External Email - Use Caution 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 <dgr...@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: > > External Email - Use Caution > 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 <fredsampe...@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 <dgr...@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! >>> >>> _______________________________________________ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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