Hi Jimmy, I think the problem, if you can call it that, is with
fslview. Below is from our FAQ. See if that makes sense.
doug
Q. Why would the orientation of my scans look wrong after
processing my DICOM files with 'mri_convert'?
A: It can be misleading to check orientation using FSLVIEW because it
orients volumes based on the way they are on disk so you often get
things looking pretty strange (e.g., upside-down). FSLVIEW does display
little letters along the side of the image to indicate what it thinks
the orientation is, so if you stick to those, then you can properly
judge whether the orientation is correct.
Jimmy Ghaziri wrote:
> Dear FreeSurfer community,
>
> I'm using the mri_label2vol, the output is in .mgz. I then use
> mri_convert to convert it to .nii.gz.
> When I do so, the output is corrupted (see attached images). Some
> colleagues told me that it was because my FreeSurfer had a bug so I
> uninstalled and installed it back again but nothing changed. I then
> tried to run it on some other colleague's machine and it worked fine
> (on one subject just to test).
>
> Any ideas what could be the problem ? I tried to flip the image 90
> degrees but it won't flip, nothing changes.
>
> Here are the commands I'm launching :
>
> mri_label2vol --seg
> ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz --temp
> ~/Documents/freesurfer/subjects/pre_al_t1/mri/rawavg.mgz --o
> ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg_t1ref.mgz
> --regheader ~/Documents/freesurfer/subjects/pre_al_t1/mri/aparc+aseg.mgz
>
> mri_convert aparc+aseg_t1ref.mgz aparc+aseg_t1ref.nii.gz
>
>
> The data looks fine when I open it with tkmedit but it's inverted and
> cut when opened with fslview.
>
> I cannot continue my analyses even if the data looks fine on tkmedit.
> When I apply a flirt transformation on the data I get the same cut and
> inverted brain than on fslview (see flirt attached image).
>
> Is it a problem with my FreeSurfer or a command I'm running the wrong
> way ? Is there another software to convert .mgz to .nii.gz ?
>
>
> Thank you very much !
>
>
> Jimmy
>
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>
>
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>
>
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>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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