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Dear Dr Greve, I apologies if I was not clear.

I ran voxel-wise analysis between two groups. I thresholded the resultant statistical map at p<0.05 then I binarized it. This volumetric statistical map is in MNI152. I would like to move it to fsaverage then run group comparisons using it in the flag "--mask" in the command "mri_glmfit".  I highly appreciate if you guide me to the correct procedure.

John

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:


‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On July 26, 2018 5:19 PM, John Anderson <John.anderso@protonmail.com> wrote:

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