Yes
On 11/30/2020 10:45 AM, Alberto Del Cerro Leon wrote:
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Then, now that I have the AAL in the surface I should make a label for every
region in the AAL_surface image with mri_vol2label with surf option and run
mri_label2label for every label and every subject in my study. Is this the
correct workflow?
El lun, 30 nov 2020 a las 16:26, Greve, Douglas N.,Ph.D.
(<[email protected]<mailto:[email protected]>>) escribió:
Oh, don't use .img as it cannot handle the surface dimensions. Technically,
nifti cannot either, but I hacked our nifti version to accommodate. Or use mgh
as you have done.
On 11/30/2020 8:31 AM, Alberto Del Cerro Leon wrote:
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First of all, thanks you Douglas for the support.
As I said i run the mri_vol2surf and I obtained an error:
mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI
--projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img
srcvol = /home/neuroimage/fsl/FreeSurfer/AAL.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
Done loading volume
Computing registration from header.
Using /usr/local/freesurfer/subjects/MNI/mri/orig.mgz as target reference.
Reading surface /usr/local/freesurfer/subjects/MNI/surf/lh.white
Done reading source surface
Reading thickness /usr/local/freesurfer/subjects/MNI/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 104840
Writing to /home/neuroimage/fsl/FreeSurfer/AAL-lh.img
Dim: 161783 1 1
ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768
However I noticed that if i use the format .guii or .mgh this error message
doesn't appear. Could I continue with the image in this format? What's the
difference that makes this error appear with .img format?
El dom, 29 nov 2020 a las 18:26, Greve, Douglas N.,Ph.D.
(<[email protected]<mailto:[email protected]>>) escribió:
Can you send the full terminal output?
On 11/18/2020 6:41 AM, Alberto Del Cerro Leon wrote:
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I tried to run mri_vol2surf with the following command: mri_vol2surf --src
/home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5 --hemi
lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img, however i obtain an error
ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768. How can i fix it?
El lun., 16 nov. 2020 a las 17:10, Douglas N. Greve
(<[email protected]<mailto:[email protected]>>) escribió:
Which MNI space? If mni152, then run recon-all on the mni152 template, then run
mri_vol2surf with --regheader mni152subjectname; also include --projfrac 0.5.
But before you do that , load the AAL atlas onto the mni152subject with the
surfaces to make sure everything aligns. You might want to do this with the
colin27 brain instead because I think that is what the AAL atlas is defined on.
On 11/16/2020 5:30 AM, Alberto Del Cerro Leon wrote:
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Hello everyone, I tried to follow your instruction about how to get the
fresurfer stats in AAL ROIs. I have an image .nii with the labels of the AAL in
the MNI space (i submit this image in the e-mail). Can I use this image in the
mri_vol2surf? If so, i suppose that this image would be the input one, but i
don't know what is registration file in the syntax of mri_vol2surf
Sorry for the inconvenience, Alberto
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