Yes, since it appears fine when I open it with tkmedit. But once I apply a flirt transformation I get the same image on tkmedit than the one on fslview. I tried to flip the image but it won't change anything since the brain is cut. Also, I followed the same steps on my colleagues machine and it worked fine on his...
Thank you Jimmy On Fri, Feb 24, 2012 at 14:27, Douglas N Greve <gr...@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 >> >> ------------------------------**------------------------------** >> ------------ >> >> >> ------------------------------**------------------------------** >> ------------ >> >> >> ------------------------------**------------------------------** >> ------------ >> >> ------------------------------**------------------------------** >> ------------ >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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