Dear all, I have not received any advice about this point. Can somebody help me? thank you!
I followed the instructions found in Freesurfer tutorials ('cortical thickness of a volume-defined ROI'). However, in the point 4 of the procedure I am not able to change the --reshape default. My run is:
mri_surf2surf --s subj001 --trgsubject fsaverage --hemi rh --sval rh.thickness --tval rh.thickness.fsaverage.mgh --reshape-factor 7
but it continues to create (like default) a reshape with 6.
For this reason, I think, the following command: mri_segstats --seg $SUBJECTS_DIR/rh.fsaverage.mask21.mgh --in rh.thickness.fsaverage.mgh --sum segstats-mask21.txt
give:
ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7
What can I do to solve this problem?
Thank you for your help!
Angela
Angela Favaro, MD, PhD, MSc Psychiatric Clinic Department of Neurosciences via Giustiniani 3 35128 Padova Italy
Hi Angela Doug as been away and this is really his domain. If you haven't gotten an answer in a week so please repost one more time Bruce
On Dec 29, 2010, at 5:35 AM, angela.favaro@unipd.it wrote:
Dear all, I have not received any advice about this point. Can somebody help me? thank you!
I followed the instructions found in Freesurfer tutorials ('cortical thickness of a volume-defined ROI'). However, in the point 4 of the procedure I am not able to change the --reshape default. My run is:
mri_surf2surf --s subj001 --trgsubject fsaverage --hemi rh --sval rh.thickness --tval rh.thickness.fsaverage.mgh --reshape-factor 7
but it continues to create (like default) a reshape with 6.
For this reason, I think, the following command: mri_segstats --seg $SUBJECTS_DIR/rh.fsaverage.mask21.mgh --in rh.thickness.fsaverage.mgh --sum segstats-mask21.txt
give:
ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7
What can I do to solve this problem?
Thank you for your help!
Angela
Angela Favaro, MD, PhD, MSc Psychiatric Clinic Department of Neurosciences via Giustiniani 3 35128 Padova Italy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try removing the --reshape from both steps 3 and 4.
doug
On 12/29/10 5:35 AM, angela.favaro@unipd.it wrote:
cortical thickness of a volume-defined ROI
Dear all, I have not received any advice about this point. Can somebody help me? thank you!
I followed the instructions found in Freesurfer tutorials ('cortical thickness of a volume-defined ROI'). However, in the point 4 of the procedure I am not able to change the --reshape default. My run is:
mri_surf2surf --s subj001 --trgsubject fsaverage --hemi rh --sval rh.thickness --tval rh.thickness.fsaverage.mgh --reshape-factor 7
but it continues to create (like default) a reshape with 6.
For this reason, I think, the following command: mri_segstats --seg $SUBJECTS_DIR/rh.fsaverage.mask21.mgh --in rh.thickness.fsaverage.mgh --sum segstats-mask21.txt
give:
ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7
What can I do to solve this problem?
Thank you for your help!
Angela
Angela Favaro, MD, PhD, MSc Psychiatric Clinic Department of Neurosciences via Giustiniani 3 35128 Padova Italy
freesurfer@nmr.mgh.harvard.edu
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angela.favaro＠unipd.it -
Bruce Fischl -
Douglas Greve