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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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
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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/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
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