On Fri, Feb 24, 2012 at 14:27, Douglas N Greve <
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu>> wrote:
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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