On 7/15/2020 10:59 AM, Eleni Nikalexi wrote:
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Dear Douglas and Bruce, on the same subject, I wanted to ask two questions:
- since the ROIs were obtained on 2mm voxels, is the command
$ mri_vol2surf --mov ROI_set1/LeftAngG.img--regheader MNI_1mm --interp nearest --hemi lh --out Left_AngG_tmpfs.mgh --projdist-max 0 1 0.1 --noreshape --trgsubject fsaverage
correct, or should I run it on the MNI152 2mm?
This is probably fine, but you can run tkregisterfv --mov MNI152_2mm.nii.gz --s MNI_1mm --regheader --reg junk.lta these should come up registered, if not then there might be a problem.
- how can I create afterwards labels for reconned subjects of 1mm
voxel size? I already tried the $ mri_vol2label --i Left_AngG_tmpfs.mgh --id 1 --l LeftAngG_tmp.label --surf fsaverage lh white
but permission was denied, so then I tried to use tksurfer, but I got an error message: "surfer: Interpreting overlay volume /project/RDS-FHS-ppa2018-RW/eleni/localizers/Left_AngG_tmpfs.mgh as encoded scalar volume".
What would you suggest?
I don't understand what you are tyring to do here.
Thank you in advance! Eleni On Monday, July 6, 2020, 09:29:19 PM GMT+3, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
It has to be loaded as an overlay to a surface, not a surface itself.
On 7/3/2020 10:10 AM, Eleni Nikalexi wrote:
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Dear Douglas, thank you very much for your help; I run the recon of MNI152_T1_1mm_brain.nii.gz (which I moved into a directory called MNI_1mm). Then I run the following command, as you suggested: $ mri_vol2surf --mov ROI_set1/LeftAngG.img--regheader MNI_1mm --interp nearest --hemi lh --out LeftAngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape
But then, in freeview I get the following result:
Inline image
I also get an error when I try to load it as a surface: "LeftAngG_tmp.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!"
What could be the mistake?
Best regards, Eleni
On Thursday, July 2, 2020, 04:25:54 PM GMT+3, Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu wrote:
Try running recon-all on the MNI152. Load the ROI onto the reconned MNI152; load the surfaces as well and make sure that the ROI intersects with the surface, then use #3 below with --regheader MNI152 instead of --reg tmp.dat. You can also specify --trgsubject fsaverage and mri_vol2surf will map the ROI all the way onto the fsaverage surface
On 7/1/2020 10:03 AM, Eleni Nikalexi wrote:
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Dear Freesurfer developers,
We have a series of MRI scans and we are trying to extract cortical thickness in certain regions of interest. The ROIs already exist - some are in .img and some in NIFTI format - and we want to tranform them into labels and then register them on fsaverage. The problem is that the ROIs are in MNI152 space (from SPM), with voxel size=2mm. We have tried various commands to register one of the .img ROIs on fsaverage, but they all failed:
- $ fslregister --s fsaverage --mov ROI_set1/LeftAnGG.img --reg tmp.dat
- $ tkmedit fsaverage T1.mgz -overlay ROI_set1/LeftAngG.img -overlay-reg tmp.dat
- $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape
- $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz
The result is that the ROI is either not in the right place, or the right size or we just end up with a weird 3D cross shape in freeview.
Could you please suggest something that we could do to fix this?
Thank you so much in advance!
Best regards, Eleni
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