Great, thanks.
One more question. Doing it the mris_glm way, is there somehow I can turn the beta files (bfloat) into ascii surface format? Thanks,
-Aaron-
________________________________
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, January 05, 2006 3:08 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness
The easiest way is probably to build an average subject (make_average_subject). This will create ?h.thickness in the surf dir which will be the average across the input subjects. You could also use mris_glm with a design matrix of all 1s. The beta output will then be the average thickness.
Goldman, Aaron (NIH/NIMH) [F] wrote:
Hi, I feel like I used to know this, but how do I make a map of average thickness for a group of subjects? Also, is there a way I can make a similar map showing the variance of thickness values? Thanks,
-Aaron-
Aaron L. Goldman
Post-Bacc IRTA
Genes, Cognition and Psychosis Program, NIMH
Building 10, Room 3C108
Phone: (301) 435-0944
Email: aarong@mail.nih.gov
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'd recommend using mgh instead of bfloat, but in either case you'd do something like:
mris_convert -c beta.mgh $SUBJECTS_DIR/yoursubject/surf/lh.white beta.asc
(or use beta.bhdr for bfloat).
The ability of mris_convert to read any "volume" format was added fairly recently, so if yours does not do it, you can get a new one from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert
doug
Goldman, Aaron (NIH/NIMH) [F] wrote:
Great, thanks.
One more question. Doing it the mris_glm way, is there somehow I can turn the beta files (bfloat) into ascii surface format? Thanks,
-Aaron-
From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, January 05, 2006 3:08 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness
The easiest way is probably to build an average subject (make_average_subject). This will create ?h.thickness in the surf dir which will be the average across the input subjects. You could also use mris_glm with a design matrix of all 1s. The beta output will then be the average thickness.
Goldman, Aaron (NIH/NIMH) [F] wrote:
Hi, I feel like I used to know this, but how do I make a map of average thickness for a group of subjects? Also, is there a way I can make a similar map showing the variance of thickness values? Thanks,
-Aaron-
Aaron L. Goldman
Post-Bacc IRTA
Genes, Cognition and Psychosis Program, NIMH
Building 10, Room 3C108
Phone: (301) 435-0944
Email: aarong@mail.nih.gov mailto:aarong@mail.nih.gov
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Hi, I've been getting the following error message when running autorecon2-wm with some of my images.Any idea as to what might be causing this? Thanks, Alex
Fill Fri Jan 6 14:15:18 EST 2006 Using transforms/talairach.lta mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz /data/flanders/work/alex/freesurfer/subjects_fe/1000795_fixwm/mri logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.120 0.025 -0.148 4.472; 0.007 1.256 0.182 -50.337; 0.160 -0.148 1.109 -29.027; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.120 0.025 -0.148 4.472; 0.007 1.256 0.182 -50.337; 0.160 -0.148 1.109 -29.027; 0.000 0.000 0.000 1.000; mri_fill: could not find any points where lh and rh wm are nbrs INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst reading segmented volume aseg.mgz... INFO: Modifying dst c_(r,a,s), using the transform dst ERROR: mri_fill exited with non-zero status Linux flanders 2.4.26 #2 SMP Tue Dec 14 03:07:23 EST 2004 i686 GNU/Linux recon-all exited with errors at Fri Jan 6 14:16:07 EST 2006
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
check the aseg and see if it's reasonable. Something is badly wrong if there are no lh and rh white matter points that are nbrs.
cheers, Bruce On Fri, 6 Jan 2006, Fornito, Alexander wrote:
Hi, I've been getting the following error message when running autorecon2-wm with some of my images.Any idea as to what might be causing this? Thanks, Alex
Fill Fri Jan 6 14:15:18 EST 2006 Using transforms/talairach.lta mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz /data/flanders/work/alex/freesurfer/subjects_fe/1000795_fixwm/mri logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.120 0.025 -0.148 4.472; 0.007 1.256 0.182 -50.337; 0.160 -0.148 1.109 -29.027; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.120 0.025 -0.148 4.472; 0.007 1.256 0.182 -50.337; 0.160 -0.148 1.109 -29.027; 0.000 0.000 0.000 1.000; mri_fill: could not find any points where lh and rh wm are nbrs INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst reading segmented volume aseg.mgz... INFO: Modifying dst c_(r,a,s), using the transform dst ERROR: mri_fill exited with non-zero status Linux flanders 2.4.26 #2 SMP Tue Dec 14 03:07:23 EST 2004 i686 GNU/Linux recon-all exited with errors at Fri Jan 6 14:16:07 EST 2006
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
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Doug Greve -
Fornito, Alexander -
Goldman, Aaron (NIH/NIMH) [F]