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Thank you very much Prof Greve! I'm almost done! Now, using mri_volcluster I can identify the vertex number with highest significance within a ROI in a surface sig.mgh map (see attached txt). However I don't know how to compute the corresponding MNI coordinates of a specific vertex number (say 122288 in the file). I already checked the very helpful page https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems, but I did not see the precise calculation "from a single vertex number to (MNIx, MNIy,MNIz)". Maybe I missed something but the mri_volcluster output only displayed the vertex number (i.e no RAS coords) to work with. I am always working on fsaverage space.Thanks a lot in advance!
On Tue, Sep 15, 2020 at 5:27 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Use mri_annotation2label to convert the, eg, ?h.aparc.annot to a segmentation (--seg output), then use mri_binarize with 1031._______________________________________________
On 9/15/2020 10:41 AM, Fred Sampedro wrote:
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Thats precisely the point that I should be missing. To recap, I'm interested in knowing the MNI coordinates of the vertex with highest significance within a specific atlas-ROI (e.g. ctx-lh-supramarginal) from a surface sig.mgh map (e.g. group comparison in cortical thickness).
If I understood correctly, first I need a "surface binary mask" of the atlas ROI, which I tried to get using mri_binarize but I am not sure if I did it correctly. Then, I would fscalc mul the sig.mgh map with the surface binary mask, and finally apply mri_volcluster. I'm stuck in the first step of obtaining the desired surface binary mask from the default FS atlas.
On Tue, Sep 15, 2020 at 4:10 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
What do you mean you are trying to overlay it on lh.inflated? the output of mri_binarize will be a volume, so you'd have to sample it onto the surface in some way_______________________________________________
On 9/14/2020 9:28 AM, Fred Sampedro wrote:
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Thanks a lot in advanceCould you please help me with exact commands? I'm sure this should be easy but I lost this battle!!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..).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.mri_binarize --i aparc+aseg.mgz --o leftsupramarg.mgh --match 1031Just 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:
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:
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Thanks a lot in advance!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).Dear FS experts,I have a rather simple question:
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?
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