[Freesurfer] Aseg2feat: Missing segmentations
Hello,
This is regarding the registration of functional data to freesurfer
parcellations
(http://freesurfer.net/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace).
The rsfMRI is sampled at 2x2x2.
After running reg-feat2anat and aseg2feat
a = MRIread('aparc+aseg'); %Original aparc+aseg output from freesurfer
recon-all
size(unique(a.vol(:))) % 114 segs
a = MRIread('aparc+aseg'); % this is the output file after aseg2feat
size(unique(a.vol(:))) % 98 segs
Any advice?
Thanks
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[Freesurfer] recon-all error MRIthickenThinWMStrands
Hi ERROR: MRIthickenThinWMStrands: invalid x,y,z! Numerical result out of range Any tips? S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] reg-feat2anat failure..
Hi, recon-all was successful. But when I try reg-feat2anat --feat '/home//func/2_reg' --subject xyz I get an error with MRISread(/home/sudhin/Data/freesurfer_subjects//xyz/surf/lh.white): could not open file Loading mov Projecting LH Surfs Loading lh.white surf No such file or directory Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all error: v5.0.0 - dataset 1
BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries = [27,14799] ERROR: _FindFacePath: could not find path! Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all error: v5.0.0 - dataset 3
CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s ghjG exited with ERRORS at Thu May 16 05:11:49 EDT 2013 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all error: v5.0.0 - dataset 2
=== *WATERSHED** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s cbvfB exited with ERRORS at Fri May 17 17:45:23 EDT 2013 == ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all errors: v5.0.0; dataset 4
CORRECTING DEFECT 1 (vertices=33, convex hull=57) After retessellation of defect 1, euler #=-41 (88676,260208,171491) : difference with theory (-61) = -20 CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s IN387G exited with ERRORS at Thu May 16 05:11:49 EDT 2013 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all error: v5.0.0 - dataset 1
Hi! Can you please send this to me? On May 28, 2013, at 4:24 PM, Bruce Fischl wrote: the new topo fixer will correct this problem Bruce On Tue, 28 May 2013, Sudhin A. Shah wrote: BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries = [27,14799] ERROR: _FindFacePath: could not find path! Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 3 recon-all errors: v5.0.0
1) BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries = [27,14799] ERROR: _FindFacePath: could not find path! Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013 === 2)*WATERSHED** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s cbvfB exited with ERRORS at Fri May 17 17:45:23 EDT 2013 == 3)CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s ghjG exited with ERRORS at Thu May 16 05:11:49 EDT 2013 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all errors: v5.0.0
1) BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries = [27,14799] ERROR: _FindFacePath: could not find path! Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013 === 2)*WATERSHED** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s cbvfB exited with ERRORS at Fri May 17 17:45:23 EDT 2013 == 3)CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s ghjG exited with ERRORS at Thu May 16 05:11:49 EDT 2013 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all error: Correcting Defect 2
v5.0.0 On May 16, 2013, at 2:18 PM, Bruce Fischl wrote: Hi Sudhin what FS version are you running? Bruce On Thu, 16 May 2013, Sudhin A. Shah wrote: Hi, I got the following error: CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all error: Correcting Defect 2
Hi, I got the following error: CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all completes without all the info..
Hi! I am running this on ~26 datasets and some have exited with errors and others have not completed (~ 2 days). Sorry, but what should I be running to get the following files? 1) T1.mgz 2) wm.mgz 3) aparc+aseg.mgz 4) brainmask.mgz 5) ribbon.mgz 6) And I need to run reg-feat2anat I am quite certain that what I ran (successfully) before was recon-all -s xyx -i xyz -autorecon1 but when I ran this recently, all the files above did not populate. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] Sent: Tuesday, May 07, 2013 12:05 PM To: Sudhin A. Shah Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all completes without all the info.. Yes, the -all flag will run autorecon1, autorecon2, and autorecon3. recon-all -all -i path to dicom/nii/mgz T1 image -s subjID For that uncompleted subject you have though if sounds like you just need to run autorecon2 and 3 recon-all -autorecon2 -autorecon3 -s subjID On Tue, 7 May 2013, Sudhin A. Shah wrote: Is there 1 command line? I used to just run the 1 line. On May 7, 2013, at 10:19 AM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Sudhin, You'll need to also run -autorecon2 and -autorecon3 in order to get surfaces and all the cortical/sub-cortical measures. -Louis On Tue, 7 May 2013, Sudhin A. Shah wrote: On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote: Hi, This is a new issue as it used to run well before.. I run recon-all ... ... -autorecon1 - force and it completes without error but I don't have all the files.. Attached is a screenshot. On the right is the output from a file that worked before and on the left is a newer folder.. Screenshot.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all completes without all the info..
On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote: Hi, This is a new issue as it used to run well before.. I run recon-all ... ... -autorecon1 - force and it completes without error but I don't have all the files.. Attached is a screenshot. On the right is the output from a file that worked before and on the left is a newer folder.. Screenshot.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all completes without all the info..
Is there 1 command line? I used to just run the 1 line. On May 7, 2013, at 10:19 AM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Sudhin, You'll need to also run -autorecon2 and -autorecon3 in order to get surfaces and all the cortical/sub-cortical measures. -Louis On Tue, 7 May 2013, Sudhin A. Shah wrote: On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote: Hi, This is a new issue as it used to run well before.. I run recon-all ... ... -autorecon1 - force and it completes without error but I don't have all the files.. Attached is a screenshot. On the right is the output from a file that worked before and on the left is a newer folder.. Screenshot.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] labels to lobes
Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] labels to lobes
Also, is there a way to associate these labels with motor/auditory/visual cortices? Or do I have to use the specific parcellations? On Feb 28, 2013, at 9:25 AM, Sudhin A. Shah sut2...@med.cornell.edu wrote: Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels to lobes
Thank you! Is there something similar to assign labels to functional cortices eg. motor, visual, auditory? Thanks S On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote: After a conventional FS run you can do the following: $mri_annotation2label --subject subj --hemi hemi --lobesStrict hemi.lobesStrict.annot Which will create an annotation file hemi.lobesStrict.annot containing the lobar labels. To extract these into their own individual label files, do $mri_annotation2label --subject subj --hemi hemi --annotation lobesStrict --outdir subj/label This will populate the subj/label directory with files: hemi.frontal.label hemi.parietal.label hemi.temporal.label hemi.occiptal.label hemi.cingulate.label So, to be pendantic, if you want the lobar labels for the left hemisphere of a subject called 'sub1', you would $mri_annotation2label --subject sub1 --hemi lh --lobesStrict lh.lobesStrict.annot $mri_annotation2label --subject sub1 --hemi lh --annotation lobesStrict --outdir sub1/label HTH -=R On Thu Feb 28 09:24:58 2013, Sudhin A. Shah wrote: Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels to lobes
Hi I got an error -lobesStrict unknown. I am running mri_annotation2label version stable5. Is there a workaround? On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote: After a conventional FS run you can do the following: $mri_annotation2label --subject subj --hemi hemi --lobesStrict hemi.lobesStrict.annot Which will create an annotation file hemi.lobesStrict.annot containing the lobar labels. To extract these into their own individual label files, do $mri_annotation2label --subject subj --hemi hemi --annotation lobesStrict --outdir subj/label This will populate the subj/label directory with files: hemi.frontal.label hemi.parietal.label hemi.temporal.label hemi.occiptal.label hemi.cingulate.label So, to be pendantic, if you want the lobar labels for the left hemisphere of a subject called 'sub1', you would $mri_annotation2label --subject sub1 --hemi lh --lobesStrict lh.lobesStrict.annot $mri_annotation2label --subject sub1 --hemi lh --annotation lobesStrict --outdir sub1/label HTH -=R On Thu Feb 28 09:24:58 2013, Sudhin A. Shah wrote: Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] labels to lobes
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 On Feb 28, 2013, at 12:12 PM, Rudolph Pienaar wrote: It looks like you might be running a too-old version of mri_annotation2label. What FS build/version are you running? On Thu Feb 28 11:36:50 2013, Sudhin A. Shah wrote: Hi I got an error -lobesStrict unknown. I am running mri_annotation2label version stable5. Is there a workaround? On Feb 28, 2013, at 10:47 AM, Rudolph Pienaar wrote: After a conventional FS run you can do the following: $mri_annotation2label --subject subj --hemi hemi --lobesStrict hemi.lobesStrict.annot Which will create an annotation file hemi.lobesStrict.annot containing the lobar labels. To extract these into their own individual label files, do $mri_annotation2label --subject subj --hemi hemi --annotation lobesStrict --outdir subj/label This will populate the subj/label directory with files: hemi.frontal.label hemi.parietal.label hemi.temporal.label hemi.occiptal.label hemi.cingulate.label So, to be pendantic, if you want the lobar labels for the left hemisphere of a subject called 'sub1', you would $mri_annotation2label --subject sub1 --hemi lh --lobesStrict lh.lobesStrict.annot $mri_annotation2label --subject sub1 --hemi lh --annotation lobesStrict --outdir sub1/label HTH -=R On Thu Feb 28 09:24:58 2013, Sudhin A. Shah wrote: Hello, Is there a lookup table I can use to convert free surfer labels to lobes? Either label nos (1006, 2006 etc) or label names (ctx-rh-superiorfrontal)? I have 86 labels and want an easy way to differentiate them into the corresponding lobes. Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix..
Hi Doug,
Is the BBR cost function in anat2exf.register.dat.bbr.init?
mwtp5
3.75
4.00
0.15
9.689088e-01 6.952747e-02 -2.374479e-01 6.737892e+00
2.456762e-01 -1.566831e-01 9.566056e-01 -2.835866e+01
2.930631e-02 -9.851995e-01 -1.688930e-01 1.765446e+01
0 0 0 1
round
Or in anat2exf.register.dat.mincost
0.545185 785.020257 804.709380 1.199352
This looks ok under manual inspection - although the head was not in an ideal
position (patient data). However, I cannot extract data from ROI label 2013.
Thanks,
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 25, 2013 11:39 AM
To: Sudhin A. Shah; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Registration segmentation with FSL -
obtaining correlation matrix..
First check the value of the BBR cost function. If it is over .8, then
something is wrong. To check whether it is an LR flip, you can flip the
volume LR and re-run the registration to see if it gets better.
doug
On 02/25/2013 11:19 AM, Sudhin A. Shah wrote:
Hi Doug,
When I initially pulled out the correlation values (using the matlab code
below) after the automated registration process: regfeat2anat aseg2feat,
some ROIS reported NaNs.
When I manually checked the registration and adjusted it using tkregister2, I
found myself stretching/scaling to make it fit. Consequently I do not have
NaNs BUT I am now realising that I should'nt have to scale.
1) How can I check if left-right reversals have happened - its not obvious by
eye
2) I am going to re-run the automated registration and I can send you a pic
and the cost function..
Thanks,
S
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 25, 2013 10:44 AM
To: Bruce Fischl
Cc: Sudhin A. Shah
Subject: Re: [Freesurfer] Registration segmentation with FSL -
obtaining correlation matrix..
Hi Sudhin, I'm not sure what the problem is. NaNs in the data?
Stretching the registration? You should not need to stretch the reg.Are
you 100% positive that the func and anat come from the same subject and
there have been on left-right reversals? What is the final value of the
cost function?
doug
On 02/25/2013 10:06 AM, Bruce Fischl wrote:
Hi Sudhin
Doug would have some. You definitely shouldn't have to stretch/scale
to get it to fit. If you do, something critical is wrong. Also, please
cc the list so that the right person (Doug in this case!) can answer.
cheers
Bruce
On Mon, 25 Feb 2013, Sudhin A. Shah wrote:
Hi Bruce,
They were a result of the registration (between structural and
functional) being 'off'. When I manually correct this using
tkregister2, they were fine. However, I found that I had to stretch
(scale) to get them to fit so (i started a new thread regarding this)
are there image examples on what this should look like so I can use
as a guide?
Thanks,
S
On Feb 25, 2013, at 9:27 AM, Bruce Fischl wrote:
Hi Sudhin
are you sure that the NaNs don't exist before registration and
extraction? Cany you check? I don't see why anything we would have
done would introduce them.
cheers
Bruce
On Fri, 22 Feb 2013, Sudhin A. Shah wrote:
Hello
I have run free surfer and co-registered with the rsfMRI via FSL
(reg-feat2anat aseg2feat)
When I extract the values (as per the matlab code below), I see
NaNs in certain regions. Of the 19 datasets that I have analyzed I
have
see NaNs for the following labels
10061033200620132033
Is this a known problem? Is there a solution?
Thanks,
S
On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:
Sorry, I don't think we have such a program. You could do it
in matlab
fairly easily, eg,
f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
ind = find(a.vol == seglist(nthseg));
roimean(:,nthseg) = mean(fmat(:,ind),2);
end
m = roimean'*roimean;
On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:
Hello,
This worked perfectly 2 years ago :), but now I am
having some trouble.
I run reg-feat2anat aseg2feat with no problem.
I now need a correlation matrix of every ROI (created by
freesurfer)
against every other ROI. For this I used @ROI_Corr_Mat
(http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html).
Again - this worked fine in the past.
Now I get an error (working with AFNI to see if it can
be fixed).
Question: Is there any alternative to getting this
correlation matrix?
i.e every ROI against every other ROI?
Thanks,
S
Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix..
Hi! It turns out the 3T scans have a lot of susceptibility artifact so it might not be the registration failing but more of the signal :( Unfortunately I will just leave out those ROIs for my analysis.. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, February 25, 2013 3:28 PM To: Sudhin A. Shah Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix.. It may be that there is a lot of T2* decay around the edge of the brain. See slide 13 from this presentation: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fs.multimodal-integration.ppt To check your data, turn off the intensity normalization by clicking in the image window and hitting 'i'. In the control window, increase the value of fmov to brighten the image. It may be that there is actually tissue outside of those areas but they are very dark. Adjusting the fmov will also allow you to get better contrast which may help to evaluate whether the surfaces inside the brain are correct. doug ps. what was your TE and echo spacing? Is this at 3T? On 02/25/2013 02:52 PM, Sudhin A. Shah wrote: w/attachment From: Sudhin A. Shah Sent: Monday, February 25, 2013 2:52 PM To: Douglas N Greve Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix.. Here is the last subject - coronal view.. This is where I started scaling/stretching :( From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sudhin A. Shah [sut2...@med.cornell.edu] Sent: Monday, February 25, 2013 1:29 PM To: Douglas N Greve Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix.. Here is another example registration (different subject). Here I cannot extract values for label 1006 and 2006.. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sudhin A. Shah [sut2...@med.cornell.edu] Sent: Monday, February 25, 2013 12:49 PM To: Douglas N Greve Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix.. Sorry - this doesn't look bad. Still I cannot extract values for the ROI label 2013.. On Feb 25, 2013, at 12:43 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It does not look bad to me. Why do you think it looks wrong? On 02/25/2013 12:29 PM, Sudhin A. Shah wrote: Hi Doug, Here's an example view... It looks fine to me. See attached.. From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, February 25, 2013 12:12 PM To: Sudhin A. Shah Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix.. The cost (from .mincost) looks fine. Can you send a pic of the registration inaccuracy? doug On 02/25/2013 11:53 AM, Sudhin A. Shah wrote: Hi Doug, Is the BBR cost function in anat2exf.register.dat.bbr.init? mwtp5 3.75 4.00 0.15 9.689088e-01 6.952747e-02 -2.374479e-01 6.737892e+00 2.456762e-01 -1.566831e-01 9.566056e-01 -2.835866e+01 2.930631e-02 -9.851995e-01 -1.688930e-01 1.765446e+01 0 0 0 1 round Or in anat2exf.register.dat.mincost 0.545185 785.020257 804.709380 1.199352 This looks ok under manual inspection - although the head was not in an ideal position (patient data). However, I cannot extract data from ROI label 2013. Thanks, From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, February 25, 2013 11:39 AM To: Sudhin A. Shah; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix.. First check the value of the BBR cost function. If it is over .8, then something is wrong. To check whether it is an LR flip, you can flip the volume LR and re-run the registration to see if it gets better. doug On 02/25/2013 11:19 AM, Sudhin A. Shah wrote: Hi Doug, When I initially pulled out the correlation values (using the matlab code below) after the automated registration process: regfeat2anat aseg2feat, some ROIS reported NaNs. When I manually checked the registration and adjusted it using tkregister2, I found myself stretching/scaling to make it fit. Consequently I do not have NaNs BUT I am now realising that I should'nt have to scale. 1) How can I check if left-right reversals have happened - its not obvious by eye 2) I am going to re-run
Re: [Freesurfer] tkregister2 window error: Remote login
On Feb 21, 2013, at 2:16 PM, Sudhin A. Shah wrote: Hello, I am remotely logged in to my Ubuntu system(from Mac). I have previously run tkregister2 but am now having trouble; Opening window subj Window type not found register: tkoinitwindow(name) failed. Is there a solution to this? Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix..
Hello
I have run free surfer and co-registered with the rsfMRI via FSL (reg-feat2anat
aseg2feat)
When I extract the values (as per the matlab code below), I see NaNs in certain
regions. Of the 19 datasets that I have analyzed I have see NaNs for the
following labels
10061033200620132033
Is this a known problem? Is there a solution?
Thanks,
S
On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:
Sorry, I don't think we have such a program. You could do it in matlab
fairly easily, eg,
f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
ind = find(a.vol == seglist(nthseg));
roimean(:,nthseg) = mean(fmat(:,ind),2);
end
m = roimean'*roimean;
On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:
Hello,
This worked perfectly 2 years ago :), but now I am having some trouble.
I run reg-feat2anat aseg2feat with no problem.
I now need a correlation matrix of every ROI (created by freesurfer)
against every other ROI. For this I used @ROI_Corr_Mat
(http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html).
Again - this worked fine in the past.
Now I get an error (working with AFNI to see if it can be fixed).
Question: Is there any alternative to getting this correlation matrix?
i.e every ROI against every other ROI?
Thanks,
S
___
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:
www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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[Freesurfer] tkregister2 - stretching..
Hello, I manually checked the registration of my free surfer parcellations to the rsfMRI data after reg-feat2anat and aseg2feat. Problem is that I had to scale (stretch) the functional to make a good fit in several cases. Is this recommended? How can I avoid this? Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix..
On Feb 20, 2013, at 3:02 PM, Sudhin A. Shah wrote:
Hello
I have run free surfer and co-registered with the rsfMRI via FSL (reg-feat2anat
aseg2feat)
When I extract the values (as per the matlab code below), I see NaNs in certain
regions. Of the 19 datasets that I have analyzed I have see NaNs for the
following labels
10061033200620132033
Is this a known problem? Is there a solution?
Thanks,
S
On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:
Sorry, I don't think we have such a program. You could do it in matlab
fairly easily, eg,
f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
ind = find(a.vol == seglist(nthseg));
roimean(:,nthseg) = mean(fmat(:,ind),2);
end
m = roimean'*roimean;
On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:
Hello,
This worked perfectly 2 years ago :), but now I am having some trouble.
I run reg-feat2anat aseg2feat with no problem.
I now need a correlation matrix of every ROI (created by freesurfer)
against every other ROI. For this I used @ROI_Corr_Mat
(http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html).
Again - this worked fine in the past.
Now I get an error (working with AFNI to see if it can be fixed).
Question: Is there any alternative to getting this correlation matrix?
i.e every ROI against every other ROI?
Thanks,
S
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:
www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] tkregister2 window error: Remote login
Hello, I am remotely logged in to my Ubuntu system(from Mac). I have previously run tkregister2 but am now having trouble; Opening window subj Window type not found register: tkoinitwindow(name) failed. Is there a solution to this? Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Registration segmentation with FSL - obtaining correlation matrix..
Hello
I have run free surfer and co-registered with the rsfMRI via FSL (reg-feat2anat
aseg2feat)
When I extract the values (as per the matlab code below), I see NaNs in certain
regions. Of the 19 datasets that I have analyzed I have see NaNs for the
following labels
10061033200620132033
Is this a known problem? Is there a solution?
Thanks,
S
On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:
Sorry, I don't think we have such a program. You could do it in matlab
fairly easily, eg,
f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
ind = find(a.vol == seglist(nthseg));
roimean(:,nthseg) = mean(fmat(:,ind),2);
end
m = roimean'*roimean;
On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:
Hello,
This worked perfectly 2 years ago :), but now I am having some trouble.
I run reg-feat2anat aseg2feat with no problem.
I now need a correlation matrix of every ROI (created by freesurfer)
against every other ROI. For this I used @ROI_Corr_Mat
(http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html).
Again - this worked fine in the past.
Now I get an error (working with AFNI to see if it can be fixed).
Question: Is there any alternative to getting this correlation matrix?
i.e every ROI against every other ROI?
Thanks,
S
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Re: [Freesurfer] Two timepoints - same subject, correlation matrix
Hi, So I think I found the solution - (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical) reg-feat2anat aseg2feat or aparc2feat New question: Is there anyway to combine aseg2feat and aparc2feat? i.e. get all subcortical and cortical segmentations registered to functional space? Thanks, S On 06/21/11, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Sudhin, this looks like an AFNI question. Have you tried posting to the AFNI list? doug Sudhin A. Shah wrote: On Jun 17, 2011, at 6:25 PM, Sudhin A. Shah sut2...@med.cornell.edu mailto:sut2...@med.cornell.edu sut2...@med.cornell.edu wrote: Hi, Can somebody please help me figure out how to correct this issue? 1 subject - 2 functional scans 1) run recon-all on subject anatomical. 2) process functional series (using AFNI/FSL) - each individually. 3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html%29) @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually) This works (I don't know why since I am not doing anything to register them to a common space). 4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 112 in 2nd timepoint. I would like to get the /exact same number /so I can compare them! Of course I can manually adjust the rows/columns later, but I am not sure this is the smartest way to do this. Can I do all the steps in Freesurfer? Thank you, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Two timepoints - same subject, correlation matrix
Got it : aseg2feat --feat featdir --seg aparc+aseg On 06/22/11, Sudhin A. Shah sut2...@med.cornell.edu wrote: Hi, So I think I found the solution - (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical) reg-feat2anat aseg2feat or aparc2feat New question: Is there anyway to combine aseg2feat and aparc2feat? i.e. get all subcortical and cortical segmentations registered to functional space? Thanks, S On 06/21/11, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Sudhin, this looks like an AFNI question. Have you tried posting to the AFNI list? doug Sudhin A. Shah wrote: On Jun 17, 2011, at 6:25 PM, Sudhin A. Shah sut2...@med.cornell.edu mailto:sut2...@med.cornell.edu sut2...@med.cornell.edu wrote: Hi, Can somebody please help me figure out how to correct this issue? 1 subject - 2 functional scans 1) run recon-all on subject anatomical. 2) process functional series (using AFNI/FSL) - each individually. 3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html%29) @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually) This works (I don't know why since I am not doing anything to register them to a common space). 4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 112 in 2nd timepoint. I would like to get the /exact same number /so I can compare them! Of course I can manually adjust the rows/columns later, but I am not sure this is the smartest way to do this. Can I do all the steps in Freesurfer? Thank you, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514 -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Two timepoints - same subject, correlation matrix
On Jun 17, 2011, at 6:25 PM, Sudhin A. Shah sut2...@med.cornell.edu wrote: Hi, Can somebody please help me figure out how to correct this issue? 1 subject - 2 functional scans 1) run recon-all on subject anatomical. 2) process functional series (using AFNI/FSL) - each individually. 3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually) This works (I don't know why since I am not doing anything to register them to a common space). 4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 112 in 2nd timepoint. I would like to get the exact same number so I can compare them! Of course I can manually adjust the rows/columns later, but I am not sure this is the smartest way to do this. Can I do all the steps in Freesurfer? Thank you, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Two timepoints - same subject, correlation matrix
Hi, Can somebody please help me figure out how to correct this issue? 1 subject - 2 functional scans 1) run recon-all on subject anatomical. 2) process functional series (using AFNI/FSL) - each individually. 3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually) This works (I don't know why since I am not doing anything to register them to a common space). 4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 112 in 2nd timepoint. I would like to get the exact same number so I can compare them! Of course I can manually adjust the rows/columns later, but I am not sure this is the smartest way to do this. Can I do all the steps in Freesurfer? Thank you, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_annotation2labels
Hi Actually, its the opposite. I'm trying to get a volume from the label aka http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ On 06/16/11, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: If you're trying to create a label from a volume then use mri_cor2label. doug Sudhin A. Shah wrote: Hi, I am trying to use this for the aparc+aseg-in-highres.mgz file instead of the default aparc mri_annotation2label --subject AY --hemi lh --outdir $fsfolder/AY/labels this works But how do I specify aparc+aseg-in-highres.mgz I tried --aparc+aseg-in-highres but it was not recognised.. Thank you, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Whole brain parcellation contd..
Thank you.
I just found this:
http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/
1) Is it better to extract the masks from the .mgz file (as explained on this
site) as opposed to converting the aparc+aseg-inhighres.mgz file to .nii.gz and
then extracting masks with FSL/AFNI?
2) Is there anyway to loop through all the labels instead of specifying by hand
in this command:
mri_label2vol –label ./lh.entorhinal.label –temp \
/Applications/freesurfer/subjects/${blindnum}/mri/rawavg.mgz –subject
${blindnum} –hemi lh –o \${blindnum}_lh_entorhinal.nii.gz –proj frac 0 1 .1
–fillthresh .3 –reg ../mri/register.dat
Thank you,
S
On 06/15/11, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
You are guaranteed not to have overlap regardless of what you do as
there is only one label at each voxel. For Cortex, what you have is
fine. For subcortical, you can use what is in
$FREESURFER_HOME/ASegStatsLUT.txt. This has {Left,Right}-Cerebral-Cortex
which can be ignored.
doug
Sudhin A. Shah wrote:
Hi,
Is there anyway to know all the label #s that are in
aparc+aseg-inhighres.mgz.
Thank you,
S
On 06/13/11, *Sudhin A. Shah * sut2...@med.cornell.edu wrote:
Hi Sorry for bothering you again, but I am not sure I understand.
I was running whole brain correlation analysis (voxel by voxel). BUT
for comparison purposes, I want to compute region by region
correlation matrix.
So, I want to divide up the brain into freesurfer parcellated regions
- i.e. with no overlap, but with full coverage of whole brain.
I have looked at FreeSurferColorLUT.txt and am confused because there
are several sets and overlap (eg. 19 and 55 vs 2035..)
If I use the following, can I ensure no overlap and full coverage?
1)Subcortical: 9-13, 16-19, 48-55, 58 - 59, 85,86
2)Cortex: 1002- 1034, 2002- 2034
I am asking if there is an established list of whole brain
parcellations before I rely on label names to choose the ROIS
On 06/13/11, *Douglas N Greve * gr...@nmr.mgh.harvard.edu wrote:
Anything that is non-0 will cover the whole brain.
doug
Sudhin A. Shah wrote:
Hi, thank you. Is there a range in the labels that will ensure
that I am including the whole brain? I.e. I see labels for Cx, but
not subcortical..
If I take labels 1001 to 2001 ( for eg ) will that cover whole brain?
Thank you,
S
On Jun 13, 2011, at 10:59 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
That is fine, or you can use mri_binarize with the --match
option. The numbers that correspond to each label can be found in
$FREESURFER_HOME/FreeSurferColorLUT.txt. You can also get at them
visual as I described in my previous email with tkmedit:
tkmedit subject orig.mgz -aux aseg.mgz -aseg
doug
Sudhin A. Shah wrote:
I mean that I am using FSL to create binary masks from
freesurfer parcellated regions. Unless there is a better way :)
S
On Jun 10, 2011, at 7:13 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
What do you mean you are doing it with FEAT?
Sudhin A. Shah wrote:
Hello,
I am a beginner so please bear with me. I want to obtain
binary masks for every region (Cortical + subcortical). I am using
FSL(feat) to do this BUT am not sure what the labels would be.
I have looked at FreeSurferColorLUT.txt for
aparc+aseg-in-highres.mgz BUT do not know which labels to use to
avoid overlap and ensure full coverage.
Thank you,
S
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Re: [Freesurfer] Whole brain parcellation contd..
Hi, Is there anyway to know all the label #s that are in aparc+aseg-inhighres.mgz. Thank you, S On 06/13/11, Sudhin A. Shah sut2...@med.cornell.edu wrote: Hi Sorry for bothering you again, but I am not sure I understand. I was running whole brain correlation analysis (voxel by voxel). BUT for comparison purposes, I want to compute region by region correlation matrix. So, I want to divide up the brain into freesurfer parcellated regions - i.e. with no overlap, but with full coverage of whole brain. I have looked at FreeSurferColorLUT.txt and am confused because there are several sets and overlap (eg. 19 and 55 vs 2035..) If I use the following, can I ensure no overlap and full coverage? 1)Subcortical: 9-13, 16-19, 48-55, 58 - 59, 85,86 2)Cortex: 1002- 1034, 2002- 2034 I am asking if there is an established list of whole brain parcellations before I rely on label names to choose the ROIS On 06/13/11, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Anything that is non-0 will cover the whole brain. doug Sudhin A. Shah wrote: Hi, thank you. Is there a range in the labels that will ensure that I am including the whole brain? I.e. I see labels for Cx, but not subcortical.. If I take labels 1001 to 2001 ( for eg ) will that cover whole brain? Thank you, S On Jun 13, 2011, at 10:59 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: That is fine, or you can use mri_binarize with the --match option. The numbers that correspond to each label can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt. You can also get at them visual as I described in my previous email with tkmedit: tkmedit subject orig.mgz -aux aseg.mgz -aseg doug Sudhin A. Shah wrote: I mean that I am using FSL to create binary masks from freesurfer parcellated regions. Unless there is a better way :) S On Jun 10, 2011, at 7:13 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: What do you mean you are doing it with FEAT? Sudhin A. Shah wrote: Hello, I am a beginner so please bear with me. I want to obtain binary masks for every region (Cortical + subcortical). I am using FSL(feat) to do this BUT am not sure what the labels would be. I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz BUT do not know which labels to use to avoid overlap and ensure full coverage. Thank you, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe
[Freesurfer] mri_annotation2labels
Hi, I am trying to use this for the aparc+aseg-in-highres.mgz file instead of the default aparc mri_annotation2label --subject AY --hemi lh --outdir $fsfolder/AY/labels this works But how do I specify aparc+aseg-in-highres.mgz I tried --aparc+aseg-in-highres but it was not recognised.. Thank you, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Whole brain parcellation.
Hi Sorry for bothering you again, but I am not sure I understand. I was running whole brain correlation analysis (voxel by voxel). BUT for comparison purposes, I want to compute region by region correlation matrix. So, I want to divide up the brain into freesurfer parcellated regions - i.e. with no overlap, but with full coverage of whole brain. I have looked at FreeSurferColorLUT.txt and am confused because there are several sets and overlap (eg. 19 and 55 vs 2035..) If I use the following, can I ensure no overlap and full coverage? 1)Subcortical: 9-13, 16-19, 48-55, 58 - 59, 85,86 2)Cortex: 1002- 1034, 2002- 2034 I am asking if there is an established list of whole brain parcellations before I rely on label names to choose the ROIS On 06/13/11, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Anything that is non-0 will cover the whole brain. doug Sudhin A. Shah wrote: Hi, thank you. Is there a range in the labels that will ensure that I am including the whole brain? I.e. I see labels for Cx, but not subcortical.. If I take labels 1001 to 2001 ( for eg ) will that cover whole brain? Thank you, S On Jun 13, 2011, at 10:59 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: That is fine, or you can use mri_binarize with the --match option. The numbers that correspond to each label can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt. You can also get at them visual as I described in my previous email with tkmedit: tkmedit subject orig.mgz -aux aseg.mgz -aseg doug Sudhin A. Shah wrote: I mean that I am using FSL to create binary masks from freesurfer parcellated regions. Unless there is a better way :) S On Jun 10, 2011, at 7:13 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: What do you mean you are doing it with FEAT? Sudhin A. Shah wrote: Hello, I am a beginner so please bear with me. I want to obtain binary masks for every region (Cortical + subcortical). I am using FSL(feat) to do this BUT am not sure what the labels would be. I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz BUT do not know which labels to use to avoid overlap and ensure full coverage. Thank you, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline (http://www.partners.org/complianceline) . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail
[Freesurfer] Whole brain parcellation.
Hello, I am a beginner so please bear with me. I want to obtain binary masks for every region (Cortical + subcortical). I am using FSL(feat) to do this BUT am not sure what the labels would be. I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz BUT do not know which labels to use to avoid overlap and ensure full coverage. Thank you, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
