DBP2:Harvard:Brain Segmentation Roadmap - Revision history

Sylvain: /* Related Clinical Projects */

2010-11-02T20:24:20Z

Related Clinical Projects

Sylvain: /* Related Clinical Projects */

2010-11-02T20:18:52Z

Related Clinical Projects

Sylvain: /* Module */

2010-11-02T19:14:30Z

Module

Sylvain: /* Module */

2010-11-02T19:14:14Z

Module

Kubicki: /* Work in Progress */

2010-10-29T21:23:11Z

Work in Progress

Kubicki: /* Work Accomplished */

2010-10-29T21:21:25Z

Work Accomplished

Kubicki: /* Work in Progress */

2010-10-29T21:08:47Z

Work in Progress

Kubicki: /* Staffing Plan */

2010-10-29T20:55:27Z

Staffing Plan

Kubicki: /* Staffing Plan */

2010-10-29T20:54:54Z

Staffing Plan

Kubicki: /* Work in Progress */

2010-10-29T20:53:11Z

Work in Progress

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 We use stochastic tractography to segment thalamus into discrete ROIs based on its connectivity to 10 cortical ROIs (for each hemisphere) of the frontal lobe. Cortical ROIs are extracted using free surfer, and co-registered to DTI space using FSL. Thalamus is painted by connectivity using additional in-house matlab script (available after request). Volumes of the thalamic ROIs as well as FA for each individual connection are our measures of interest.
 :* Results presentation and paper submission. Data analysis and paper in preparation.
 ;* Tractography Comparison Project

@@ Line 126: / Line 126: @@
 We are using stochastic tractography to examine white matter connectivity between medial anterior and posterior OFC and rostral ACC (cognitive part of ACC).
 :* Results presentation and paper submission. Data was analyzed for 27 SZ and 256 HC subjects. Schizophrenia group demonstrated significant mean FA reduction in the connection between left anterior OFC and ACC, and between bilateral posterior OFC. Poster was presented at Annual Biological Psychiatry Meeting, paper in preparation.
 ;* Study of thalamus segmentation based on cortical connectivity in Chronic Schizophrenia

@@ Line 63: / Line 63: @@
 :* Module documentation and training data can be found here:
-:**[[Slicer3:Stochastic_tractography]]]
+:**[[Slicer3:Stochastic_tractography]]
 ==Work Accomplished==

@@ Line 62: / Line 62: @@
 Then, probability maps can be saved as ROIs, and either used directly, or thresholded (at certain probability, step claimed by few publications to remove noise) in slicer to mask and compute average FA, Mode, Trace for entire connection. Diffusion indices can be also weighted by the probability of connection for each voxel.
-:* Module documentation can be found here:
+:* Module documentation and training data can be found here:
-:**[[Media:IJdata.tar.gz|Training Dataset]]
+:**[[Slicer3:Stochastic_tractography]]]
 ==Work Accomplished==

@@ Line 81: / Line 81: @@
 :* Algorithm was also used to trace smaller white matter fiber tracts, such as Cingulum, Fornix, Uncinate Fasciculus, Arcuate Fasciculus on 3T "Santa Fe" dataset (http://www.na-mic.org/Wiki/index.php/SanteFe.Tractography.Conference)
-== Work in Progress ==
+== Related Clinical Projects ==
-−
 ;* Arcuate Fasciculus Extraction and Analysis in Schizophrenia
 [[Image:STArcuate.jpg|thumb|right|200px|<font size=1>Figure 7: The arcuate fasciculus including seed, midpoint and target ROI's.</font>]]
@@ Line 137: / Line 135: @@
 ;* Tractography Comparison Project
 We are also working on a [http://www.na-mic.org/Wiki/index.php/SanteFe.Tractography.Conference tractography comparison project]dataset, where we apply stochastic tractography to phantom, as well as test dataset.
 ===Staffing Plan===

@@ Line 95: / Line 95: @@
 ; - Related Clinical Projects
-;* Arcuate Fasciculus Extraction Project
+;* Arcuate Fasciculus Extraction and Analysis in Schizophrenia
 [[Image:STArcuate.jpg|thumb|right|200px|<font size=1>Figure 7: The arcuate fasciculus including seed, midpoint and target ROI's.</font>]]
 We are investigating Arcuate Fasciculus using Stochastic Tractography (Figure 7). This structure is especially important in both VCFS and schizophrenia, as it connects language related areas (Brocka and Wernicke's), and is involved in language processing quite disturbed in schizophrenia patients. It also can not be reliably traced using deterministic tractography.
@@ Line 108: / Line 108: @@
 [[Image:connectivity1.jpg|thumb|right|200px|<font size=1>Figure 8: Maps of inferior frontal cortex (Broca) connectivity in controls and patients with schizophrenia.</font>]]
-;* Semantic Network Connectivity Project
+;* Semantic Network Connectivity in Schizophrenia
 We use combination of fMRI and DTI data to define and characterize functional and anatomical connectivity within the semantic processing network in schizophrenia.
 :Project involves:
@@ Line 133: / Line 133: @@
 [[Image:Anna.png|thumb|right|200px|<font size=1>Figure 10: Max Plank data showing tracts through the corpus connecting 2 cortical ROIs defined by fMRI activations.</font>]]
-;* Study of Default Network
+;* Study of Default Network in Psychosis
 We are collaborating with the Department of Neurophysiology Max Planck Institute in Frankfurt (Anna Rotarska contact person), where we use stochastic tractography to measure integrity of anatomical connections within the default network in schizophrenia. The fMRI resting state results (ROIs) have been co-registered with anatomical scans, and then again registered to DTI space. Figure 8 shows pilot data of the white matter connections through the corpus callosum between the left and the right auditory cortex ROIs as defined by fMRI data.
 :* Results presentation and paper submission. We are in the process of analyzing results.
 ;* Tractography Comparison Project

@@ Line 142: / Line 142: @@
 ===Staffing Plan===
-* Sylvain and Yogesh are the DBP resources charged with adapting the tools in the NA-MIC Kit to the DBP needs
+* Sylvain and Ryan are the DBP resources charged with adapting the tools in the NA-MIC Kit to the DBP needs
-* Andrew Rauch, our NAMIC RA is our NAMIC RA.
+* Andrew Rauch is our NAMIC RA.
 * Ryan is our NAMIC software engineer. He is responsible for improving the STM (Stochastic Tractography Module), and making sure software works with STM compliant datasets.
 * Polina is the algorithm core contact

@@ Line 93: / Line 93: @@
 == Work in Progress ==
-; A - Optimization and Testing of stochastic tractography module :
+; - Related Clinical Projects
 ;* Arcuate Fasciculus Extraction Project
 [[Image:STArcuate.jpg|thumb|right|200px|<font size=1>Figure 7: The arcuate fasciculus including seed, midpoint and target ROI's.</font>]]
-We have started the project of investigating Arcuate Fasciculus using Stochastic Tractography (Figure 7). This structure is especially important in both VCFS and schizophrenia, as it connects language related areas (Brocka and Wernicke's), and is involved in language processing quite disturbed in schizophrenia patients. It also can not be reliably traced using deterministic tractography.
+We are investigating Arcuate Fasciculus using Stochastic Tractography (Figure 7). This structure is especially important in both VCFS and schizophrenia, as it connects language related areas (Brocka and Wernicke's), and is involved in language processing quite disturbed in schizophrenia patients. It also can not be reliably traced using deterministic tractography.
 :Project involves:
 :* Whole brain segmentation, and automatic extraction of regions interconnected by Arcuate Fasciculus (Inferior frontal and Superior Temporal Gyri).
 :* White matter segmentation, in order to prevent algorithm from traveling through the ventricles, where diffusivity is high.
 :* Non-linear registration of labelmaps to the DTI space.
-:* Seeding tracts. We have piloted it using 5000 seeds per voxel, however it is quite time consuming running it on even most powerful computers in the lab, so we have experimented with smaller number of seeds per voxel. We tested 1000 seeds, which gave virtually identical results.
+:* Seeding tracts within both ROIs.
 :* Extracting path of interest, and calculating FA along the path for group comparison. Presentation of previous results for 7 schizophrenics and 12 control subjects, can be found here: [[Media:NAMIC_AHM_Arcuate.ppt|Progress Report Presentation]].
-:* Results presentation and paper submission. Abstract was accepted and results presented at the World Biological Psychiatry Symposium in Venice, Italy. Paper is in preparation.
+:* Results presentation and paper submission. Abstract was accepted and results presented at the World Biological Psychiatry Symposium in Venice, Italy. Paper has been submitted to Neuroimage.
 [[Image:connectivity1.jpg|thumb|right|200px|<font size=1>Figure 8: Maps of inferior frontal cortex (Broca) connectivity in controls and patients with schizophrenia.</font>]]
@@ Line 121: / Line 116: @@
 :* Use of stochastic tractography to identify connections between functional nodes
 :* Correlational analysis involving anatomical and functional connectivity data.
-:* Results presentation and paper submission. Data was presented at HBM conference in 2007, paper has been submitted to HBM.
+:* Results presentation and paper submission. Data was presented at HBM conference in 2007, paper has been accepted for publication at HBM.
 :* <font color="red">'''New: '''</font>June 10th 2009, paper accepted for publication in Human Brain Mapping: "Functional and Anatomical Connectivity Abnormalities in Left Inferior Frontal Gyrus in Schizophrenia" by Jeong, Wible, Hashimoto and Kubicki, HBM in Press
@@ Line 134: / Line 129: @@
 :* Extracting paths of interest, and calculating FA along the paths for group comparison.
 :* Correlational analysis involving anatomical and connectivity data, clinical information and genetic data.
-:* Results presentation and paper submission. First step of data analysis has been already accomplished, we are in the process of registering structural and DTI data and preparing DTI data for stochastic tractography analysis. We plan to submit an abstract with study results for Biological Psychiatry symposium (dedline December 2009).
+:* Results presentation and paper submission. We plan to submit an abstract with study results for Biological Psychiatry symposium (dedline December 2010).
 [[Image:Anna.png|thumb|right|200px|<font size=1>Figure 10: Max Plank data showing tracts through the corpus connecting 2 cortical ROIs defined by fMRI activations.</font>]]
 ;* Study of Default Network
-We have started collaboration with Department of Neurophysiology Max Planck Institute in Frankfurt (Anna Rotarska contact person). They have dataset containing DTI and resting state fMRI in schizophrenia, and want to use stochastic tractography to measure integrity of anatomical connections within the default network in schizophrenia. Their fMRI data has been co-registered with anatomical scans, and has been put it into  DTI space. Figure 8 shows pilot data of the white matter connections through the corpus callosum between the left and the right auditory cortex ROIs as defined by fMRI data.  This data will be also used to test robustness of our module, since data was collected on a different scanner (3T Philips).
+We are collaborating with the Department of Neurophysiology Max Planck Institute in Frankfurt (Anna Rotarska contact person), where we use stochastic tractography to measure integrity of anatomical connections within the default network in schizophrenia. The fMRI resting state results (ROIs) have been co-registered with anatomical scans, and then again registered to DTI space. Figure 8 shows pilot data of the white matter connections through the corpus callosum between the left and the right auditory cortex ROIs as defined by fMRI data.
 ;* Tractography Comparison Project
@@ Line 147: / Line 143: @@
 * Sylvain and Yogesh are the DBP resources charged with adapting the tools in the NA-MIC Kit to the DBP needs
-* Doug Markant, our NAMIC RA has left the lab, and now Doug Terry, is a new NAMIC RA.
+* Andrew Rauch, our NAMIC RA is our NAMIC RA.
-* Julien is our new NAMIC software engineer. He is responsible for improving the STM (Stochastic Tractography Module), and making sure software works with STM compliant datasets.
+* Ryan is our NAMIC software engineer. He is responsible for improving the STM (Stochastic Tractography Module), and making sure software works with STM compliant datasets.
   [[Link Progress| Development Progress]]
 * Polina is the algorithm core contact
@@ Line 170: / Line 166: @@
 * '''07/2009''' - Continue working on clinical collaborative studies using stochastic tractography module.
 * '''12/2009''' - Submission of abstracts reporting findings of several clinical studies involving stochastic tractography, including anatomical connectivity abnormalities in patients with VCFS and anatomical and functional connectivity abnormalities in schizophrenia.
 ===Team and Institute===
 *PI: Marek Kubicki (kubicki at bwh.harvard.edu)
-*DBP2 Investigators: Sylvain Bouix,  Yogesh Rathi, Julien de Siebenthal
+*DBP2 Investigators: Sylvain Bouix,  Yogesh Rathi, Ryan Ecbo
 *NA-MIC Engineering Contact: Brad Davis, Kitware
 *NA-MIC Algorithms Contact: Polina Gollard, MIT