I'm trying to understand why the coregistration for a bunch of subjects are bad/failing (mincost value > 8).
The orientation for the anatomical matches the functional (after FSL unpacking) but visual inspection shows that they are actually reversed. Then I used mri_convert to change the orientation of the anatomical but the coregistration is still failing. So I still have no idea what's causing the coreg to fail or how to fix it. -Afsana ________________________________________ 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 5:51 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed 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 _______________________________________________ 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 . 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