Try using mri_convert to convert one set and see if that fixes it. If so, then never use unpack_fsl.sh again. Note that unpack_fsl.sh is not part of the FSL suit of tools, so don't blame them ...
On 08/17/2016 01:57 PM, Afzal, Afsana wrote: > I opened up the functional and anatomical (original and reversed) in freeview > and the functional volume is better aligned with the reversed anatomical than > with the original anatomical. I realize this is a gross visual check that is > probably unreliable but I don't have any other guesses as so why the coreg is > failing for over 150 subjects. > > ______________________________ > 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: Wednesday, August 17, 2016 1:44 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed > > what do you mean "visual inspection shows that they are actually > reversed"? Please give details > > On 08/17/2016 01:31 PM, Afzal, Afsana wrote: >> 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 >> >> > -- > 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.
