Hello,
I'm trying to get this ROI drawn on a brain surface.
http://www.sal.mvm.ed.ac.uk/images/MT_roi.png
To do this, I first ran a script (of the form)[1]:
mri_cor2label --i ~/roi.nii --l ~/roi.label --id 1
Then opened the new roi.label file in tksurfer:
:~$ tksurfer s01 lh orig
The ROI seemed very small and in the wrong place:
http://www.sal.mvm.ed.ac.uk/images/MT_scatter2.png http://www.sal.mvm.ed.ac.uk/images/MT_scatter3.png (the purple labelled areas are sulci contours)
I'm guessing some form of registration went wrong. I tried to first convert it to .nii/.tgh but using the -rl option of mri_convert:
:~$ mri_convert -rl ~/fs_subjects/s01/mri/T1.mgz -rt nearest ~/mainpref_mask_1_3.nii ~/test_mask.mgh
This still looked ok, when I checked the ROI.
I tried mri_cor2label again, but found the region was still in the wrong place.
I figured I needed to give it more info about the surface that it's to be drawn on, so I tried: :~$ mri_cor2label --i ~/test_mask.mgh --l ~/test_mask.label --id 1 --surf s01 lh $Id: mri_cor2label.c,v 1.8.2.2 2009/02/20 16:37:50 greve Exp $ Loading mri /home/s0783410/test_mask.mgh Loading /home/s0783410/fs_subjects/s01/surf/lh.white ERROR: dim mismatch between surface (127260) and input (16777216)
but that didn't seem to work.
To see what might be going on, I tried out the whole thing on V1, which I got segmented by the v1_segment function I asked about in my last email. The output seemed reasonable:
http://www.sal.mvm.ed.ac.uk/images/V1before.tiff
and I was able to get it to a nice ROI in a nii file (thanks doug!):
http://www.sal.mvm.ed.ac.uk/images/V1_nii.png
and I got the nii file back to a surface using:
:~$ mri_cor2label --i ~/imageA.nii --l ~/imageA.label --id 1
Then viewing it in:
:~$ tksurfer s01 lh orig (and loading the imageA.label file).
Which is a little odd: http://www.sal.mvm.ed.ac.uk/images/V1mess.tiff (although it seems to be lined up properly, it has a little extra region selected in the Lingual(?) Gyrus).
I thought the difference might be because the V1 ROI came from the original T1 image used by freesurfer, while the ROI I'm trying to use is from a functional image. However, to check, I coregistered (resliced) the function ROI to the original anatomical image, but this didn't seem to make any different.
Any suggestions or ideas about where I should be looking? This is I guess one of the most common tasks people use freesurfer for, so I guess I just need to look in the right place for help.
Thanks for the help!
Mike.
[1] Actual output: s0783410@spatial2:~$ mri_cor2label --i ~/mainpref_mask_1_3.nii --l ~/mainpref_mask_1_3.label --id 1 $Id: mri_cor2label.c,v 1.8.2.2 2009/02/20 16:37:50 greve Exp $ Loading mri /home/s0783410/mainpref_mask_1_3.nii ------- Vox2RAS of input volume ----------- -1.719 0.000 0.000 110.003; 0.000 0.000 2.400 -30.001; 0.000 -1.719 0.000 110.003; 0.000 0.000 0.000 1.000; Scanning the volume Found 473 label voxels Writing label file /home/s0783410/mainpref_mask_1_3.label LabelWrite: saving to /home/s0783410/mainpref_mask_1_3.label Centroid: -0.91 -6.49 54.15 mri_cor2label completed SUCCESSFULLY