Hi,
if I apply the following command:
preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm -fwhm 0 -per-run -nosmooth -force
The preprocessing runs into trouble at the following point
mri_vol2vol done
mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /...path.../bold/001/masks/brain.mni305.1mm.nii freadFloat: fread failed ERROR: dimension mismatch between source and mask
As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which results in the dimension mismatch. How can I get rid of this problem?
Cheers Joerg
Yep, that's a bug. I've fixed it in my version. To fix it in yours, do the following two steps:
Step 1: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/subcort.mask.1mm.mgz cp subcort.mask.1mm.mgz $SUBJECTS_DIR/fsaverage/mri
Step 2: In rawfunc2tal-sess, change:
set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
To
if($res == 2) then set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz else set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri/subcort.mask.1mm.mgz endif
doug
On 11/27/2012 04:48 AM, Jörg Pfannmöller wrote:
Hi,
if I apply the following command:
preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm -fwhm 0 -per-run -nosmooth -force
The preprocessing runs into trouble at the following point
mri_vol2vol done
mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /...path.../bold/001/masks/brain.mni305.1mm.nii freadFloat: fread failed ERROR: dimension mismatch between source and mask
As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which results in the dimension mismatch. How can I get rid of this problem?
Cheers Joerg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Note that each of those set commands should be a single line. The file to change is $FREESURFER_HOME/fsfast/bin/rawfunc2tal-sess
doug
On 11/27/2012 01:23 PM, Douglas N Greve wrote:
Yep, that's a bug. I've fixed it in my version. To fix it in yours, do the following two steps:
Step 1: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/subcort.mask.1mm.mgz cp subcort.mask.1mm.mgz $SUBJECTS_DIR/fsaverage/mri
Step 2: In rawfunc2tal-sess, change:
set subcortmask =$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
To if($res == 2) then set subcortmask =$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz else set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri/subcort.mask.1mm.mgz endif
doug
On 11/27/2012 04:48 AM, Jörg Pfannmöller wrote:
Hi,
if I apply the following command:
preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm -fwhm 0 -per-run -nosmooth -force
The preprocessing runs into trouble at the following point
mri_vol2vol done
mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /...path.../bold/001/masks/brain.mni305.1mm.nii freadFloat: fread failed ERROR: dimension mismatch between source and mask
As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which results in the dimension mismatch. How can I get rid of this problem?
Cheers Joerg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
A last question to this topic. Does the resolution of the MNI305 brain affected the surface based analysis or is it exclusively affecting the subcortical analysis?
On Tue, 27 Nov 2012 13:30:04 -0500 Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Note that each of those set commands should be a single line. The file to change is $FREESURFER_HOME/fsfast/bin/rawfunc2tal-sess
doug
On 11/27/2012 01:23 PM, Douglas N Greve wrote:
Yep, that's a bug. I've fixed it in my version. To fix it in yours, do the following two steps:
Step 1: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/subcort.mask.1mm.mgz cp subcort.mask.1mm.mgz $SUBJECTS_DIR/fsaverage/mri
Step 2: In rawfunc2tal-sess, change:
set subcortmask =$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
To if($res == 2) then set subcortmask =$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz else set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri/subcort.mask.1mm.mgz endif
doug
On 11/27/2012 04:48 AM, Jörg Pfannmöller wrote:
Hi,
if I apply the following command:
preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm -fwhm 0 -per-run -nosmooth -force
The preprocessing runs into trouble at the following point
mri_vol2vol done
mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /...path.../bold/001/masks/brain.mni305.1mm.nii freadFloat: fread failed ERROR: dimension mismatch between source and mask
As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which results in the dimension mismatch. How can I get rid of this problem?
Cheers Joerg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Just subcortical. BTW, going to 1mm will probably create very large files. doug
On 11/28/2012 03:52 AM, Jörg Pfannmöller wrote:
A last question to this topic. Does the resolution of the MNI305 brain affected the surface based analysis or is it exclusively affecting the subcortical analysis?
On Tue, 27 Nov 2012 13:30:04 -0500 Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Note that each of those set commands should be a single line. The file to change is $FREESURFER_HOME/fsfast/bin/rawfunc2tal-sess
doug
On 11/27/2012 01:23 PM, Douglas N Greve wrote:
Yep, that's a bug. I've fixed it in my version. To fix it in yours, do the following two steps:
Step 1: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/subcort.mask.1mm.mgz cp subcort.mask.1mm.mgz $SUBJECTS_DIR/fsaverage/mri
Step 2: In rawfunc2tal-sess, change:
set subcortmask =$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
To if($res == 2) then set subcortmask =$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz else set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri/subcort.mask.1mm.mgz endif
doug
On 11/27/2012 04:48 AM, Jörg Pfannmöller wrote:
Hi,
if I apply the following command:
preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm -fwhm 0 -per-run -nosmooth -force
The preprocessing runs into trouble at the following point
mri_vol2vol done
mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /...path.../bold/001/masks/brain.mni305.1mm.nii freadFloat: fread failed ERROR: dimension mismatch between source and mask
As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which results in the dimension mismatch. How can I get rid of this problem?
Cheers Joerg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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@nmr.mgh.harvard.edu
-
Douglas N Greve -
Jörg Pfannmöller