text:
The Geology of Indonesia/The lesser Sunda Islands
The Lesser Sunda islands (LSI) are defined as a group of small islands situated between east of Java Island and Banda Islands, which are part of Western Banda Arc. Geologically, they constitute the inner outer arc built by Tertiary volcanic arc and some of the young volcanoes are still active. The arc is a south-facing island arc, which is the eastward continuation of the Sumatra-Java island arc system of Indonesia (Cardwell and Isack 1981). In terms of Plate Tectonic theory, the series of volcanoes built in the LSI is due to the subduction of Indo-Australian Oceanic crust beneath the LSI, and it is interpreted that the sources of melted magma from the subducted oceanic is about 165-190 Km depth (Hamilton 1979).
The oldest rock exposed in LSI is of Miocene age. Whereas to the western part of the islands (Sunda Arc) Mesozoic sequences are common (Foden and Varne 1981, Katili 1975). This indicates that the arc is relatively young tectonic product in the Indonesian Archipelago.
The systematic relationship between volcanoes, earthquake and active tectonics features at the region can give a better understanding of the present tectonics of the LSI. Although these phenomena are mainly considered due to the fact that the lithosphere of the Indian-Australian plate is being subducted beneath the Banda Arc, but the tectonic process are different from one place to other places along the subduction. These result in different type of volcanic composition and tectonic style along the arc.
I. INTRODUCTION Edit
The Lesser Sunda Islands (LSI) are defined as an area situated between eastern part of Java Island and Western part of Banda Arc, consisting of group of small islands and basins (Figure 1). Physiographically, It is bounded to the west by the Java Island, to the east by the Banda arc, to the north by the Flores Sea and to the south by Indian Ocean. Geologically, the Lesser Sunda Islands (LSI) is located in the center of Banda Arc, which were built by the young volcanoes forming geanticline. On the basis of Plate Tectonic Theory, the series of volcanoes built in the LSI is due to the subduction of Indo-Australian oceanic crust beneath the LSI, and it is interpreted that the sources of melted magma is about 165-200 km depth based on Hamilton's tectonic map (1979).
II. TECTONIC SETTING Edit
In terms of Plate tectonic setting the Indonesian archipelago is situated in the triple junction of the three major plates, they are the Indo-Australian, the Eurasian and the Pacific Plates (Figure 2). The interaction of the three major plates creates a complex tectonic especially in the plate boundary that is situated in Eastern Indonesia. The LSI is mainly form as a result of the subduction of the Indo-Australian plate beneath the Sunda-Banda Arc during the upper Tertiary in which this subduction formed the inner volcanic arc of the LSI. However, there are differences in relation to the chemical analyses among the volcanic rocks in the LSI. The volcanic arc in the east Sunda region, which rests directly on oceanic crust and is bounded by ocean crust on both sides, has lavas with chemical characteristics that distinguish them from lavas in the western parts of the arc (Barber et al 1981). Hamilton (1979) suggested the inner ridge is formed of upper Cenozoic calc-alkalic rocks.
The volcanic rocks in the inner Banda Arc of the LSI in which the oldest known rocks are Early Miocene are found about 150 Km above the inclined zone of earthquake (Hamilton 1979, Audley-Charles 1981). The very active Benioff Zone was contoured by Hatherton and Dickinson (1989) and updated by Hamilton (1978) (Figure 3). Seismicity in the Java Sector extends to a maximum depth of about 600 Km. This indicates subduction of sub-ocean lithosphere belonging to the Australian/New Guinea Plate below the Banda Arc, and the cessation of volcanism in the Early Pliocene opposite Timor suggests collision of Timor with Alor and Wetar, after all the oceanic lithosphere had been consumed by subduction.
The size of the islands of this volcanic chain gradually is getting smaller eastward from Java through Bali, Lombok, Sumbawa, Flores, Wetar to Banda. This decreasing, which is most noticeable east of Wetar, may reflect the amount of ocean floor subducted, implying either that dip-slip motions have been more important westwards from Wetar and strike-slip motions increasingly important eastwards. Alternatively, it may be that the present volcanic arc east of Wetar is younger and perhaps that the original volcanic arc east of Wetar has been overridden by the Australian continental margin (Bowin et al. 1980)
III. TECTONO-STRUCTURAL UNITS Edit
Based on Plate Tectonic Theory, the LSI can be divided into four tectono-structural units consisting of from north to south (Figure 4); The back arc unit which is occupied by the Flores Sea; The inner arc unit which is built by a series of volcanic island consisting of Bali, Lombok, Sumbawa, Komodo, Rinca, Flores, Adonora, Solor, Lomblen, Pantar, Alor, Kambing and Wetar; The outer arc unit which is formed by non volcanic island of Dana, Raijua, Sawu, Roti, Semau and Timor; And the fore arc unit which is situated between the inner arc and outer arc and is part of deep basins consisting of Lombok and Savu basins.
In this paper, the author will mainly discuss the geology and geophysics of the inner arc and back-arc of the LSI. Whilst the rest will be discussed somewhere in this book by another author.
III.1.1 Introduction
The back arc region of the LSI is mainly occupied by the Flores Sea which can be divided into three morphological units (van Bemmelen 1949); the NW Flores sea, The central Flores Basin, the east Flores Sea (see Figure 1). Bathymetric contours in the Flores Sea are oriented E-W (see Fig. 1). The most prominent phenomena is the symmetrical Flores Depression, where the water depth exceeds 5000 meters. Towards the volcanic arc, the continental shelf is narrow and very steep, suggesting structural control.
The NW Flores Sea is the broad and shallow platform connecting the south Arm of Sulawesi and Sunda Shelf with the water depth less than 1000 m. The Central Flores Basin has a triangular form with the top of triangular pointing to the direction of the Lampobatang volcano. Whilst the east Flores Sea comprise the ridges and interjacent trough, which connect the South Arm of Sulawesi with the submarine Batu Tara Ridge in the west of South Banda Basin.
III.1.2 Back-arc thrusting
In the Flores Sea, the phenomena of back-arc thrusting have attracted considerable attention and various hypotheses have been proposed to explain its initiation and driving mechanism. Silver et al. (1983) listed some of these hypotheses, including gravitational body forces as the sole mechanism, gravity spreading as a result of existing relief or injection of magma in the volcanic arc, low angle subduction resulting in back arc thrusting and collisional stress. Silver et al.(1983; 1986) considered back-arc thrusting to be a precursor of arc polarity reversal.
There are two major zones in the back-arc region of the LSI where back arc thrusting occurs (Silver et al. 1986; Prasetyo and Dwiyanto 1986); one is to the north of Wetar and Alor (Wetar Thrust), the other is to the north of Flores and Sumbawa islands (Flores Thrust). Hamilton (1979) proposed that these back arc thrusts indicated subduction polarity reversal due to the difficulty of subducting the buoyant continental margin of Australia, whereas Silver et al. (1983) related the distribution of back arc thrusts to the thickness of the forearc crust. Thick forearc crust, represented by Sumba Island and Timor Island, respectively is correlated with the formation of the Flores and Wetar thrusts.
III.1.3 stratigraphy and structure
Silver et al. (1986) divided the outer slope and trench sediments in the Flores Basin into five recognizable seismic stratigraphic units (Fig. 5), but not all units appear on all sections. The following divisions are based on their description. The lowest reflector (B) is irregular, hummocky, and considered to be acoustic basement. It was suggested that on Line 14, at least, this basement may consist of young (Pliocene ?) lava flows, consistent with the occurrence of volcanic products on the islands of the Bonerate Group to the north. Unit 1, which immediately overlies basement, is highly reflective and very variable in thickness. On Lines 8-12 this unit can be seen clearly and may thicken westward. Above Unit 1 is a poorly reflective Unit 2 which is inferred to have been deposited under pelagic or hemipelagic conditions. Unit 3 is well layered with variable thickness and is interpreted as a turbidite deposit. Above Unit 3 is another poorly bedded hemipelagic layer that generally forms the top of the slope sequence. This unit appears on all sections and is very thick in some places, although the average thickness is nearly constant at a few hundred meters. Unit 5 consists of trench turbidites. These are present on all profiles but vary greatly in thickness and lateral extent.
The stratigraphic framework in the western part of Flores Sea near the Bali Basin can be described in terms of four major units(Guntoro 1999), these being metamorphic basement, pre-rift sediments, syn-rift sediments and post rift sediments (Figure 6a and b). In some places diapiric intrusions reach up to the post rift sediments. The movement of diapirs was associated with Neogene compression, which resulted in the formation of thrust faults.
The structure of the western part of the Flores Sea as shown in Figure 6a and b is based on seismic reflection profile (Guntoro 1999). The interpretation indicates the presence of rift structure in the Palaeogene which later on experienced compressional tectonics in the Pliocene forming inverse structure. This seismic section can be described in terms of two major depressions (north and south), separated by the Lombok High. Structures can be recognized as due to folding, thrusting, block faulting, diapiric intrusion and igneous intrusion.
The older thrust faults, extending from basement through the pre-rift sediment units, were associated with Cretaceous compression which caused uplift of the region which was followed by erosion. Normal faults, extending from basement through the syn-rift sediments, were associated with the Paleocene-Eocene extension which produced horst and graben structures. Younger thrusts, extending from basement into the post-rift sediments, were associated with the reactivation of normal faults. The timing of inversion can be deduced from flexures observed in seismic sequences identified as post Middle Miocene to Pliocene.
Figure 7 shows seismic, bathymetric and gravity data obtained along the Mariana 09 line which crossed the Flores Sea from south to near Kabaena Island in the northeast, a total distance of about 400 km. The seismic profile shows that the region is dominated by series of down thrown basement blocks and magmatic activity. The Flores Ridge, the Flores Thrust, the Flores Basin, Selayar Ridge, Selayar Basin, Bone Ridge, Kabaena Basin and Kabaena Ridge can all be identified. The sediments accumulated in several sub basins separated by oceanic topographic highs. There are two principal types of reflectors. The first is characterised by rounded, conelike structures, irregular surfaces and high morphology, can be seen in the Selayar Ridge, Bone Ridge and Kabaena Ridge. The second reflector type is sub-parallel to horizontal. In the Kabaena and Selayar basins this reflector is interpreted as indicating flat-lying sediments but in the Flores Basin, where reflectors are smoother than in the Kabaena and Selayar basins, they probably mark basaltic lava flows with thin sedimentary cover.
From stratigraphic and structural point of views, it is clear that the back arc unit of the LSI have different history and evolution. The western part of the Flores Sea show similar to the basin in the Java Sea in which the history started since Mesozoikum. In contrast, the central Flores Sea indicates young basin of Pliocene age.
III.2.1 Introduction
The inner arc region of the LSI is situated on a geanticlinal ridge (van Bemmelen 1949), which has a width of about 100 km in its western end, gradually diminishing eastward to about 40 km. It consists of a row of young volcanic islands, 1400 km long, connecting the volcanic inner arc of the Banda system with the volcanic Java-Sumatra arc, they are of Bali, Lombok, Sumbawa, Komodo, Rinca, Flores, Adonora, Solor, Lomblen, Pantar, Alor, Kambing and Wetar; Van Bemmelen (1949) divided this volcanic inner row into an eastern and western part. The eastern part (from Romang to Komodo) represents the volcanic inner arc of the Timor orogene. Whereas the western part (From Sumbawa to Bali) is more closely related with the Java sector of the Sunda Mountain System.
III.2.2 Geology of the LSI
The geology and tectonic setting of the Lombok and Sumbawa are described below (qf. Foden and Varne 1981b). The islands of Lombok and Sumbawa lie in the central portion of the Sunda Arc. The oldest exposed rocks are Miocene, suggesting that subduction and volcanism began considerably later than in Java and Sumatra to the west, where there are abundant volcanic and intrusive rocks of Late Mesozoic age. The islands are located on the eastern edge of the Sunda shelf, in a zone where crustal thickness is apparently rapidly diminishing, from west to east (Curray et al, 1977). The seismic velocity structure of the crust in this region is transitional between typical oceanic and continental profiles and the Moho appears to lie at about 20 km (Curray et al. 1977). These factors tend to suggest that there has been limited opportunity for crustal contamination of magmas erupted on the islands of Lombok and Sumbawa. In addition, these islands lie to the west of those parts of the eastern-most Sunda and west Banda arcs where collision with the Australian continental plate is apparently progressing.
The volcanoes considered are located between 165 and 190 km above the benioff Zone (Hamilton 1979) (see Fig. 3). Rinjani, Tambora and Sangeang Api Volcanoes are still active, while Sangenges and Soromundi are eroded cones of Quaternary age (Sudrajat 1975). There is a marked offset in the line of active volcanoes between the most easterly Sumbawa Volcano (Sangeang Api) and the line of active volcano in the Flores. This suggests that a major transcurrent fault cut across the arc between Sumbawa Island and Flores. Audley-Charles (1975) considered that this feature represented a major tectonic discontinuity between the east and west Sunda Arcs (the Sumba Fracture). Further, Hedervari (1978) and Ritsema (1954) found a market absence of shallow and intermediate earthquake activity in the region to the south of Lombok and Sumbawa, a feature they interpreted to represent a marked break in the Sunda Arc Zone.
Faulting and folding caused strong deformation in the eastern part of Lombok Basin and is characterized by block faulting, shale diapirs and mud volcano (Prasetyo 1992). Abbot and Chamalaun (1978) suggested that Wetar formed island as part of island arc by the Late Miocene and great uplift occurred during Plio-Pleistocene.
III.2.3 Stratigraphy
The stratigraphy of the inner arc region of the LSI can be seen in Tables 1 and 2 (Suwarno and Noya 1985). The following stratigraphy description is quoted from these authors. The oldest rock exposed is Early Miocene volcanic rocks consisting of andesitic-basaltic breccia volcanic unit deposited in the marine environment. This unit is interfingering with tuffaceous sandstone unit (occur in Ruteng, Ende, Lomblen and Sumbawa islands) and limestone unit (occur in Komodo and Sumbawa), both units are also interfingering. Conformably, but in some other areas are unconformable, overlying the Early Miocene volcanic rocks is the reef unit (occur in Bali, Lombok, Sumbawa, Komodo, Ruteng) and lava dacitic unit (occur in Lombok, Komodo, Ruteng, Alor & Wetar Barat). Reef unit and lava dacitic units are interfingering with upper part of tufaceous sandstone (in Bali). Late Middle Miocene basaltic-granitic dykes intruded all rock units above.
Unconformably overlain tufaceous sandstone unit, reef unit, and dacitic lava are andesitic-basaltic tuff unit (occurred in Sumbawa, Ruteng, Ende, Lomblen, Alor and Wetar Barat), coral reef unit (occurred in Sumbawa, Komodo, Ruteng, Ende, Lomblen), and andesitic- basaltic lava unit (occurred in Alor, Lomblen, Alor & Wetar Barat, Wetar) in which those three units are interfingering and also Naumantang Formation (in Wetar). The age of andesitic-basaltic tuff unit, coral reef unit, and andesitic-basaltic lava range from Late Miocene to Pliocene, whereas the age of Naumantang Formation is Late Miocene.
In the eastern part of LSI, some dioritic - granodioritic intrusion rocks are part of andesitic-basaltic lava unit and Naumantang Formation. Toward the western part (Bali), equivalent with andesitic-basaltic tuff unit, coral reef unit and andesitic-basaltic lava unit is Selatan Formation (Msl) consisting of limestone covered conformably Ulakan Formation (Mu). It is suggested that conformably above the Selatan Formation is Prapatagung Formation (Ppa) and Pulaki volcanic rocks (Pp). Above Prapatagung Formation and Pulaki volcanic rocks are conformably overlain by Asah Formation (Pa) consisting of volcanic rocks and locally calcareous.
Covered unconformably most of the area is the old volcanic products (Qtv, Qot, and Qv) consisting of lava, breccia, agglomerate and andesitic sandy tuff of Plio-Pleistocene age.
The volcanic activity in the LSI continues up to the present time. The result can be seen as volcanic cones built by andesitic-basaltic rocks (qhv, Qyt, A, B, P, Qbb, Qvb, Qvc, Qvd, Qve). Those volcanoes grow well in land as well as on offshore.
The rocks which are considered as young products are coral reef (Ql), Terraces (Qt, Qct, Qalk), and alluvium deposits and beach (kW/qAL). All those rocks are deposited unconformably above the surrounding rocks.
Volcanic activity with strong explosion can be seen in Bali and Lombok with the result of caldera such as Buyan-Bratan Caldera, Batur Caldera, Rinjani Caldera. Th occurrence of batur Caldera is approximately 22.000+/-1500 years.
Based on stratigraphical and structural data above, Suwarno and Noya (1985) proposed the geological history of the inner arc of the LSI. The geological history started in Early Miocene when the area constitutes a basin. The first deposition was clastic sediments forming tufaceous sandstone and limestone which were deposited in the marine environment with the depth of about 20-100 m (neritic). Before these clastic sediments were deposited, the area is influenced by marine volcanic activity forming andesitic-basaltic volcanics which were called andesitic-basaltic breccia volcanics. This volcanic activity indicates the subduction resulting volcanic arc in the LSI initially occurred in pre-Miocene and at least in Oligo-Miocene (Katili 1975).
In the mid Miocene, the andesitic-basaltic volcanic activity decreased, but it was replaced by the appearance of dacitic -rhyolitic composition material. They are represented by dacitic lava unit, upper part of tuffaceous sandstone unit, reef limestone unit and upper part of Mulakan Formation (Mu).
In Middle Miocene, locally in Sumbawa and Komodo there was tectonic activity indicated by unconformity between andesitic-basaltic volcanic breccia and reef limestone unit and dacitic lava unit.
In late Middle Miocene to early Upper Miocene, there were tectonic activity causing uplifting, faulting, and folding trending in NE-SW to NNW-SSE and also was associated with magmatic activity of various compositions. From Lombok up to Wetar, this event caused an obvious gap, but in Bali, this event is not clear. In Bali, marine sedimentary deposition continues up to Pliocene and even Quaternary producing Surga Formation, Selatan Formation, Prapatagung Formation and Pulaki volcanic rocks. from this fact, it is suggested that between Lombok and Bali, it was cut off by a fault trending in N-S with upthrown in the Lombok and downthrown in Bali.
Post early Upper Miocene, all area from Sumbawa to Wetar experienced subsidence. In contrast Lombok was part of a high separated basin in the eastern part (Sumbawa to Wetar) and in the western part (Bali), so it is suggested that Lombok was a high. In the eastern basin, there were deposition of tuff, tuffaceous sandstone and limestone, which are grouped in the andesitic-basaltic tuff unit and reef limestone unit with neritic-bathyal environment. Whilst in Wetar and Bali occurred marine volcanic activity producing lava, breccia, agglomerate and tuff in basaltic-andesitic and dacitic composition with calcareous intercalation. These rocks are grouped into andesitic-basaltic lava unit and Naumantang formation. This deposition activity lasted up to Early Pliocene whereas in general volcanic activity on Early Pliocene wanned and produced tuff only.
In Plio-Pleistocene, the basins in Sumbawa-Wetar were uplifted with the formation of moderate-strong folding on late Pliocene or early Pleistocene. In that time, volcanic activity was increasing again producing andesitic-basaltic volcanic rocks (Qtv, Qot) and locally produced tephrite-lesit (Qv ls/le) like in Sumbawa.
In Late Pliocene to Pleistocene, Bali was also uplifted followed by volcanic activity producing non-marine andesitic-basaltic volcanic rocks (Qd, Qba, Qsv). This also occurred in Lombok (v1, v2, v3) and in Sumbawa-Wetar (upper part Qtv and Qvb, Qvs, Qvsa, Qvl, Qvm, Qvyo, Qv ls/le, Qvd dan Qvg). Locally in Bali was also deposited conglomerate, sandstone, and coral reef of Palasari Formation (Qp).
In Late Pleistocene, all area was uplifted and was followed by faulting and folding. Miocene to Pliocene rock units show faulting trending in NE-SW to NW-SE.
Late Pleistocene or Early Holocene volcanic activity lasts up to present day marked by the presence of 17 active volcanoes (Figure 3). This fact cannot be separated by the movement of Indo-Australian oceanic plate. Volcanoes in Bali-Sumbawa occupy northern part of the arc, whilst in Flores occupy the southern part of the arc. This volcanic activity produces andesitic-basaltic volcanic rocks which are grouped into young volcanic rocks (Qhv, Qyt, Qpb, Qvb, Qvc, Qvd, Qve, A, B, P) and cover some of the older rocks.
The presence of beach and river terraces (Qt and Qct), uplifted lacustrine deposits (Qalk) and coral reef (Ql), indicate that this area is still uplifting up to now. For Bali, the Quaternary uplifting produced Palasari Formation. The uplifting movement maybe still continue and cause the tilting of Bali island in which the northern part is steeper than the southern part.
IV. VOLCANIC ACTIVITY AND COMPOSITION Edit
IV.1 Introduction
Frequent earthquake shocks and active volcanoes in the LSI indicate to the active tectonic process, which are currently in progress in response to the continued movement of the Indo-Australian Plate beneath the arc. However toward the eastern of the subduction, in Alor and Wetar, the volcanoes is no longer active since the Pleistocene and it is interpreted due to the cease of subduction as the collision of the northern margin of Australian beneath the arc occurred.
Many authors assumed that the Sunda arc and Banda arcs are continues. However, some other authors suggested as discontinues. Some hypothesis have been put forward to support this opinion as explained below. Cardwell and Isack (1978) show no evidence of a major discontinuity in the seismic records. However; Audley-Charles (1975) proposed the Sumba fracture between Sumbawa and Flores as the structural discontinuity of the two arcs. Nishimura et al. (1981) proposed that a major tectonic discontinuity separates Eastern Indonesia from Western Indonesia between Sumbawa and Flores, this view being based on investigations of the differences in geophysical, geochemical and submarine morphological features. The regional Bouguer gravity anomaly patterns change considerably in the area between Sumbawa and Flores (Chamalaun et al. 1976). East of Flores Island, there are east-west gravity anomalies along the outer Banda Arc with high positive values in the north. West of Sumbawa Island there are also east-west gravity anomalies associated with the Java Trench system, but in the field decreases from high positive values to the south to low or negative values to the north. Between these two regions of opposite gradient is a region in which contour lines trend north-south. In geochemical studies, there are differences in the chemical characters of the Quaternary volcanic rocks of Lombok, Sumbawa and Bali on the one side and Flores on the other side. Discontinuity in the distribution of earthquake shocks beneath the Sunda Arc indicate that the underthrusting of the Indian ocean plate is actively in progress in this segment of the arc. Whist, shallow shocks are absent in the western segment of the Banda arc, indicating that to the east of Sumba underthrusting has ceased. Discontinuity in the trend of the volcanic arc, with volcanoes on eastern side of the discontinuity displaced southward with respect to those on the west. This offset occurred along an extension of the Palu-Koro transcurrent fault recognized in Sulawesi.
IV.2 Volcanic composition
The Sunda Arc is complicated by the change in the converging Indian Ocean Australian Plate, which is oceanic west of Timor and to the east is of 40 km thick continental crust, depressed by 3 km at the axis of the Timor trough (Bowin et al. 1980). The presence of active volcanoes from Bali to Flores indicate subduction related subduction. However, toward Alor and Wetar the volcanism is no longer active. This suggests that the geometry of subduction is not homogeneous along the arc. Volcanism in the islands of Alor and Wetar in the inner Banda Arc ceased in Early Pliocene time, it is due to the Australian continental margin had collided with this part of arc (Audley –Charles 1980). Hutchison (1981) found that the chemical characteristics of volcanoes around the arc systems could be correlated directly with their tectonic environment. Factors which influence the composition of the lavas included depth to the underlying Benioff zone, and whether the volcanoes are constructed on continental or oceanic crust. Petrography and geochemistry of the Quaternary-recent volcanoes of Lombok and Sumbawa arc is unusual in which the volcanic arc rests directly on oceanic crust (Foden and Varne 1981b). The oceanic crust occurs on both sides of the arc. The depth to the underlying Benioff Zone beneath the volcanoes is 165 km - 190 km. The volcanic rocks vary in composition from calk-alcaline to highly potassic, but there is no correlation between their composition and depth to the underlying Benioff Zone. Since there is no continental material in the surrounding of the arc, the highly potassic potassic leucitites cannot be attributed to contamination by continental material. He concluded that variations in the compositions of the lavas can only be attributed to inhomogeneities in the source region.
In Lombok, Rinjani Volcano lies approximately 300 km north of the Java trench and is situated about 170 km above the active north dipping Benioff seismic zone (Hamilton 1979). Foden and Varne (1981) based on the composition of andesites which have very low Ni concentrations and low Mg/Mg+Fe, he suggested that the Rinjani suite is of mantle origin, but that all the andesites and dacites as well as many of the basalts have probably been modified by fractional crystallization processes. In brief, Foden and Varne concluded that the Rinjani calc-alkaline suite, which in many respects is typical of many suites erupted by circum-pacific volcanoes, probably originated by partial melting of the peridotite mantle-wedge overlying the active Benioff Zone beneath Lombok Island.
V. EARTHQUAKE Edit
The LSI and its surrounding area is considered as an area of high seismicity, and several large earthquakes associated with tsunami have been recorded in this area. Figure 3 show the distribution of earthquake in this area from 1900 to 1988 with the magnitude varying from 3 to 7 Richter scale ((Ismanto and Prajuto 1989). Figure 2 also shows the depth and magnitude of the earthquake in north-south direction with the depth of epicenter reaching 550 km but other reports mentioned the depth up to 720 Km. The distribution of the earthquake indicate that the Australian Plate has been subducting to the north at an inclination of about 63 degree, and also the subduction of the oceanic crust in the Flores Sea to the south due to the subduction reversal polarity (See Figure 1 from Ismanto and Prajuto, 1989).
VI. CONCLUSIONS Edit
1. The LSI can be divided into four structural tectonic units, they are; The back-arc unit, the inner arc unit, the foe arc unit, and the outer arc unit. Each unit has different stratigraphic and structural styles. 2. From the information of Well JS 25-1, basement complexes are present in the Central Lombok Block. These are suggested to be part of the Late Cretaceous accretionary complexes formed at the southeastern margin of the Sundaland. Whilst, the basement in the Flores Sea may consist of young (Pliocene) lava flows (Silver et al. 1986), and thin sedimentary covers. 3. The western part of Flores Sea has experienced three major tectonic events, these being Cretaceous crustal compression, Palaeogene crustal extension and Neogene inversion. The changes between these structural regimes, indicated by distinct basin geometries, styles of faulting and structural deformation since the Cretaceous, imply changes in the intraplate stresses or plate boundaries and movements which can be linked to the evolution of subduction and collision around the SE Sunda Shelf. 4. The presence of back-thrust in the Flores Sea associated with high seismicity in this area of about 30 km depth indicates the initial stage of arc reversal polarity with the subduction of oceanic crust in the Flores Sea to the south toward the LSI. This has been interpreted due to the choked subduction of the Indo-Australian plate in the south towards the LSI. 5. Based on the similarity of lithology, depositional environment and age, it is interpreted that the area in the LSI is a basin during Early Miocene - Late Miocene. After the Late Miocene, Bali Island became a separate basin to the basin in the eastern part and were separated by a ridge in the Lombok Island. 6. The seismic velocity structure of the crust in this region is transitional between typical oceanic and continental profiles and the Moho appears to lie at about 20 Km (Curray et al. 1977).
BIBLIOGRAPHY Edit
Audley-Charles, M.G., (1980). Geological history of the region of Wallace's line: In Wallace's line and Plate Tectonics, Edited by T.C Whitmore, Clarendon Press, Oxford 1981.
Audley-Charles, M.G., (1980). Geometrical problems and implications of large scale overthrusting in the Banda Arc –Australian margin collision zone. In thrust and nappe tectonics (ed. K. McClay and N.J. Price). Geological Society of London Special Publication 9, 407-16.
Barber et al. 1981. The geology and tectonics of Eastern Indonesia: Review of the Seatar workshop, 9-14 July 1979, Bandung, Indonesia. In the geology and tectonics of Eastern Indoensia, GRDC, Special Publication, No. 2, 1981, pp. 7-28. Cardwell and Isack, 1981> Special publication GRDC
Ismanto, W., and Prajuto, 1989. Penyebaran gempa bumi di nusa tenggara dan sekitarnya. Majalah Ikatan Ahli Geologi Indonesia, vol. 12, No. 1, July 1989.
Katili, J.A., 1975. Volcanism and plate tectonics in the indonesian island arrc. Tectonophysics, 26, 165-188.
Suwarno, N., and Y. Noya., 1985. Stratigraphy regional wilayah Busur Bergunungapi Nusatenggara. Proceeding PIT XIV Ikatan Ahli Geologi Indonesia, Jakarta 10-11 Desember 1985, pp. 71-79.


text:
TALLAHASSEE — Gov. Rick Scott said Wednesday he supports expanding Medicaid and funneling billions of federal dollars to Florida, a significant policy reversal that could bring health care coverage to 1 million additional Floridians.
"While the federal government is committed to pay 100 percent of the cost, I cannot, in good conscience, deny Floridians the needed access to health care," Scott said at a hastily called news conference at the Governor's Mansion.
Scott, a former hospital executive, spoke with unusual directness about helping the "poorest and weakest" Floridians — a stunning about-face for a small-government Republican who was one of the loudest voices in an aggressive, and ultimately unsuccessful, legal strategy to kill a law he derided as "Obamacare."
Throughout his 2010 campaign for governor, as Scott sought support from tea party members, he called the law a "job killer" that would hurt Florida.
On Wednesday, he called the proposed Medicaid expansion, at least for an initial period, "common sense."
Tea party activists bitterly criticized Scott's declaration.
"This is just another example of Republicans lying to Floridians," said Everett Wilkinson of Palm Beach Gardens, calling Scott "the Benedict Arnold to the patriot and tea party movement in Florida."
Scott was careful to point out that the Republican-controlled Florida Legislature will ultimately decide whether or not his proposal is worth implementing. That is far from certain, particularly in the more partisan House.
"Gov. Scott has made his decision, and I certainly respect his thoughts," said House Speaker Will Weatherford, R-Wesley Chapel. "However, the Florida Legislature will make the ultimate decision. I am personally skeptical that this inflexible law will improve the quality of health care in our state and ensure our long-term financial stability."
"I respect the governor for staking out a clear position," added Sen. Joe Negron, R-Stuart, who chairs a Senate committee studying the health care law. He said senators would reach their own conclusions likely in early March.
Scott said he would support an initial three-year expansion of Medicaid but made clear he would not twist legislators' arms to make it happen. He reiterated that his top priorities are a $2,500 pay raise for teachers and a sales tax break for manufacturers' equipment purchases.
Under the governor's proposal, after three years the Legislature would have to vote to reauthorize the program to keep it going.
"It is not a white flag of surrender to government-run health care," he said, as if anticipating a political backlash from his most conservative supporters.
Part of his self-described "new perspective" came from the death of his mother, Esther, last year, he said.
"A few months ago, my mother passed away, and I lost one of the only constants in my life," Scott said. "Losing someone so close to you puts everything in new perspective . . . especially the big decisions."
For weeks, Scott has said the debate on expanding Medicaid was directly tied to the state's application for waivers it needs to allow private companies to run the program.
His endorsement of the expansion came hours after the federal government agreed to grant Florida a conditional waiver to privatize Medicaid statewide for the state's more than 3 million current recipients, more than half of which are children or people under age 21.
Scott and GOP lawmakers have repeatedly warned that Medicaid's roughly $21 billion annual costs were consuming Florida's budget and proposed the managed care plan to save money and improve care.
The privatization expands on a five-county pilot program that has been rife with problems. Critics worry for-profit providers are scrimping on patient care and denying medical services to increase profits. Some doctors have dropped out of the pilot program, complaining of red tape and that the insurers deny the tests and medicine they prescribe. Patients have complained they struggled to get doctor's appointments.
Several health plans also dropped out of the pilot program, saying they couldn't make enough money. Patients complained they were bounced from plan to plan with lapses in care. Nearly half of the 200,000 patients enrolled in the pilot have been dropped from at least one plan, federal health officials noted at one point during negotiations.
Lawmakers say they have fixed the pilot program's shortcomings, with provisions including increased oversight and more stringent penalties, including fining providers up to $500,000 if they drop out. The measures also increase doctors' reimbursement rates and limit malpractice lawsuits for Medicaid patients in hopes of increasing doctor participation in the program.
Medicaid, a joint state-federal, government-run health care program, is voluntary for states. But every state participates, in part because of the good financial terms. The federal government covers about 55 percent of all Medicaid costs in Florida and covered about 68 percent in recent years with additional stimulus funding.
The health care law tried to entice states to expand eligibility to Medicaid by raising income eligibility limits. To do so, the federal government agreed to fund 100 percent of the cost for states to expand Medicaid for three budget years. The federal government would then cover 95 percent of the costs in 2017, 94 percent of the costs in 2018, 93 percent of the costs in 2019 and 90 percent of the costs in 2020 and beyond.
Recent polls conducted by the American Cancer Society's Cancer Action Network and the Florida Hospital Association indicated that most Floridians supported the Medicaid expansion.
Scott said Wednesday that he had to look past his long-standing opposition to the health care law to reach his decision.
"It doesn't matter what I believe. It doesn't matter what anybody believes," Scott said. "The Supreme Court's already made their decision. We had an election in the fall, and the public made their decision."
Information from the Associated Press was used in this report.
The story
. Federal government conditionally approves Florida plan to privatize Medicaid system.
. Hours later, Scott endorses plan to expand Medicaid eligibility.
. Top GOP lawmakers, who must sign off, remain noncommittal.
Case for the economy
A report for two consumer groups cites economic benefits. 4A
The story
. Federal government conditionally approves Florida plan to privatize Medicaid system
. Hours later, Scott endorses plan to expand Medicaid eligibility
. Top GOP lawmakers, who must sign off on expansion, remain non-committal
tease hed goes right
1 inch 1 inch of body type 1 inch 1 inch of body type 1 inch 1. 4A

subset: commoncrawl


text:
Tag Archives: Events
That Speaking Thing
Written by HDIAndrew on August 29, 2015 — Leave a Comment
No, not RPGBaby's speaking. While she coos a lot, she is only speaking in my wife and my heads, and we get to make up the words. This is about public speaking, as we have opened SIEGE for speaker requests. I can't even begin to count the number of presentations I have given at conventions, […]
Posted in SIEGE | Also tagged Blog Post, convention, Event, keynote, public speaking, Scott Steinberg, Speaker


text:
Skip Navigation
Search the Archives
The NIDA Archive contains:
Archive content is not current information, is not being updated, and may contain broken links. If you wish to search for current content, go to the NIDA Home Page.
If you need a alternative means of access to any information please contact us. Let us know the nature of your accessibility problem, the Web address of the required information, and your contact information.


text:
Create a Website Account - Manage notification subscriptions, save form progress and more.
Show All Answers
The City maintains the street lights along Main Street from Highway 1 to Filbert Street and the 300-500 blocks of Seymour Street. Pacific Gas & Electric Company (PG&E) maintains all the other street lights. To contact PG&E lights, you may click the link or call them at 800-743-5002, for City Lights call 650-726-7177 or email Public Works. Please provide the following:
- Provide your name and phone number if case additional information is needed
- Street name and address where the light pole is located and if possible, the pole number, and a cross street
- Type of problem with the street light: i.e. burn-out, cycles on and off repeatedly, light burns 24 hours a day, broken glassware
Graffiti Abatement Hotline at 650-712-7310. To report graffiti vandalism in progress, residents should call 911. If you want to report information about "taggers" anonymously, please call the HMB Sheriff Sub Station at 650-726-8288. When reporting graffiti, the following should be included:
- Location: The address, or closest address, of the affected area. If graffiti is located at an intersection, include cross roads and directional clues (NE, SE, SW, NW).
- Type: Include the type of property that received the graffiti, such as a wall, curbside, telephone pole or fence. If graffiti is located on utility poles, boxes and/or phone booths please include the company name (PG&E, Comcast, etc.) and any other identifying information that will help pin-point the location.
- Business Name: Permission must be obtained from the property owner to clean private property.
- Contact Information: name and phone number. Your contact information will not be shared.
- Photos are instrumental.


text:
Emily Johnson on "Niicugni"
I saw Emily Johnson's The Thank-you Bar in fall 2011 at NYLA. The show began with a walk through the backstage area of the theater, signs mischievously posted along the way with incongruous labels: a white brick wall held one that read "Vaux Swifts nest in this beam." We entered the stage floor to take one of the 30 seats available in the limited capacity show, sitting either in chairs or cushions on the floor. Our seats, located in the middle of the space, rather than along an edge, meant we were surrounded by the show's installation, which through its simple construction prevented this immersion from overwhelming. The remainder of the performance—roughly an hour's worth of interweaving story, music, movement, and light—continued with this intimate yet nimble quality that created a real sense of gentleness that was as soothing as it was powerful.
I left this performance with a strange confusion: I liked it, yet felt as though I shouldn't like it. I couldn't deny my positive reaction to the piece, but some part of me thought it might be in bad taste to admit to liking it.
This confusion took a few days to process. The performance was so pleasant, and direct in its presentation, that it was as though the piece violated an aesthetic taboo that put it out of bounds. I had to confront a clash between my felt enjoyment of the work and some nagging thought that the performance was manipulative. Happily, the conflict resolved soon enough: there was a real depth to the work that removed any hesitation I felt. I saw that what I was holding up to mark something as out of bounds needed to be reevaluated. It's a powerful performance that allows you to see the boundaries of your own aesthetic territory.
Pleasure has become a problematic sensation to deal with and use in art. Some critics and artists have argued that by its very nature pleasure is manipulative, and thus precludes criticality. Things that are pleasurable present themselves as desirable (this connection is readily used in marketing, for example), so how can something that encourages you to desire it allow you to form your own judgement of it? The Thank-you Bar gave me space to consider these questions.
The Thank-you Bar was indeed a lovely piece, speaking directly to the audience with a sincere presentation. There was no aesthetic facade built up between the work's intention and its audience. When I shared my musings with Johnson, she perceptively reflected back to me:
"Was it really the pleasurable experience, or the sincerity that made you nervous?"
Sincerity can be hard to accept. It's easy to be caught off guard when presented with a sincere statement or action, because much of socialization and communication is about learning to read signs. In sidestepping how I anticipated a performance to code its meaning, The Thank-you Bar at first felt somehow off. It took some time to process all this—pleasure, sincerity, enjoyment and appreciation—but the more I thought about the performance, the easier the supposed conflict was to dismiss.
I think, in the end, that it was precisely the sincerity, of both Johnson (and her collaborators), and the work itself, that made space for me to accept the difficult aspects of pleasure in the performance. The theoretical problems of pleasure—its relation to the good, whether it is manipulative—were in this instance neutralized through an honest presentation of the sensation. There is no sense of manipulation when all cards are laid bare.
These thoughts, in some form, were the starting point of a conversation Johnson and I had a few weeks ago, before we turned to talking about her newest work Niicugni, having its NYC premiere this week at BAC as part of the PS122 COIL Festival.
"In Niicugni, we're dancing on a stage floor. But we're trying at certain moments to think about reaching down into the ground all the way beneath the building that supports and houses us all. Trying to connect the piece to this place. Also spreading out in all directions, and connecting to all the places in this city. And also connecting us to all the places we're from."
Niicugni is the second work in what Johnson envisions as a trilogy. Though it was created after The Thank-you Bar, the works don't necessarily have a chronological order. The way Johnson describes it makes me think of a russian matryoshka doll where, conceptually, "The Thank-you Bar sits inside Niicugni", rather than preceding it. Ideas of land, location, and identity, central to The Thank-you Bar, are also spoken about regarding Niicugni.
The process for Niicugni began over two years ago, in August 2010 at Vermont Performance Lab. In some important ways, however, the "process" of creating this piece cannot be separated from the performance that happens onstage in various theaters. A central aspect of the work is the fish-skin lanterns that form the majority of the set. These lanterns were handmade by volunteers, created in workshops lead by Johnson in Vermont, Minnesota, and Arizona, as well as by friends and family members in California and Alaska. The 51 lanterns hang throughout the space, over both the stage and and audience, creating both a light and sound installation.
The workshops that helped produced this set are part of the concept of the piece. Producing all 51 lanterns was a painstaking process, and each remains individually identifiable, distinct from every other lantern, and is marked by a unique background. The lanterns are identified on a map (created by Max Wirsing) included in the program that provides a range of information on the origins of each lantern, from the individual(s) who worked to create it, to the type of fish, to the distance traversed by the lantern (starting from the river the fish came from, to where the lantern was made, and the subsequent miles traveled on tour, ending with the current theater). This map locates the lantern in the present, physical theater, and to a web of efforts and places already past.
This important work is part of the ground of Niicugni. Johnson observes, "The actual labor and effort of people who volunteered is now housed in these objects. You can see the stitching, the craft—you can probably see their fingerprints. It's a different story for everybody. I can recognize who made each lantern.
"The lanterns hold their own story, each one—but I don't know that it's necessary to know that. That story can be known and voiced, or be kept with the object. And either one is fine. The story is offered, but not forced."
This speaks to the many layers that make up Johnson's work. She notes that she calls her work "performance installation", as a way to indicate the shared importance of the work's various elements. Sound, story, light, set, performance—all are integral to the experience. Though this is not an unusual position for a contemporary dance-maker (notions of boundaries between disciplines are decades out of fashion), what is interesting in Niicugni is that Johnson insists on a parity between what might be considered the "preparation" for creating the piece and the live performance that happens onstage. "From the first workshop we had at Vermont Performance Lab over two years ago—that was the show. And so is what we're doing at BAC this January. They are equal parts." The intimation is that Niicugni is not only what audiences will see onstage, but was also the labor and the stories that went in to creating the stage performance. Those are not discrete efforts that contributed to some later, final piece, but are part of the work as much as the live performance is a part.
Thinking back to Johnson explaining how, during the performance, they are sometimes thinking about "reaching down" or "spreading out" in attempts to connect to various places, I start to get a sense that Niicugni is a work that extends. It extends the present moment to feature the energy that went into creating it; it extends spaces to bring in the locales of present participants origins; and extends meaning to make use of stories that might not be heard. Referencing the lanterns and the living stories present in each, Johnson suggests that "while it isn't necessary that the audience knows the story behind each lantern, it's still important that the lanterns are there." By way of analogy, she observes, "The ground is below us, whether or not we think about it."
Circling back again to The Thank-you Bar, we start discussing performance personas and notions of honesty. I suggest that, even as she tells stories, Johnson does not "perform" as a character distinct from her off-stage person, but speaks directly to her audience, as a person speaking to another person (or group of people). She agrees with my perspective, "When I'm performing, I'm not trying to take a position other than 'me'. And the stories I tell aren't all 'true' (in the sense that they are not all based in 'fact'), and therefore aren't all 'honest'. But they come from an honest place, they come from my experience. It really is just me talking. And dancing, for that matter."
At this point, laughter starts to trickle in, and Johnson brings out a story in the moment, to illustrate the idea:
"I think it's really funny that I can kick my leg really high! I think it's hilarious that that is a thing we do onstage. And I do that onstage, sometimes. And I do it, and I'm laughing at it as I'm doing it, and acknowledging it as a funny thing (for me anyway). And it's also a very classical thing, and a very strong thing. It's all of those things, and somehow that is also honest. I'm not doing it to show 'I can do that', I'm doing it to offer, 'Look, I can do this! Isn't it a funny thing? What can you do?'"
As we wrap up our conversation, another story follows. Johnson muses, "You've got me on this 'honest' track."
"Sounds terrible," I reply.
Here is a snippet of audio of Emily telling a story about "bowling shoes…":


text: These are unedited, "as shot" images uploaded directly from my camera. don't worry if the photo appears too dark, or the dog looks too far away. All purchased images with be cropped, brightened and other wise edited for best composition or to your specifications. All images are © Barry Rosen and may not be downloaded or posted on Facebook, Twitter or other websites without my permission. Of course, my copyright overprint will be removed on all purchased images.


text:
Back to list of all tutorials
Back to course page
Longitudinal Tutorial (FreeSurfer Version 6.0)
This page will take you through the steps of processing your longitudinal data:
After the tutorial (if you want to learn more) you can read details about the longitudinal stream at LongitudinalProcessing, LongitudinalEdits and LongitudinalStatistics.
1. Preparations
If you are taking one of the formally organized courses, everything has been set up for you on the provided laptop. The only thing you will need to do is run the following commands in every new terminal window (aka shell) you open throughout this tutorial. Copy and paste the commands below to get started:
export SUBJECTS_DIR=$TUTORIAL_DATA/long-tutorial cd $SUBJECTS_DIR
To copy: Highlight the command in the box above, right click and select copy (or use keyboard shortcut Ctrl+c), then use the middle button of your mouse to click inside the terminal window to paste the command (or use keyboard shortcut Ctrl+Shift+v). Press enter to run the command.
These two commands set the SUBJECTS_DIR variable to the directory where the data is stored and then navigates into this directory.
If you are NOT taking one of the formally organized courses, click here.
2. Longitudinal Image Processing
All data for this tutorial has already been processed for you since processing can take up to 24h. However, to continue you need to understand the three processing steps (cross, base, long) and associated directory names.
For example, assume you have a subject with two time points: OAS2_0001_MR1 and OAS2_0001_MR2.
[CROSS]: You would process these two images independently first (we call that cross as in crossectional analysis/processing) using the regular FreeSurfer processing stream (recon-all). You end up with two directories with the names OAS2_0001_MR1 and OAS2_0001_MR2
[BASE]: Then you would run the second step to create the within subject template (also called base) and end up with a new directory. There is only one base directory per subject. We decide to name the base: OAS2_0001. Inside this directory are the results for the average anatomy of your subject across time. You don't use this data in any analysis, and only look at it for quality checking or editing.
[LONG]: Finally you would create the two longitudinal runs (the ones you are actually interested in). You end up with two more directories (these names get automatically assigned): OAS2_0001_MR1.long.OAS2_0001 and OAS2_0001_MR2.long.OAS2_0001. They contain the final, most reliable and accurate processing results.
For the subjects described above, the commands for creating the cross, base, and long are the following. For a subject with two time points OAS2_0001_MR1 and OAS2_0001_MR2 you would run the independent runs first by typing (don't do it, it has already been done for you) in two separate terminals or on different computers:
Don't run these recon-all commands
It will take a while and has already been done for you.
recon-all -subjid OAS2_0001_MR1 -all
recon-all -subjid OAS2_0001_MR2 -all
If you work with your own data, you'd have to import the dicoms first recon-all -i path_to_your_dcm1 ... -subjid your_subject_name. In this command you can pass several within-session scans by specifying multiple -i flags instead of the "...". You then run the above recon-all comands to process the imported data. We call these runs the cross sectionals (or cross runs) because the two time points are processed completely independently as if they were from different subjects.
Once the norm.mgz is available on both time points, you can create the unbiased subject template/base. We decide to name it OAS2_0001 :
recon-all -base OAS2_0001 -tp OAS2_0001_MR1 -tp OAS2_0001_MR2 -all
This will create the within-subject template (we will refer to these type of runs as base) and run it through recon-all. It will take approximately the same time as a regular recon-all run, a little more because of the initial averaging of time points. A directory OAS2_0001 will be created.
Finally once the base and the two cross sectionally processed time points are fully completed, you can run the longitudinal runs (again in two different terminals or different computers) by typing:
Don't run these recon-all commands
It will take a while and has already been done for you.
recon-all -long OAS2_0001_MR1 OAS2_0001 -all
recon-all -long OAS2_0001_MR2 OAS2_0001 -all
These runs create the directories OAS2_0001_MR1.long.OAS2_0001 and OAS2_0001_MR2.long.OAS2_0001 containing the final results. These are complete subjects directories and we will use them for any post-processing or analysis as the results are more sensitive and repeatable than the independent cross runs. These longitudinal processes run much faster than the cross and base above. We call them the longitudinal or simply long runs, because they make use of common information taken from the template.
You can now continue with the next section (inspecting the data).
If you want to learn about the exact commands for processing your data, click here.
3. Inspecting Longitudinal Data
We use freeview (FreeviewGuide) as a viewer in this tutorial.
First let's check the base (subject template) of a single subject. Open the norm.mgz and surfaces with freeview. If you run the following command and freeview opens, switch to the coronal view in order to see the same as the images below:
freeview -v OAS2_0001/mri/norm.mgz \ -f OAS2_0001/surf/lh.pial:edgecolor=red \ OAS2_0001/surf/rh.pial:edgecolor=red \ OAS2_0001/surf/lh.white:edgecolor=blue \ OAS2_0001/surf/rh.white:edgecolor=blue
This will show you the within-subject template (base), i.e., the average anatomy of this subject across time overlayed with the pial and white surface. If the across-time registration failed you would see a blurry image or ghosting. You should inspect the surfaces on this image. This will be important later as the surfaces are transferred into the longitudinal runs and therefore should be accurate in the base. Move back and forth to inspect all slices and see if the surfaces follow the white matter and gray matter boundaries.
Now it is time to look at the longitudinal results. Starting with FreeSurfer 5.1, the base and the long volumes are all in the same voxel space, meaning that volumes across time are anatomically aligned and can be directly compared if opened on top of each other ). Close any open freeview window to reduce memory usage and run the following command:
freeview -v OAS2_0001_MR1.long.OAS2_0001/mri/norm.mgz \ OAS2_0001_MR2.long.OAS2_0001/mri/norm.mgz \ -f OAS2_0001_MR1.long.OAS2_0001/surf/lh.pial:edgecolor=red \ OAS2_0001_MR1.long.OAS2_0001/surf/lh.white:edgecolor=blue \ OAS2_0001_MR2.long.OAS2_0001/surf/lh.pial:edgecolor=255,128,128 \ OAS2_0001_MR2.long.OAS2_0001/surf/lh.white:edgecolor=lightblue
This might take a while to load (check the progress bar). You will see the normalized skull stripped images (norm.mgz) of both time points on top of each other (the second time point is the top-most layer and so the only one visible at the moment). You also see the white and pial surface for each time point, drawn on top of each other (we only show the left hemisphere here to reduce memory usage for older computers). Time point 1 uses red and blue while time point 2 uses pink and light blue for the surface colors. The surfaces do not change much across time. You can also compare the images directly. For this, uncheck the 4 check boxes in front of all the surfaces, or press 'Ctrl-f'. Select the first (top) norm volume and use the opacity slider to blend between the two images. You can also switch back and forth between the two images by pressing 'Alt-c' or using the opacity slider. This way you can spot longitudinal deformations (atrophy) and also potential global alignment problems (not in this case). You will mainly notice that the ventricles are getting larger in the second time point. You can use the Up and Down arrow keys to scroll through the slices. Close freeview when done.
4. Post-Processing Longitudinal Data
4.1. Longitudinal Table
(Also: LongitudinalStatistics)
To get the longitudinal data ready for the statistical analysis, you need to create a table (space separated as a text file) in the following format:
where the first column is called fsid (containing each time point) and the second column is fsid-base containing the base name, to group time points within subject. You can have many more columns such as gender, age, group, drug, etc. Make sure there is a column containing an accurate time variable (optimally measured in years if you are interested in yearly change) such as age or the duration of the study (time from initial scan). Here we use years to measure the time from baseline scan (=tp1). You can see in the table that the two subjects OAS2_0001 and OAS2_0004 each have two time points (MR1,MR2) that are not equally spaced (approx 15 and 18 months apart). We have created this table for you in the qdec subdirectory for the tutorial data and can get started right away. You can look at the file by opening it in your favourite spreadsheet editor, e.g.:
libreoffice -calc qdec/long.qdec.table.dat
or, if that fails, a simple text editor:
gedit qdec/long.qdec.table.dat
NOTE: For Mac users, you can try Numbers, Excel or a simple text editor:
open qdec/long.qdec.table.dat -a Numbers
open qdec/long.qdec.table.dat -a "Microsoft Excel"
open -e qdec/long.qdec.table.dat
4.2. What kind of statistical analysis to perform?
FreeSurfer offers different ways to analyze longitudinal data (details: LongitudinalStatistics). The GLM group analysis tutorials teach you how to run some simple statistical analyses on thickness maps (e.g. to find cortical regions with different thickness across groups). In this tutorial we will describe how to get your longitudinal data ready for statistical analysis, but not to do the actual model fitting.
The two most frequently used models are the simple two-stage model (LongitudinalTwoStageModel) and a fully flexible mixed effects model (LinearMixedEffectsModels) (LME), which is recommended for statistical analysis but requires Matlab knowledge. LME can, for example, deal with different time deltas and time points, missing data, and include subjects with only a single time point. The 2-stage model on the other hand, first performs a linear fit in each subject independently to reduce the repeated measures to a single number (slope, such as mm/year) and then performs a regular cross sectional analysis across subjects (e.g. to look for age or group effects).
Users who are interested in preparing data for the more powerful and complex mixed effects modeling can see how it is done by clicking here.
In this tutorial, we will prepare the data for a simple statistical model for longitudinal data, consisting of two stages:
- We reduce repeated measures to a single number for each subject. For example, quantifying atrophy rates (as mm/year thinning or percent change).
- This measure can then be compared across groups (e.g. with a standard glm_fit analysis) to detect disease or treatment effects.
4.3. Preparing the Thickness Data - QCACHE
The following command can be used to prepare the data:
Don't run this command
It will take a while and has already been done for you.
long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR
This will:
- (--qdec) read in the table
- (--meas thickness) take the thickness measure of each time point
- (--hemi) specify which hemisphere to work on (here 'lh' specified)
- (--do-avg) compute the temporal average (thickness at midpoint of linear fit, here it is just the average)
- (--do-rate) compute the rate of change (thickening in mm/year)
- (--do-pc1) compute the percent change (with respect to time point 1)
- (--do-spc) compute a symmetrized percent change (with respect to the temporal average)
- (--do-stack) output a stacked thickness file for each subject (time series)
- (--do-label) intersect the cortex label to ensure we don't include non-cortex regions
- (--time) specify the column in the longqdec.table.dat that contains the time variable (here 'years' specified)
- (--qcache) and automatically smooth everything on different levels and map it to fsaverage (note how this is specified after the flag)
- (--sd) specify the subject directory (needs to be passed explicitly since FS 5.2)
We pass all these parameters as an example. Usually you will not compute the average, select rate, pc1 or spc (depending on what you are interested in) and not explicitly write out the stack which is used for debugging (so drop --do-avg and --do-stack and select from --do-rate, --do-pc1 or do-spc). You then need to run the same command for the right hemisphere (--hemi rh).
(Note, if you split your table up into smaller tables containing only information for a specific subject each, you can run this on a cluster in parallel for each subject to speed things up (you can use the commands below to split the table up into individual subjects inside the qdec directory).
cd qdec long_qdec_table --qdec ./long.qdec.table.dat --split fsid-base cd ..
Now before continuing, let's get an idea about what the above four measures mean in our setting (with only two time points):
The temporal average is simply the average thickness: avg = 0.5 * (thick1 + thick2), usually you don't want to analyse this, as you are mainly interested in change.
The rate of change is the difference per time unit, so rate = ( thick2 - thick1 ) / (time2 - time1), here thickening in mm/year. In aging or disease we expect it to be negative in most regions (because of noise not necessarily for a single subject, but on average). For more than two time points, this is the slope of the linear fit.
The percent change (pc1) is the rate with respect to the thickness at the first time point: pc1 = rate / thick1. We also expect it to be negative and it tells how much percent thinning we have at a given cortical location.
The symmetrized percent change (spc) is the rate with respect to the average thickness: spc = rate / avg. This is a more robust measure than pc1, because thickness at time point 1 is more noisy than the average. Also spc is symmetric: when reversing the order of tp1 and tp2 it switches sign. This is not true for pc1. Therefore, and for other reasons related to increased statistical power, we recommend to use spc.
So let's investigate (some of) the results, which can be found in each base surf directory. Call this to open up the pial surface (left hemi) of subject OAS2_0001:
freeview -f OAS2_0001/surf/lh.pial:overlay=OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=OAS2_0001/surf/lh.long.thickness-stack.mgh:annot=OAS2_0001/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale --viewport 3d
Click on the 3D view button if freeview opens in a different view from what is depicted in the screenshot below, then click somewhere on the cortex to see the time course data at that location.
You are looking at the smoothed average thickness (color overlay) with values between 1 (red) and >3 mm (yellow). If you click at any location on the surface you can see a plot of the two original (unsmoothed) thickness values at the two time points. We also opened the cortical parcellation (aparc, using the annot flag) in outline style, which can be switched on and off. It helps to find out what region you are inspecting when clicking on the surface. For a single subject values are often noisy even after smoothing and show local thinning and thickening. That is why for a group analysis one needs several subjects in each group. The yellow lines/curves in the main window on the surface show the intersection of the three planes with the cortex at the selected location, and can be ignored.
For users with only an older Freeview version (no support for time course), you can use tksurfer to achieve the same (no need to do it in the course):
tksurfer OAS2_0001 lh pial -overlay $SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh -timecourse $SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-stack.mgh -aparc
In a similar fashion, you can open, for example, the symmetrized percent change. Close any open freeview windows. This time we open the overlay on fsaverage, an average subject provided with FreeSurfer and often used as the common target to compare results across subjects. The --qcache flag of long_mris_slopes has conveniently registered and mapped all results to this average subject:
freeview -f $FREESURFER_HOME/subjects/fsaverage/surf/lh.pial:overlay=$SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-spc.fwhm15.fsaverage.mgh:overlay_threshold=2,5
note the 'fsaverage' in the filename. Because there is not much change on the surfaces, the SPC will be even more noisy than the average. You can use the above commands to investigate individual results, but this is rarely necessary.
Since FS5.2: Similar to the long_mris_slopes command above to compute thickness change, you can use long_stats_slopes to compute subject rates, percent changes, etc. for the ROI stats (aseg or aparc, i.e. subcortical and cortical ROI volumes and average thickness). Once you reduced the measures to a single number per subject, you can compare groups similar to a cross sectional analysis (e.g. using mri_glm_fit).
Close freeview when finished.
5. Editing Longitudinal Data
Editing longitudinal data can be complicated, but in some cases you actually save time, as some edits are only necessary in the base. You should be familiar with Edits and might want to check also the page about LongitudinalEdits. To refresh how to perform edits using Freeview, navigate to the FreeviewGuide.
Here are some examples of some common errors you can encounter with your data. Notes: Because some of the recons take a while to run and it is not practical for you to run them during this short period of time, we ran the edits ahead of time. You will see that the edited and re-processed version have the postfix '_fixed'.
Don't run the recon-all commands on this page
It will take hours and has already been done for you.
5.1. Skullstrip Error
The most common type of skull strip failures you probably will see has to do with the cerebellum: Often, part of the cerebellum is stripped off (as you have seen in the skull strip tutorial in the troubleshooting portion earlier). Sometimes skull stripping will also leave too much dura behind. For either case, the best way to solve the problem is to adjust the watershed parameters.
Very rarely, you will see FreeSurfer fail completely in the skullstrip step (usually associated with many other errors) as is clearly the case in the following example. For the purpose of this tutorial, we will only focus on and fix the skull strip error in this case.
Before starting this section, change your SUBJECTS_DIR to where the skullstrip example data is:
export SUBJECTS_DIR=$TUTORIAL_DATA/long-tutorial/skullstrip cd $SUBJECTS_DIR
Let's take a look at the base for subject OAS2_0004:
freeview -v OAS2_0004/mri/T1.mgz \ OAS2_0004/mri/brainmask.mgz \ -f OAS2_0004/surf/lh.pial:edgecolor=red \ OAS2_0004/surf/rh.pial:edgecolor=red \ OAS2_0004/surf/lh.white:edgecolor=blue \ OAS2_0004/surf/rh.white:edgecolor=blue
You are looking at a completely misaligned average image in the base for this subject. In order to find out what causes these problems, it is important to also check the cross-sectional runs for the same subject to see if the problem is present there. While looking at the base helps to see that this subject's processing has a problem, you should always check to see whether the initial cross sectional processing already fails.
You can open the cross subjects with the commands below. NOTE: We suggest only opening one freeview window at a time if you are using an old computer or one without much RAM. Freeview uses a large amount of memory, and may slow down your computer.
freeview -v OAS2_0004_MR1/mri/T1.mgz \ OAS2_0004_MR1/mri/brainmask.mgz \ -f OAS2_0004_MR1/surf/lh.pial:edgecolor=red \ OAS2_0004_MR1/surf/rh.pial:edgecolor=red \ OAS2_0004_MR1/surf/lh.white:edgecolor=blue \ OAS2_0004_MR1/surf/rh.white:edgecolor=blue
freeview -v OAS2_0004_MR2/mri/T1.mgz \ OAS2_0004_MR2/mri/brainmask.mgz \ -f OAS2_0004_MR2/surf/lh.pial:edgecolor=red \ OAS2_0004_MR2/surf/rh.pial:edgecolor=red \ OAS2_0004_MR2/surf/lh.white:edgecolor=blue \ OAS2_0004_MR2/surf/rh.white:edgecolor=blue
These commands will open the brainmask.mgz volume, the T1.mgz, and the surfaces for both hemispheres. You can check the brainmask.mgz volume and compare it to the T1.mgz volume (use Alt+v to toggle between them).
As you can see, the skull strip for this subject is very poor for both timepoints MR1 and MR2 (cross), therefore affecting the results of the base and the longitudinals downstream. Don't be overwhelmed by other problems presented in this case. You should always find out if there is a skullstrip error first, fix that, then attack the rest of the problems. You'll be surprised how much less you'll have to go through in the end. Take it one step at a time.
5.1.1. Fixing a bad skull strip
First, take a look at the coronal slice 125 for OAS2_0004_MR1, you can see that the entire neck is still present.
Now look at OAS2_0004_MR2. This timepoint looks even worse with parts of the skull still present and parts of the brain stripped off. If you scroll to slice 66, you will see that a great part of the brain is missing. Below is the comparison between the brainmask.mgz (left) and T1.mgz (right) for slice 66.
The best way to fix a problem like this is to adjust the watershed parameters. As mentioned earlier, this can only be done on the cross-sectionals, and you'll have to use the edited cross-sectionals to recreate the base and the longitudinals afterwards. Adjust the watershed parameters for both MR1 and MR2 using the following commands. Feel free to run these commands (separately) since this step is fairly quick (This command is optional).
Don't run the recon-all commands on this page
It will take hours and has already been done for you.
recon-all -subjid OAS2_0004_MR1 -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas
recon-all -subjid OAS2_0004_MR2 -skullstrip -wsthresh 55 -clean-bm -no-wsgcaatlas
For OAS2_0004_MR1, the brain is intact while a lot of the skull is left behind, therefore we decreased the watershed threshold. As for OAS2_0004_MR2, we don't want to strip away more brain so we increased the threshold. Play around with different numbers and see what you get. If you ran the commands, take a look at your output volumes (directory w/o _fixed), or simply check our edited volumes, and verify that the result of the new skull stripping is correct.
It is necessary to run the rest of the cross sectional recon-all steps for all timepoints that you made an adjustment to:
recon-all -subjid OAS2_0004_MR1 -autorecon2 -autorecon3
recon-all -subjid OAS2_0004_MR2 -autorecon2 -autorecon3
These _fixed versions were already run with -autorecon2 and -autorecon3.
freeview -v OAS2_0004_MR1_fixed/mri/T1.mgz OAS2_0004_MR1_fixed/mri/brainmask.mgz
freeview -v OAS2_0004_MR2_fixed/mri/T1.mgz OAS2_0004_MR2_fixed/mri/brainmask.mgz
To save time, you can check in with the recon-all-status.log in the scripts directory of these subjects to see if the normalization step is complete. Once that step is complete, you can start recreating your base (remove/rename the base dir if it existed, e.g. mv OAS2_0004 OAS2_0004_old, before running this). Alternatively, you can wait until the recons are complete to check whether all surfaces are updated as desired. Here are the results for OAS2_0004_MR1 slice 125 and OAS2_0004_MR2 slice 66.
*Notice the huge improvement between OAS2_0004_MR2_fixed and the original one. You might not arrive at this output if you just ran the watershed parameter with threshold 55 and rerunning -autorecon2 -autorecon3 once.
After those initial runs, we noticed that there was still a good amount of skull left over, so we ran the following commands:
Don't run the recon-all commands on this page
It will take hours and has already been done for you.
recon-all -skullstrip -subjid OAS2_0004_MR2
recon-all -autorecon2 -autorecon3 -subjid OAS2_0004_MR2
Sometimes just rerunning the -skullstrip step will help fix the problem without you having to do any extra adjustments. This is because during this step, FreeSurfer uses the existing brainmask.mgz as input and that can make a big difference on the output.
5.1.2. Recreating base and longs
Now you are ready to recreate the base.
Don't run the recon-all commands on this page
It will take hours and has already been done for you.
recon-all -base OAS2_0004 -tp OAS2_0004_MR1 -tp OAS2_0004_MR2 -all
Then, the final step is to recreate the longitudinals once the base and cross sectional runs are complete:
recon-all -long OAS2_0004_MR1 OAS2_0004 -all
recon-all -long OAS2_0004_MR2 OAS2_0004 -all
**NOTE**: When recreating the base and longitudinals, it is recommended to remove or rename the existing base and longitudinal directories and start those processes from scratch, if possible.
5.1.3. Viewing final results
You can examine the corrected version of the base and longitudinals by using the following commands in separate terminals.
freeview -v OAS2_0004_fixed/mri/T1.mgz \ OAS2_0004_fixed/mri/brainmask.mgz \ -f OAS2_0004_fixed/surf/lh.pial:edgecolor=red \ OAS2_0004_fixed/surf/rh.pial:edgecolor=red \ OAS2_0004_fixed/surf/lh.white:edgecolor=blue \ OAS2_0004_fixed/surf/rh.white:edgecolor=blue
freeview -v OAS2_0004_MR1.long.OAS2_0004_fixed/mri/T1.mgz \ OAS2_0004_MR1.long.OAS2_0004_fixed/mri/brainmask.mgz \ -f OAS2_0004_MR1.long.OAS2_0004_fixed/surf/lh.pial:edgecolor=red \ OAS2_0004_MR1.long.OAS2_0004_fixed/surf/rh.pial:edgecolor=red \ OAS2_0004_MR1.long.OAS2_0004_fixed/surf/lh.white:edgecolor=blue \ OAS2_0004_MR1.long.OAS2_0004_fixed/surf/rh.white:edgecolor=blue
freeview -v OAS2_0004_MR2.long.OAS2_0004_fixed/mri/T1.mgz \ OAS2_0004_MR2.long.OAS2_0004_fixed/mri/brainmask.mgz \ -f OAS2_0004_MR2.long.OAS2_0004_fixed/surf/lh.pial:edgecolor=red \ OAS2_0004_MR2.long.OAS2_0004_fixed/surf/rh.pial:edgecolor=red \ OAS2_0004_MR2.long.OAS2_0004_fixed/surf/lh.white:edgecolor=blue \ OAS2_0004_MR2.long.OAS2_0004_fixed/surf/rh.white:edgecolor=blue
If you were horrified while looking at the base earlier, which is the left image at coronal slice 120 below, compare it to the right image, also at coronal slice 120, after the skullstrip fix.
And here are the longitudinals for OAS2_0004_MR2.long.OAS2_0004. Before (left) at slice 145 and after (right) at the same slice.
Note that, although much has been fixed, there are still problems here that need special treatment (e.g. exclusion of wm from the surfaces at various places). With these, you can start making manual edits on the wm or you can use other appropriate methods. *Take home message* - although your case might appear like this one we just went through, and you might think that it's impossible to remedy, take it one step at a time. Usually several adjustments to the skullstrip parameters can make this big of a difference.
For more details on skull strip errors and the different ways to fix them, refer back to the Troubleshooting Skull Strip Tutorial.
5.2. Pial/Brainmask Edits
Before starting this section, set your SUBJECTS_DIR back to the parent directory for this tutorial:
export SUBJECTS_DIR=$TUTORIAL_DATA/long-tutorial/ cd $SUBJECTS_DIR
Sometimes you will come across a case where you need to make edits to the brainmask.mgz to correct the pial surfaces. Open subject OAS2_0057 to see where and how this type of edit should be done.
First, open the base:
freeview -v OAS2_0057/mri/T1.mgz \ OAS2_0057/mri/brainmask.mgz \ -f OAS2_0057/surf/lh.pial:edgecolor=red \ OAS2_0057/surf/rh.pial:edgecolor=red \ OAS2_0057/surf/lh.white:edgecolor=blue \ OAS2_0057/surf/rh.white:edgecolor=blue
This will open the brainmask.mgz volume, T1.mgz volume, and all surfaces. You can also check out the cross-sectionals and the longitudinals of this subject to check if the problem is present in all parts of the stream. NOTE: We suggest only opening one freeview window at a time if you are using an old computer or one without much RAM. Freeview uses a large amount of memory, and may slow down your computer.
freeview -v OAS2_0057_MR1/mri/T1.mgz \ OAS2_0057_MR1/mri/brainmask.mgz \ -f OAS2_0057_MR1/surf/lh.pial:edgecolor=red \ OAS2_0057_MR1/surf/rh.pial:edgecolor=red \ OAS2_0057_MR1/surf/lh.white:edgecolor=blue \ OAS2_0057_MR1/surf/rh.white:edgecolor=blue
freeview -v OAS2_0057_MR2/mri/T1.mgz \ OAS2_0057_MR2/mri/brainmask.mgz \ -f OAS2_0057_MR2/surf/lh.pial:edgecolor=red \ OAS2_0057_MR2/surf/rh.pial:edgecolor=red \ OAS2_0057_MR2/surf/lh.white:edgecolor=blue \ OAS2_0057_MR2/surf/rh.white:edgecolor=blue
freeview -v OAS2_0057_MR1.long.OAS2_0057/mri/T1.mgz \ OAS2_0057_MR1.long.OAS2_0057/mri/brainmask.mgz \ -f OAS2_0057_MR1.long.OAS2_0057/surf/lh.pial:edgecolor=red \ OAS2_0057_MR1.long.OAS2_0057/surf/rh.pial:edgecolor=red \ OAS2_0057_MR1.long.OAS2_0057/surf/lh.white:edgecolor=blue \ OAS2_0057_MR1.long.OAS2_0057/surf/rh.white:edgecolor=blue
freeview -v OAS2_0057_MR2.long.OAS2_0057/mri/T1.mgz \ OAS2_0057_MR2.long.OAS2_0057/mri/brainmask.mgz \ -f OAS2_0057_MR2.long.OAS2_0057/surf/lh.pial:edgecolor=red \ OAS2_0057_MR2.long.OAS2_0057/surf/rh.pial:edgecolor=red \ OAS2_0057_MR2.long.OAS2_0057/surf/lh.white:edgecolor=blue \ OAS2_0057_MR2.long.OAS2_0057/surf/rh.white:edgecolor=blue
See if you can find the slices where you will need to edit the braimask.mgz in order to correct the surfaces. Continue reading for a detailed description on how and at which stage you can fix this problem.
6. Making Pial Surfaces Edits
Towards the anterior region of the brain, notice that there's a lot of dura remaining from the skullstrip making the pial surface extend farther out from the grey matter. In these cases, manual edits will be the quickest way to fix the problem. Also notice that this problem exists in all three stages: cross, base, and long. Except for very special cases (e.g. comparing cross sectional vs. longitudinal processing) you will not need the final cross-sectional results, but instead use the longitudinal results for downstream analysis. Therefore, it is easiest and quickest now to just edit the base, and then rerun the base and longitudinal data from there. If you prefer to correct the cross-sectionals, you can also do that, the base should automatically be fixed, but needs to be checked.
Remember to delete the base directory when you are recreating a new base from your edited cross time points, or at least delete the brainmask.mgz file from the mri directory of the base before rerunning it, to make sure that the updates are transferred.
The following are before images from the base OAS2_0057 coronal slices 174 and 203, respectively.
We will step through the quick route of just editing the base. After deleting the extra dura from brainmask.mgz, rerun the base with the following command:
Don't run any of the following recon-all commands It will take hours to run and has already been done for you.
recon-all -base OAS2_0057 -autorecon-pial
To rerun the longitudinals, use the following commands (note - it is better if you delete or rename the existing longitudinal directories for this subject. Or you can delete the brainmask.mgz in the mri directories if you don't want to delete the whole subjectdir, maybe because of other edits in the long runs.)
recon-all -long OAS2_0057_MR1 OAS2_0057 -all
recon-all -long OAS2_0057_MR2 OAS2_0057 -all
Here is the final output of the base for the same coronal slices, 174 and 203:
Compare the output volumes of the long (time point MR1) with the before-edit versions:
freeview -v OAS2_0057_MR1.long.OAS2_0057/mri/T1.mgz \ OAS2_0057_MR1.long.OAS2_0057/mri/brainmask.mgz \ -f OAS2_0057_MR1.long.OAS2_0057/surf/lh.pial:edgecolor=red \ OAS2_0057_MR1.long.OAS2_0057/surf/rh.pial:edgecolor=red \ OAS2_0057_MR1.long.OAS2_0057/surf/lh.white:edgecolor=blue \ OAS2_0057_MR1.long.OAS2_0057/surf/rh.white:edgecolor=blue
freeview -v OAS2_0057_MR1.long.OAS2_0057_fixed/mri/T1.mgz \ OAS2_0057_MR1.long.OAS2_0057_fixed/mri/brainmask.mgz \ -f OAS2_0057_MR1.long.OAS2_0057_fixed/surf/lh.pial:edgecolor=red \ OAS2_0057_MR1.long.OAS2_0057_fixed/surf/rh.pial:edgecolor=red \ OAS2_0057_MR1.long.OAS2_0057_fixed/surf/lh.white:edgecolor=blue \ OAS2_0057_MR1.long.OAS2_0057_fixed/surf/rh.white:edgecolor=blue
Here is the before image (left) of OAS2_0057_MR1.long.OAS2_0057 (slice 174) and the corresponding after image (right - slice 174).
The same improvement should have occurred in OAS2_0057_MR2.long.OAS2_0057.
7. Control Points Edits
Sometimes, there are areas in the white matter with intensity lower than 110 and where the wm is not included in the surfaces. The best way to fix this problem is to add control points.
Take a look at the next subject, OAS2_0121 in all cross, base, and long to see if you can find the places that need control points. NOTE: We suggest only opening one freeview window at a time if you are using an old computer or one without much RAM. Freeview uses a large amount of memory, and may slow down your computer.
freeview -v OAS2_0121_MR1/mri/T1.mgz \ OAS2_0121_MR1/mri/brainmask.mgz \ -f OAS2_0121_MR1/surf/lh.pial:edgecolor=red \ OAS2_0121_MR1/surf/rh.pial:edgecolor=red \ OAS2_0121_MR1/surf/lh.white:edgecolor=blue \ OAS2_0121_MR1/surf/rh.white:edgecolor=blue
freeview -v OAS2_0121_MR2/mri/T1.mgz \ OAS2_0121_MR2/mri/brainmask.mgz \ -f OAS2_0121_MR2/surf/lh.pial:edgecolor=red \ OAS2_0121_MR2/surf/rh.pial:edgecolor=red \ OAS2_0121_MR2/surf/lh.white:edgecolor=blue \ OAS2_0121_MR2/surf/rh.white:edgecolor=blue
freeview -v OAS2_0121/mri/T1.mgz \ OAS2_0121/mri/brainmask.mgz \ -f OAS2_0121/surf/lh.pial:edgecolor=red \ OAS2_0121/surf/rh.pial:edgecolor=red \ OAS2_0121/surf/lh.white:edgecolor=blue \ OAS2_0121/surf/rh.white:edgecolor=blue
freeview -v OAS2_0121_MR1.long.OAS2_0121/mri/T1.mgz \ OAS2_0121_MR1.long.OAS2_0121/mri/brainmask.mgz \ -f OAS2_0121_MR1.long.OAS2_0121/surf/lh.pial:edgecolor=red \ OAS2_0121_MR1.long.OAS2_0121/surf/rh.pial:edgecolor=red \ OAS2_0121_MR1.long.OAS2_0121/surf/lh.white:edgecolor=blue \ OAS2_0121_MR1.long.OAS2_0121/surf/rh.white:edgecolor=blue
freeview -v OAS2_0121_MR2.long.OAS2_0121/mri/T1.mgz \ OAS2_0121_MR2.long.OAS2_0121/mri/brainmask.mgz \ -f OAS2_0121_MR2.long.OAS2_0121/surf/lh.pial:edgecolor=red \ OAS2_0121_MR2.long.OAS2_0121/surf/rh.pial:edgecolor=red \ OAS2_0121_MR2.long.OAS2_0121/surf/lh.white:edgecolor=blue \ OAS2_0121_MR2.long.OAS2_0121/surf/rh.white:edgecolor=blue
Notice that the intensity for the area in the bottom corner of the right hemisphere around slice 90 is only around 90 something instead of 110, and the surfaces here do not include all of the gm and wm. Because this problem occurs in both cross-sectionals, the base and subsequently the longitudinals are also affected. In cases like this, it depends on which data you are planning to use, you can choose to edit either the cross, base, or long. Control points work in all three stages.
In this example, we're demonstrating what the effect will be when adding control points at the very beginning of the stream - in the cross-sectionals. Find all the slices that have this problem and add control points carefully on the wm voxels.
7.1. Fixing the cross
You want to add control points at the stem of white matter strands where voxel values are below 110. You can also add control points along the strand. Here is what we did. For cross sectional time point 1 (OAS2_0121_MR1), here is an example of coronal slice 90 before (left) and after (right) control points were added and the cross sectional was re-run.
For cross time point 2 (OAS2_0121_MR2), here is an example of coronal slice 92 before and after control points are added
Once you are satisfied with your control points placements, save it, and run the following commands to complete the fixed cross sectional runs:
Don't run the recon-all commands on this page
It will take hours and has already been done for you.
recon-all -subjid OAS2_0121_MR1 -autorecon2 -autorecon3
recon-all -subjid OAS2_0121_MR2 -autorecon2 -autorecon3
After that is complete (or when the CA normalization step is complete - you can check in the recon-all-status.log), you can start rerunning the base (remember to delete or rename the base if it already existed, e.g. mv OAS2_0121 OAS2_0121_old). Or, if you prefer, you can wait until the recons are complete to check whether you are satisfied with the results before beginning the next step.
To inspect the fixed version of these two timepoints, run:
freeview -v OAS2_0121_MR1_fixed/mri/T1.mgz \ OAS2_0121_MR1_fixed/mri/brainmask.mgz \ -f OAS2_0121_MR1_fixed/surf/lh.pial:edgecolor=red \ OAS2_0121_MR1_fixed/surf/rh.pial:edgecolor=red \ OAS2_0121_MR1_fixed/surf/lh.white:edgecolor=blue \ OAS2_0121_MR1_fixed/surf/rh.white:edgecolor=blue
freeview -v OAS2_0121_MR2_fixed/mri/T1.mgz \ OAS2_0121_MR2_fixed/mri/brainmask.mgz \ -f OAS2_0121_MR2_fixed/surf/lh.pial:edgecolor=red \ OAS2_0121_MR2_fixed/surf/rh.pial:edgecolor=red \ OAS2_0121_MR2_fixed/surf/lh.white:edgecolor=blue \ OAS2_0121_MR2_fixed/surf/rh.white:edgecolor=blue
7.2. Fixing/Rerunning the base
To rerun the base, you would run this command:
recon-all -base OAS2_0121 -tp OAS2_0121_MR1 -tp OAS2_0121_MR2 -all
Once you are done with the base, check to see whether the surfaces are now including all white matter (we ran the above command for you, results are in OAS2_0121_intermediate):
freeview -v OAS2_0121_intermediate/mri/T1.mgz \ OAS2_0121_intermediate/mri/brainmask.mgz \ -f OAS2_0121_intermediate/surf/lh.pial:edgecolor=red \ OAS2_0121_intermediate/surf/rh.pial:edgecolor=red \ OAS2_0121_intermediate/surf/lh.white:edgecolor=blue \ OAS2_0121_intermediate/surf/rh.white:edgecolor=blue
Notice that although the surfaces improved, it is not perfect. In this case, you can add more control points to the base and would rerun with the command below (you would re-run the edited base without the _intermediate suffix as that is just a intermediate copy that we created for you):
recon-all -base OAS2_0121 -autorecon2 -autorecon3
Now the base is much better. Compare these images at slice 106. These are taken from OAS2_0121_intermediate before more control points were added (below right) and OAS2_0121_fixed (below left). You can open these two volumes using Freeview, and also compare to the original base (OAS2_0121) before the cross sectionals were fixed if you want.
7.3. Rerunning the long
The last step is to rerun the longitudinals (also remember to remove/rename existing longitudinal directories first), which would be done with these commands:
recon-all -long OAS2_0121_MR1 OAS2_0121 -all
recon-all -long OAS2_0121_MR2 OAS2_0121 -all
Compare the output below
freeview -v OAS2_0121_MR1.long.OAS2_0121/mri/T1.mgz \ OAS2_0121_MR1.long.OAS2_0121/mri/brainmask.mgz \ -f OAS2_0121_MR1.long.OAS2_0121/surf/lh.pial:edgecolor=red \ OAS2_0121_MR1.long.OAS2_0121/surf/rh.pial:edgecolor=red \ OAS2_0121_MR1.long.OAS2_0121/surf/lh.white:edgecolor=blue \ OAS2_0121_MR1.long.OAS2_0121/surf/rh.white:edgecolor=blue
freeview -v OAS2_0121_MR1.long.OAS2_0121_fixed/mri/T1.mgz \ OAS2_0121_MR1.long.OAS2_0121_fixed/mri/brainmask.mgz \ -f OAS2_0121_MR1.long.OAS2_0121_fixed/surf/lh.pial:edgecolor=red \ OAS2_0121_MR1.long.OAS2_0121_fixed/surf/rh.pial:edgecolor=red \ OAS2_0121_MR1.long.OAS2_0121_fixed/surf/lh.white:edgecolor=blue \ OAS2_0121_MR1.long.OAS2_0121_fixed/surf/rh.white:edgecolor=blue
For the longitudinals, control points were automatically copied over from the cross-sectionals, and the surfaces were initialized from the base, therefore making a great improvement on the surfaces at this end of the stream.
The before (left) and after (right) images from OAS2_0121_MR1.long.OAS2_0121 at slice 107.
8. White Matter Edits
White matter edits are possibly the most common type of edits you will come across in data. In many cases, even a difference of 1 wm voxel can cause a huge defect in the surfaces. Take a look at the following subject. For this one, we will open the brainmask.mgz volume and compare it to the wm.mgz volume instead of T1.mgz. If you're using tkmedit instead of Freeview, load wm.mgz as your "Aux Volume". NOTE: We suggest only opening one freeview window at a time if you are using an old computer or one without much RAM. Freeview uses a large amount of memory, and may slow down your computer.
freeview -v OAS2_0185/mri/wm.mgz \ OAS2_0185/mri/brainmask.mgz \ -f OAS2_0185/surf/lh.pial:edgecolor=red \ OAS2_0185/surf/rh.pial:edgecolor=red \ OAS2_0185/surf/lh.white:edgecolor=blue \ OAS2_0185/surf/rh.white:edgecolor=blue
freeview -v OAS2_0185_MR1/mri/wm.mgz \ OAS2_0185_MR1/mri/brainmask.mgz \ -f OAS2_0185_MR1/surf/lh.pial:edgecolor=red \ OAS2_0185_MR1/surf/rh.pial:edgecolor=red \ OAS2_0185_MR1/surf/lh.white:edgecolor=blue \ OAS2_0185_MR1/surf/rh.white:edgecolor=blue
freeview -v OAS2_0185_MR2/mri/wm.mgz \ OAS2_0185_MR2/mri/brainmask.mgz \ -f OAS2_0185_MR2/surf/lh.pial:edgecolor=red \ OAS2_0185_MR2/surf/rh.pial:edgecolor=red \ OAS2_0185_MR2/surf/lh.white:edgecolor=blue \ OAS2_0185_MR2/surf/rh.white:edgecolor=blue
freeview -v OAS2_0185_MR1.long.OAS2_0185/mri/wm.mgz \ OAS2_0185_MR1.long.OAS2_0185/mri/brainmask.mgz \ -f OAS2_0185_MR1.long.OAS2_0185/surf/lh.pial:edgecolor=red \ OAS2_0185_MR1.long.OAS2_0185/surf/rh.pial:edgecolor=red \ OAS2_0185_MR1.long.OAS2_0185/surf/lh.white:edgecolor=blue \ OAS2_0185_MR1.long.OAS2_0185/surf/rh.white:edgecolor=blue
freeview -v OAS2_0185_MR2.long.OAS2_0185/mri/wm.mgz \ OAS2_0185_MR2.long.OAS2_0185/mri/brainmask.mgz \ -f OAS2_0185_MR2.long.OAS2_0185/surf/lh.pial:edgecolor=red \ OAS2_0185_MR2.long.OAS2_0185/surf/rh.pial:edgecolor=red \ OAS2_0185_MR2.long.OAS2_0185/surf/lh.white:edgecolor=blue \ OAS2_0185_MR2.long.OAS2_0185/surf/rh.white:edgecolor=blue
Toggle between the two volumes (use the opacity slider) and see if you can spot an area where a simple wm edit will make a huge difference to the surfaces.
8.1. Making white matter edits
For the longitudinal stream, it is recommended that you make wm.mgz edits to the base. This is because even though the long transfers manual wm edits from the cross, it still takes the surfaces from the base, and if the base surfaces did not improve, neither will the long. The only way to make corrections to the base surfaces themselves is to edit wm.mgz on the base. Therefore, making wm.mgz edits right on the base can save you a lot of time. Of course it is best to edit all stages (all cross time points and base), but often it is sufficient to edit only the base. Were you able to find the area that needs intervention? Here is what we found. You can see below on the brainmask.mgz (left) that the pial surface is cutting through the wm. If you toggle to the wm.mgz, you can see that there are a few wm voxels missing.
This happens at the tip of the lh temporal lobe within several slices. Below is an example of coronal slice 166.
Add wm voxels to connect the wm together in all the slices that need it. Here is an example of what we did in slice 168. Bright wm voxels in the temporal lobes have been manually added.
After you are satisfied with your edits, save the edited volume and rerun the base.
Don't run the recon-all commands on this page
It will take hours and has already been done for you.
recon-all -base OAS2_0185 -autorecon2-wm -autorecon3
After that is done, check the surfaces on base using Freeview (or tkmedit for older version of Freeview).
freeview -v OAS2_0185_fixed/mri/wm.mgz \ OAS2_0185_fixed/mri/brainmask.mgz \ -f OAS2_0185_fixed/surf/lh.pial:edgecolor=red \ OAS2_0185_fixed/surf/rh.pial:edgecolor=red \ OAS2_0185_fixed/surf/lh.white:edgecolor=blue \ OAS2_0185_fixed/surf/rh.white:edgecolor=blue
This is what it should look like now in slice 166.
When the surfaces are all corrected, you would recreate the long (make sure you remove the long directories before the rerun - or at the very least, remove the wm.mgz files in all the mri sub-directories of the long runs).
recon-all -long OAS2_0185_MR1 OAS2_0185 -all
recon-all -long OAS2_0185_MR2 OAS2_0185 -all
Inspect your output:
freeview -v OAS2_0185_MR1.long.OAS2_0185_fixed/mri/wm.mgz \ OAS2_0185_MR1.long.OAS2_0185_fixed/mri/brainmask.mgz \ -f OAS2_0185_MR1.long.OAS2_0185_fixed/surf/lh.pial:edgecolor=red \ OAS2_0185_MR1.long.OAS2_0185_fixed/surf/rh.pial:edgecolor=red \ OAS2_0185_MR1.long.OAS2_0185_fixed/surf/lh.white:edgecolor=blue \ OAS2_0185_MR1.long.OAS2_0185_fixed/surf/rh.white:edgecolor=blue
freeview -v OAS2_0185_MR2.long.OAS2_0185_fixed/mri/wm.mgz \ OAS2_0185_MR2.long.OAS2_0185_fixed/mri/brainmask.mgz \ -f OAS2_0185_MR2.long.OAS2_0185_fixed/surf/lh.pial:edgecolor=red \ OAS2_0185_MR2.long.OAS2_0185_fixed/surf/rh.pial:edgecolor=red \ OAS2_0185_MR2.long.OAS2_0185_fixed/surf/lh.white:edgecolor=blue \ OAS2_0185_MR2.long.OAS2_0185_fixed/surf/rh.white:edgecolor=blue
See here that the improved surfaces in the base also correct the surfaces in the long. Compare MR1.long slice 166 in the before (left) and after (right) images below.
The same improvement should have occurred with MR2.longitudinal run.
9. Quiz
You can test your knowledge of this tutorial by clicking here for a quiz!


text:
Berkeleyside is thrilled to announce that on Monday March 5th we will be hosting the Berkeleyside Local Business Forum 2012: Startup Berkeley.
The Forum's focus will be the strengths, and weaknesses, of the city of Berkeley for startups. What does it take to turn an idea into a successful business, how can one nurture innovation, and what can be done to improve the startup climate here?
Featured panelists joining the conversation at the Forum include: Will Wright, creator of The Sims and founder of Stupid Fun Club; David Hyman, founder and CEO of streaming music service MOG, June Taylor, founder of jam and marmalade company The Still Room; and Rauly Butler, Senior Vice President Retail at Mechanics Bank.
"An extraordinary amount of innovation comes out of Berkeley in a variety of realms," said Lance Knobel, one of the founders of Berkeleyside. "But Berkeley is still seen as rough ground for business startups. We want to examine the realities of Berkeley for new business ventures."
The Forum will have a number of panel discussions, but the format will be highly interactive. At last year's Berkeleyside Local Business Forum — to which we welcomed Autodesk CEO Carl Bass and Chris Anderson, Editor in Chief of Wired, among others — questions from the audience provided much of the impetus for the conversation.
Among the topics the Forum will concentrate on are the positive assets Berkeley offers for new businesses, the hurdles that businesses face in the city, and the wider issues of how a vigorous business culture in Berkeley can effectively tie into the innovative economy of the Bay Area.
The Berkeleyside Local Business Forum 2012 is organized in partnership with Mechanics Bank, and is sponsored by GreenerPrinter. Further details of the Forum will be posted regularly here on Berkeleyside, on the Forum Facebook page and on Twitter (#BerkForum).
Whether you are a business owner, an entrepreneur looking to start a business, an incubator, a service provider to startups, or simply a citizen interested in the future of your city, we look forward to seeing you there.
When: Monday March 5th, 7:00- 9:00 pm. Doors open at 6:00 pm (plenty of time before and after for networking).
Where: Freight & Salvage Coffeehouse, 2020 Addison Street in downtown Berkeley. Refreshments, including beer and wine, available to purchase.
Tickets: $10 ($5 for students and seniors), available through Brown Paper Tickets.