I'm still not sure why you are trying to do this. If FSL did not unpack the volumes with the correct orientation, then you need to switch to mri_convert. If they are in the right orientation, then I don't understand what you are trying to do. doug
On 08/16/2016 05:27 PM, Afzal, Afsana wrote: > Hi Doug, > > After the coregistration failed for the majority of the subjects, I visually > inspected a handful of the subjects in freeview and it looks like the > anatomical and the functional are reversed but I could be wrong. > > The nifti files are unpacked from DICOMs using unpack_fsl.sh > (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to > a specific subject directory if that would be of any help. > > Might be worth mentioning that the subjects who failed coreg were not scanned > using siemens scanners but Phillips and GE scanners. Don't know if there's > some sort of discrepancy between the scanner coordinate frames that could > potentially lead to this issue. > > Thank you very much for your help, > > Afsana > ______________________________ > Afsana Afzal > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, August 16, 2016 3:45 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed > > How do you know that the structural is left-right reversed? Or that the > fMRI is? How did you create the nifti files? > > > On 08/16/2016 01:41 PM, Afzal, Afsana wrote: >> Hi, >> >> I'm having trouble co-registering a bunch of subjects whose T1 is >> left-right reversed. While the orientation of the structural file in >> the NIfTI header is LIA and the orientation of the functional volume >> is LAS, visual inspection shows that the structural is left-right >> reversed. I then followed the steps outlined in >> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal >> <https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal> to rerun >> the reconstruction and re-registered the subject but the registration >> mincost value is still hovering around 0.9 even with the left-right >> reversed structural. >> >> I've tried running registration with SPM and FSL; neither method is >> able to register these subjects properly. >> >> With --init-fsl I get the following: >> WARNING: initial G-W contrast is negative, but expecting positive. >> If the mov data has a T1 contrast, re-run with --T1 >> >> and with --init-spm I get: >> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... >> ... continuing. >> >> At this point I'm out of ideas to try out. This issue is occurring for >> over 170 subjects (data collected outside Martinos using non-siemens >> scanners). >> >> Any help would be much appreciated! >> >> Thanks, >> >> Afsana >> >> >> >> ______________________________ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> 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 > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > 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 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
