Hi,
Here is the mri_vol2surf I run:
mri_vol2surf --src /space/data/ppolosecki/cooked/2011/110520GIZMO/bold/a2u/c13_2456/sig.nii --src_type nii --srcreg /space/data/ppolosecki/cooked/2011/110520GIZMO/t1epi/110520GIZMO_2_120509GIZMO.register.dat --projfrac 0.5 --trgsubject 120509GIZMO --surf white --hemi rh --out /rdata/space/data/ppolosecki/cooked/2011/110520GIZMO/myscripts_func_CIT/tmp_paint_/sig-rh.gii --out_type gii --frame 0
(I was using gii format hoping that I would be more caret-friendly, but I have also tried mgz) For converting my gii surface into a caret surface I was running (I case you are familiar with caret_comand, I am just starting to familiarize myslef with it):
caret_command -file-convert -fsf2c /Volumes/Polac/Desktop/fs-to-f99/120509GIZMO/func_surface/sig-rh.gii /Volumes/Polac/Desktop/fs-to-f99/120509GIZMO/surf/rh.white 120509GIZMO.R.PMAP.80672.metric -struct right
(directory names differ across commands, but don't pay attention to that, the files used are the same)
Thanks for looking into this!
On Wed, Jul 25, 2012 at 10:35 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Pablo
how did you run mri_vol2surf? Note that this isn' really a surface per-se, but rather a scalar overlay on the surface. mri_vol2surf samples the functional volume onto the surface so that you have 1 number per vertex (the functional value at that point in space). We'll need all your command lines to diagnose your problem
cheers Bruce
On Wed, 25 Jul 2012, Pablo Polosecki wrote:
Dear List,
I am trying to show my results on Caret's F99 atlas, in Caret. For this I already managed to take my anatomical (white, pial etc) surfaces and register them to F99 in Caret, which works fine. I am trying now to get my functional p-map (initially a nifti volume) into Caret too to overlay them on my anatomical surface together with the atlas information. For this my plan s the followign 1-Convert my nifti p-map volume into a surface using mri_vol2surf 2-Convert the resulting surface into caret surface using caret_command tools. 3-Apply to the resulting surface the same transformation I applied to my anatomical surfaces to have them all in register with Caret's F99 atlas.
It seems like step 1 works fine, but when I try to run step too, Caret complains that my anatomical surface doesn't have the same number of vertices as my functional surface. Indeed, when opening the anatomical surface in maltab with read_surf, it seems to have exactly twice the number of vertices that my functional surface has (I cannot open it with read_surf for some reason but I see the number when I open it with a text editor or when I look at the output of mri_vol2surf).
Would anyone have a suggestion as to why this is the way it is and how I could have my 2 surfaces have the same number of nodes?
Thank you very much,
Pablo _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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