I want to average multiple structural scans for input into the surface recon. Two are axial and one is sagittal. (I plan to correct for the gradient inhomogeneities in the sagittal images, so that shouldn't be an issue.)
Anyway, the problem comes when recon-all does "motion correction" to align the scans. For some strange reason, the axial and sagittal scan protocols use slightly different TRs and TEs (e.g. TR=7.996 vs. 8.012). For some even stranger reason, this brings recon-all to a screaching halt. I'm guessing that this is actually a MINC problem but I wonder if there is a way to make it ignore the TR and TE when aligning two structural scans.
My work around is to explicitly set the TR and TE for the sagittal scan when running mri_convert: mri_convert -tr 8.012 -te 3.136 -it dicom i*.1 $destdir/$mgzname.mgz
Can you elaborate on what "brings to a screetching halt means"? Is there an error msg or does it just hang?
doug
Don Hagler wrote:
I want to average multiple structural scans for input into the surface recon. Two are axial and one is sagittal. (I plan to correct for the gradient inhomogeneities in the sagittal images, so that shouldn't be an issue.)
Anyway, the problem comes when recon-all does "motion correction" to align the scans. For some strange reason, the axial and sagittal scan protocols use slightly different TRs and TEs (e.g. TR=7.996 vs. 8.012). For some even stranger reason, this brings recon-all to a screaching halt. I'm guessing that this is actually a MINC problem but I wonder if there is a way to make it ignore the TR and TE when aligning two structural scans.
My work around is to explicitly set the TR and TE for the sagittal scan when running mri_convert: mri_convert -tr 8.012 -te 3.136 -it dicom i*.1 $destdir/$mgzname.mgz
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry for being overly dramatic. recon-all just quits with error messages:
ERROR: TRs are inconsistent 8.012 7.996 ERROR: mri_motion_correct exited with non-zero status
From: Doug Greve greve@nmr.mgh.harvard.edu To: Don Hagler dhaglerjr@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] motion correction during recon-all Date: Mon, 28 Nov 2005 17:08:37 -0500
Can you elaborate on what "brings to a screetching halt means"? Is there an error msg or does it just hang?
doug
Don Hagler wrote:
I want to average multiple structural scans for input into the surface recon. Two are axial and one is sagittal. (I plan to correct for the gradient inhomogeneities in the sagittal images, so that shouldn't be an issue.)
Anyway, the problem comes when recon-all does "motion correction" to align the scans. For some strange reason, the axial and sagittal scan protocols use slightly different TRs and TEs (e.g. TR=7.996 vs. 8.012). For some even stranger reason, this brings recon-all to a screaching halt. I'm guessing that this is actually a MINC problem but I wonder if there is a way to make it ignore the TR and TE when aligning two structural scans.
My work around is to explicitly set the TR and TE for the sagittal scan when running mri_convert: mri_convert -tr 8.012 -te 3.136 -it dicom i*.1 $destdir/$mgzname.mgz
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Hi Don,
I've modified mri_motion_correct2 to print a warning in this case. You can make the same mod to your local or you can use the new one (attached).
doug
On Wed, 30 Nov 2005, Don Hagler wrote:
Sorry for being overly dramatic. recon-all just quits with error messages:
ERROR: TRs are inconsistent 8.012 7.996 ERROR: mri_motion_correct exited with non-zero status
From: Doug Greve greve@nmr.mgh.harvard.edu To: Don Hagler dhaglerjr@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] motion correction during recon-all Date: Mon, 28 Nov 2005 17:08:37 -0500
Can you elaborate on what "brings to a screetching halt means"? Is there an error msg or does it just hang?
doug
Don Hagler wrote:
I want to average multiple structural scans for input into the surface recon. Two are axial and one is sagittal. (I plan to correct for the gradient inhomogeneities in the sagittal images, so that shouldn't be an issue.)
Anyway, the problem comes when recon-all does "motion correction" to align the scans. For some strange reason, the axial and sagittal scan protocols use slightly different TRs and TEs (e.g. TR=7.996 vs. 8.012). For some even stranger reason, this brings recon-all to a screaching halt. I'm guessing that this is actually a MINC problem but I wonder if there is a way to make it ignore the TR and TE when aligning two structural scans.
My work around is to explicitly set the TR and TE for the sagittal scan when running mri_convert: mri_convert -tr 8.012 -te 3.136 -it dicom i*.1 $destdir/$mgzname.mgz
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
freesurfer@nmr.mgh.harvard.edu
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Don Hagler -
Doug Greve