Core1 - Revision history

Andy: Update from Wiki

2006-12-18T13:57:14Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T13:57:13Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T13:21:30Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T13:21:29Z

Update from Wiki

New page

= Harvard =

= Diffusion Data =

== 1.5T ==

So far, we recruited and shared with Core 1: 40 chronic schizophrenics and 40 controls scanned with the old DTI LSDI protocol (1.7x1.7x5 mm, 6 directions, 1 baseline ).

== 3.0T ==

We started acquiring images on the 3T GE scanner. So far, we recruited and scanned 14 schizophrenics and 12 normal controls with SENSE EPI protocol (1.7x1.7x1.7 mm, 51 directions, 8 baselines). All these subjects have also 1x1x1 structural scans available. We will either make the complete set of 26 cases available or the 12 normal controls.

<br /> The following scanner settings were used

000001.SER Volume- 3D localizer

000002.SER ASSET- parallel calibration scan

000003.SER DTI Volume - R= 17000, TE Min= 78.3, FOV= 24.0, #Slices= 81, Resolution= 144x144, NEX= 1, directions 51, + 8 x T2, 1.7 mm X 1.7 mm X 1.7 mm

000004.SER 3D FSPGR Axial, EDR, Fast, IvR, Asset - R= 7.5, TE= 3.0, FA=15 degrees, FOV= 25.6, 1 Phase FOV, Bandwith=15.63, Resolution= 256x256, Slice thickness 1

000005.SER FSE T2 Axial - R= 6200, TE= 103, FOV= 25.6, 0.75 Phase FOV, ETL=16, Bandwith=31.25, Resolution= 256x256, Slice thickness 2mm, interleaved

= Labelmaps =

== Female caudate nucleus ==

We have new manually segmented labelmaps for the caudate nucleus of 32 women with schizotypal personality disorder and 29 normal control women. The caudate nucleus was delineated on coronal axis SPGR images (0.9375x0.9375x1.5 mm, 1.5T).

See [http://pnl.bwh.harvard.edu/pub/papers_html/kooBiolPsych06.html Min-Seong et al.] for details.

= Previously available datasets =

For previously available datasets see [[DataRepository|DataRepository]].

<br />

= Dartmouth =

= 1.5T GE =

== fMRI ==

This is an EPI sequence acquired sagittally (3.75x3.75x5 mm)

'''Verbal Episodic Encoding/Recognition Task (event-related)''' - We have 14 subjects with schizophrenia and 9 normal controls.

'''Auditory-verbal n-back Working Memory Task''' - We have 20 subjects with schizophrenia and 20 normal controls.

== DTI ==

This is an EPI sequence acquired axially (1.875x1.875x3 mm reconstructed to 0.9375x0.9375x3mm).

Pre-processed and reviewed - We have 17 subjects with schizophrenia and 11 normal controls.

Awaiting pre-processing and review - 15 subjects.

Potentially 43 subjects total.

== Structural ==

All subjects have a hires SPGR 3D Volume (0.9375x0.9375x1.5 mm)

= 3.0T Philips =

Acquisition has now started. Trial case with DTI, fMRI Motor, and MPRAGE structural was incorporated in NAMIC tutorial.

= Previously available data =

For previously available datasets see [[DataRepository|DataRepository]].

@@ Line 1: / Line 1: @@
-= Harvard =
+= Introduction =
-= Diffusion Data =
+* History: During MICCAI we (Ron Kikinis, Guido Gerig, Ross Whitaker, Polina Golland, Jim Miller, Tina Kapur, Martin Styner) discussed plans for the current year of NA-MIC. Given that this is the last year for the current participants in Core 3, we need to plan specific activities.
-== 1.5T ==
+= Logistics =
-So far, we recruited and shared with Core 1: 40 chronic schizophrenics and 40 controls scanned with the old DTI LSDI protocol (1.7x1.7x5 mm, 6 directions, 1 baseline ).
+* The venue is the conference room on the second floor of our 1249 Boylston Street Facility [http://splweb.bwh.harvard.edu:8000/pages/directions/1249Boylston/Boylston-facility.html (directions)] in Boston on October 17 between 9.30am and 3pm.
-== 3.0T ==
+= Agenda =
-We started acquiring images on the 3T GE scanner. So far, we recruited and scanned 14 schizophrenics and 12 normal controls with SENSE EPI protocol (1.7x1.7x1.7 mm, 51 directions, 8 baselines). All these subjects have also 1x1x1 structural scans available. We will either make the complete set of 26 cases available or the 12 normal controls.
+* '''09.30am''' Begin
-<br /> The following scanner settings were used
+# Intro: Ron
-.SER Volume- 3D localizer
+* Identify specific analyses that should be initiated now. Specify teams, interactions and timetables (moderated by Ron Kikinis).
-.SER ASSET- parallel calibration scan
+[[Media:NA-MIC_core-3.1-10-19-06.ppt|Core 3.1 Meeting slides, including list of short- and long-term projects]]
-.SER DTI Volume - R= 17000, TE Min= 78.3, FOV= 24.0, #Slices= 81, Resolution= 144x144, NEX= 1, directions 51, + 8 x T2, 1.7 mm X 1.7 mm X 1.7 mm
+= Ongoing Projects =
-.SER 3D FSPGR Axial, EDR, Fast, IvR, Asset - R= 7.5, TE= 3.0, FA=15 degrees, FOV= 25.6, 1 Phase FOV, Bandwith=15.63, Resolution= 256x256, Slice thickness 1
+* UF: 2 ROI tractography analysis with mean FA measures, doDTI ... submitted to Brain.
-.SER FSE T2 Axial - R= 6200, TE= 103, FOV= 25.6, 0.75 Phase FOV, ETL=16, Bandwith=31.25, Resolution= 256x256, Slice thickness 2mm, interleaved
+(2) Atlas based approach warping a CC subdivision to individual cases (UNC Collaboration).
-= Labelmaps =
+* ALIC: Work in progress. Tractography from anterior and posterior limb of the internal capsule. Slicer
-== Female caudate nucleus ==
+= Core 3 Wishes =
-We have new manually segmented labelmaps for the caudate nucleus of 32 women with schizotypal personality disorder and 29 normal control women. The caudate nucleus was delineated on coronal axis SPGR images (0.9375x0.9375x1.5 mm, 1.5T).
+* Registration:
-See [http://pnl.bwh.harvard.edu/pub/papers_html/kooBiolPsych06.html Min-Seong et al.] for details.
+= List of Participants =
-= Previously available datasets =
+* Core 1
-For previously available datasets see [[DataRepository|DataRepository]].
+# Polina Golland, MIT
-<br />
+* Core 3
-= Dartmouth =
+# Martha Shenton, PNL
-= 1.5T GE =
+* Other Cores
-== fMRI ==
+# Ron Kikinis, SPL
+# Randy Gollub, MGH and Core 5
-This is an EPI sequence acquired sagittally (3.75x3.75x5 mm)
+# Steve Pieper, Core 2 and 6
+# Brad Davis, Kitware

@@ Line 1: / Line 1: @@
-= Introduction =
+= Harvard =
-* History: During MICCAI we (Ron Kikinis, Guido Gerig, Ross Whitaker, Polina Golland, Jim Miller, Tina Kapur, Martin Styner) discussed plans for the current year of NA-MIC. Given that this is the last year for the current participants in Core 3, we need to plan specific activities.
+= Diffusion Data =
-= Logistics =
+== 1.5T ==
-* The venue is the conference room on the second floor of our 1249 Boylston Street Facility [http://splweb.bwh.harvard.edu:8000/pages/directions/1249Boylston/Boylston-facility.html (directions)] in Boston on October 17 between 9.30am and 3pm.
+So far, we recruited and shared with Core 1: 40 chronic schizophrenics and 40 controls scanned with the old DTI LSDI protocol (1.7x1.7x5 mm, 6 directions, 1 baseline ).
-= Agenda =
+== 3.0T ==
-* '''09.30am''' Begin
+We started acquiring images on the 3T GE scanner. So far, we recruited and scanned 14 schizophrenics and 12 normal controls with SENSE EPI protocol (1.7x1.7x1.7 mm, 51 directions, 8 baselines). All these subjects have also 1x1x1 structural scans available. We will either make the complete set of 26 cases available or the 12 normal controls.
-# Intro: Ron
+<br /> The following scanner settings were used
-* Identify specific analyses that should be initiated now. Specify teams, interactions and timetables (moderated by Ron Kikinis).
+.SER Volume- 3D localizer
-[[Media:NA-MIC_core-3.1-10-19-06.ppt|Core 3.1 Meeting slides, including list of short- and long-term projects]]
+.SER ASSET- parallel calibration scan
-= Ongoing Projects =
+.SER DTI Volume - R= 17000, TE Min= 78.3, FOV= 24.0, #Slices= 81, Resolution= 144x144, NEX= 1, directions 51, + 8 x T2, 1.7 mm X 1.7 mm X 1.7 mm
-* UF: 2 ROI tractography analysis with mean FA measures, doDTI ... submitted to Brain.
+.SER 3D FSPGR Axial, EDR, Fast, IvR, Asset - R= 7.5, TE= 3.0, FA=15 degrees, FOV= 25.6, 1 Phase FOV, Bandwith=15.63, Resolution= 256x256, Slice thickness 1
-(2) Atlas based approach warping a CC subdivision to individual cases (UNC Collaboration).
+.SER FSE T2 Axial - R= 6200, TE= 103, FOV= 25.6, 0.75 Phase FOV, ETL=16, Bandwith=31.25, Resolution= 256x256, Slice thickness 2mm, interleaved
-* ALIC: Work in progress. Tractography from anterior and posterior limb of the internal capsule. Slicer
+= Labelmaps =
-= Core 3 Wishes =
+== Female caudate nucleus ==
-* Registration:
+We have new manually segmented labelmaps for the caudate nucleus of 32 women with schizotypal personality disorder and 29 normal control women. The caudate nucleus was delineated on coronal axis SPGR images (0.9375x0.9375x1.5 mm, 1.5T).
-= List of Participants =
+See [http://pnl.bwh.harvard.edu/pub/papers_html/kooBiolPsych06.html Min-Seong et al.] for details.
-* Core 1
+= Previously available datasets =
-# Polina Golland, MIT
+For previously available datasets see [[DataRepository|DataRepository]].
-* Core 3
+<br />
-# Martha Shenton, PNL
+= Dartmouth =
-* Other Cores
+= 1.5T GE =
-# Ron Kikinis, SPL
+== fMRI ==
-# Randy Gollub, MGH and Core 5
-# Steve Pieper, Core 2 and 6
+This is an EPI sequence acquired sagittally (3.75x3.75x5 mm)
-# Brad Davis, Kitware

@@ Line 1: / Line 1: @@
-= Harvard =
+= Introduction =
-= Diffusion Data =
+* History: During MICCAI we (Ron Kikinis, Guido Gerig, Ross Whitaker, Polina Golland, Jim Miller, Tina Kapur, Martin Styner) discussed plans for the current year of NA-MIC. Given that this is the last year for the current participants in Core 3, we need to plan specific activities.
-== 1.5T ==
+= Logistics =
-So far, we recruited and shared with Core 1: 40 chronic schizophrenics and 40 controls scanned with the old DTI LSDI protocol (1.7x1.7x5 mm, 6 directions, 1 baseline ).
+* The venue is the conference room on the second floor of our 1249 Boylston Street Facility [http://splweb.bwh.harvard.edu:8000/pages/directions/1249Boylston/Boylston-facility.html (directions)] in Boston on October 17 between 9.30am and 3pm.
-== 3.0T ==
+= Agenda =
-We started acquiring images on the 3T GE scanner. So far, we recruited and scanned 14 schizophrenics and 12 normal controls with SENSE EPI protocol (1.7x1.7x1.7 mm, 51 directions, 8 baselines). All these subjects have also 1x1x1 structural scans available. We will either make the complete set of 26 cases available or the 12 normal controls.
+* '''09.30am''' Begin
-<br /> The following scanner settings were used
+# Intro: Ron
-.SER Volume- 3D localizer
+* Identify specific analyses that should be initiated now. Specify teams, interactions and timetables (moderated by Ron Kikinis).
-.SER ASSET- parallel calibration scan
+[[Media:NA-MIC_core-3.1-10-19-06.ppt|Core 3.1 Meeting slides, including list of short- and long-term projects]]
-.SER DTI Volume - R= 17000, TE Min= 78.3, FOV= 24.0, #Slices= 81, Resolution= 144x144, NEX= 1, directions 51, + 8 x T2, 1.7 mm X 1.7 mm X 1.7 mm
+= Ongoing Projects =
-.SER 3D FSPGR Axial, EDR, Fast, IvR, Asset - R= 7.5, TE= 3.0, FA=15 degrees, FOV= 25.6, 1 Phase FOV, Bandwith=15.63, Resolution= 256x256, Slice thickness 1
+* UF: 2 ROI tractography analysis with mean FA measures, doDTI ... submitted to Brain.
-.SER FSE T2 Axial - R= 6200, TE= 103, FOV= 25.6, 0.75 Phase FOV, ETL=16, Bandwith=31.25, Resolution= 256x256, Slice thickness 2mm, interleaved
+(2) Atlas based approach warping a CC subdivision to individual cases (UNC Collaboration).
-= Labelmaps =
+* ALIC: Work in progress. Tractography from anterior and posterior limb of the internal capsule. Slicer
-== Female caudate nucleus ==
+= Core 3 Wishes =
-We have new manually segmented labelmaps for the caudate nucleus of 32 women with schizotypal personality disorder and 29 normal control women. The caudate nucleus was delineated on coronal axis SPGR images (0.9375x0.9375x1.5 mm, 1.5T).
+* Registration:
-See [http://pnl.bwh.harvard.edu/pub/papers_html/kooBiolPsych06.html Min-Seong et al.] for details.
+= List of Participants =
-= Previously available datasets =
+* Core 1
-For previously available datasets see [[DataRepository|DataRepository]].
+# Polina Golland, MIT
-<br />
+* Core 3
-= Dartmouth =
+# Martha Shenton, PNL
-= 1.5T GE =
+* Other Cores
-== fMRI ==
+# Ron Kikinis, SPL
+# Randy Gollub, MGH and Core 5
-This is an EPI sequence acquired sagittally (3.75x3.75x5 mm)
+# Steve Pieper, Core 2 and 6
+# Brad Davis, Kitware