Re: [Freesurfer] peak MNI coordinates within a masked sig.mgh

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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:

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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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