Thanks, Doug,
I never used mri_surf2surf, the latest version I downloaded.
Would you be more specific on how to convert avg_thickness to the average subject?
(I tried mri_surf2surf --srcsubject SUBJECT --tfmt avg_thickness, but it's asking a whole lot more variables...)
Nam.
Doug Greve greve@nmr.mgh.harvard.edu 10/20/06 12:34 PM >>>
Does it work if you don't use projfrac? We have a bug in the make_average_subject code that causes the average thickness (lh.avg_thickness) to be painted on the last subject in the list instead of the averaage subject. One work-around until we get this fixed is to convert the avg_thickness to the average subject with mri_surf2surf. This will require a new version of surf2surf, which you can get from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf
Run it with --tfmt curv
doug
Joongnam Yang wrote:
Dear all,
I've been waiting for an answer to the following question.
I am trying to overlay group-averaged data (FSL) on an averaged anatomical brain (Freesurfer). I did the following,
mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type
analyze
--srcreg register.dat --hemi lh --projfrac 0.5 --out AVG.gfeat/cope1.feat/thresh_zstat1-lh.w --out_type paint
and got the following error message,
MRISreadCurvature: could not open /home/nam/AVERAGE/average/surf/lh.thickness No such file or directory
In the surf directory, I DID find "lh.avg_thickness". I renamed "lh.avg_thickness" "lh.thickness", but it didn't work. Would someone please let me know how to remedy this?
Nam.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Specify the last subject in the list of subjects you used to create the average as the source subject. Specify the average subject itself as the target subject, specify lh.avg_curv as the source input and lh.curv as the output (in the average subject surf dir). You can also look at the --help
Joongnam Yang wrote:
Thanks, Doug,
I never used mri_surf2surf, the latest version I downloaded.
Would you be more specific on how to convert avg_thickness to the average subject?
(I tried mri_surf2surf --srcsubject SUBJECT --tfmt avg_thickness, but it's asking a whole lot more variables...)
Nam.
Doug Greve greve@nmr.mgh.harvard.edu 10/20/06 12:34 PM >>>
Does it work if you don't use projfrac? We have a bug in the make_average_subject code that causes the average thickness (lh.avg_thickness) to be painted on the last subject in the list instead of the averaage subject. One work-around until we get this fixed is to convert the avg_thickness to the average subject with mri_surf2surf. This will require a new version of surf2surf, which you can get from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf
Run it with --tfmt curv
doug
Joongnam Yang wrote:
Dear all,
I've been waiting for an answer to the following question.
I am trying to overlay group-averaged data (FSL) on an averaged anatomical brain (Freesurfer). I did the following,
mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type
analyze
--srcreg register.dat --hemi lh --projfrac 0.5 --out AVG.gfeat/cope1.feat/thresh_zstat1-lh.w --out_type paint
and got the following error message,
MRISreadCurvature: could not open /home/nam/AVERAGE/average/surf/lh.thickness No such file or directory
In the surf directory, I DID find "lh.avg_thickness". I renamed "lh.avg_thickness" "lh.thickness", but it didn't work. Would someone please let me know how to remedy this?
Nam.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Joongnam Yang