If the roi.nii does not include your areas of interest, then they will be masked out. The mask you create with mri_vol2surf may not be very accurate since it uses volume-based operation.
On 7/26/18 5:19 PM, John Anderson wrote:
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Dear Dr Greve, thank you so much. kindly have one additional question and I appreciate your response.
I would like to move a mask from MNI152 to fsaverage so I can use it as a mask in flag --mask in the command "mri_glmfit". Does this procedure reduces the power of the analysis, meaning instead of correcting the the between group analyses to the whole cortex. I would like to do it in the ROI? In my analyses I see results when I correct for whole brain cortex. I mean when I use the command: mri_glmfit --y data.nii.gz --fsgd fsgd.dat --C c.mtx --surf fsaverage lh --cortex --glmdir dir
I really lose these results when I use an ROI as a mask in the command mri_glmfit as follows: mri_glmfit --y data.nii.gz --fsgd fsgd.dat --C c.mtx --surf fsaverage lh --mask roi.nii --glmdir dir Thank you gain for any clarification, John
Don't use --regheader, use --reg $FREESURFER_HOME/average/mni152.register.dat
On 7/26/18 4:40 PM, John Anderson wrote:
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On July 26, 2018 4:40 PM, John Anderson John.anderso@protonmail.com wrote:
Dear Freesurfer experts, I have mask in MNI152 space. I would like to register this mask to fsaverage. How can I do this registration. I am thinking of "mri_vol2surf" as follows:
mri_vol2surf --mov mask.nii --mni152reg --regheader fsaverage --o mask_fsaverage.nii Is this command correct? Thank you for your valuable guidnace John
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