Just a follow-up, I got stuck at trying to obtain a mask from binarizing a specific ROI from the aparc+aseg.mgz, aiming to mask my sig.mgh with this ROI.If for instance, I'd like to create a ROI from the left supramarginal gyrus, I found that its label is 1031. Now, I tried:

mri_binarize --i aparc+aseg.mgz --o leftsupramarg.mgh --match 1031

however when visualizing the output of this command in freeview overlaying the mask on top of lh.inflated...it seems that this approach was wrong.

Then looking at the mail archive I thought that this is somehow more complex, involving mri_annot2label, and mri_label2label with --outmask... however I tried for 2 days and did not obtain a convincing binary ROI mgh file that I could fscalc with the sig.mgh, I got lost with several command params (srclabel/trglabel..).

Could you please help me with exact commands? I'm sure this should be easy but I lost this battle!!

Thanks a lot in advance

On Tue, Aug 4, 2020 at 5:14 PM Fred Sampedro <fredsampedro@gmail.com> wrote:

Thanks a lot!

I read the mri_volcluster doc, can you confirm that the TalX TalY TalZ coordinates are those of the vertex with maximum intensity within the cluster? (it could be those of the cluster's center of gravity)

Finally, I would be very grateful if you could help me with minor parameter tuning of the commands:

1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG?(how do I get it?) --o roimask.mgh

2) fslcalc sig.mgh mult roimask.mgh -o maskedsig.mgh

3) mri_volcluster --in maskedsig.mgh --thmin 0.001 --sum output.txt

Thanks a lot in advance!
On Mon, Aug 3, 2020 at 4:40 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Try mri_volcluster. Pass you masked sig as the input and set --thmin 0.0001 and specify a summary file with --sum. I think that should work

On 7/31/2020 9:38 AM, Fred Sampedro wrote:
External Email - Use Caution

Dear FS experts,

I have a rather simple question:

I would like to obtain the MNI coordinates of the most significant vertex in a sig.mgh map but within a specific ROI (for instance the left supramarginal region).

Here is my attempt but with practical gaps in terms of command parameters:

1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG? --o roimask.mgh

2) fslmaths sig.mgh mult roimask.mgh -o maskedsig.mgh

3) which command could I use to obtain the MNI coordinates of the peak value in maskedsig.mgh?

Thanks a lot in advance!
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