Could you explain why please ? I'm following this : http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On Fri, Feb 24, 2012 at 18:51, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > Oh, the problem may be in your label2vol cmd. Try this one > > mri_label2vol --seg ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+ > **aseg.mgz --temp ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+* > *aseg.mgz --o > ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+**aseg_t1ref.mgz > --regheader ~/Documents/freesurfer/**subjects/pre_al_t1/mri/aparc+** > aseg.mgz > > > > Jimmy Ghaziri wrote: > >> 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<mailto: >> gr...@nmr.mgh.harvard.**edu <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 >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<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 >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 >> <tel:617-726-7422> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://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> >> >> <http://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. >> >> >> ------------------------------**------------------------------** >> ------------ >> >> ______________________________**_________________ >> 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> > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
