hi folks,
does recon-all work if the input T1s for the same participant have different resolutions? (i don't have a dataset to test, but trying to debug some issues another group has been having).
cheers,
satra
No, I don't think it does
On 05/31/2016 10:13 AM, Satrajit Ghosh wrote:
hi folks,
does recon-all work if the input T1s for the same participant have different resolutions? (i don't have a dataset to test, but trying to debug some issues another group has been having).
cheers,
satra
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Do you mean several inputs for motion correction (averaging), or for a longitudinal study?
I haven't tested it, but for averaging, we use mri_robust_template and I see no reason why it should not work. It probably reslices at the resolution of the first input to create rawavg and then conforms that.
Best, Martin
On 05/31/2016 10:13 AM, Satrajit Ghosh wrote:
hi folks,
does recon-all work if the input T1s for the same participant have different resolutions? (i don't have a dataset to test, but trying to debug some issues another group has been having).
cheers,
satra
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I tried this recently and it failed. I did not pursue it any further
On 05/31/2016 01:32 PM, Martin Reuter wrote:
Do you mean several inputs for motion correction (averaging), or for a longitudinal study?
I haven't tested it, but for averaging, we use mri_robust_template and I see no reason why it should not work. It probably reslices at the resolution of the first input to create rawavg and then conforms that.
Best, Martin
On 05/31/2016 10:13 AM, Satrajit Ghosh wrote:
hi folks,
does recon-all work if the input T1s for the same participant have different resolutions? (i don't have a dataset to test, but trying to debug some issues another group has been having).
cheers,
satra
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web :http://reuter.mit.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I see. Could be we specifically test for that and stop processing. It is a bad idea to average from different resolutions. Probably averaging is not even helpful at all, especially with newer images.
Anyway, if someone points me at some data, I can take a look.
Best, Martin
On 05/31/2016 01:34 PM, Douglas N Greve wrote:
I tried this recently and it failed. I did not pursue it any further
On 05/31/2016 01:32 PM, Martin Reuter wrote:
Do you mean several inputs for motion correction (averaging), or for a longitudinal study?
I haven't tested it, but for averaging, we use mri_robust_template and I see no reason why it should not work. It probably reslices at the resolution of the first input to create rawavg and then conforms that.
Best, Martin
On 05/31/2016 10:13 AM, Satrajit Ghosh wrote:
hi folks,
does recon-all work if the input T1s for the same participant have different resolutions? (i don't have a dataset to test, but trying to debug some issues another group has been having).
cheers,
satra
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web :http://reuter.mit.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Satra
it will probably reject this by default, which you can get around be reslicing one of them to be like the other. Or "conforming" both of them.
cheers Bruce On Tue, 31 May 2016, Satrajit Ghosh wrote:
hi folks, does recon-all work if the input T1s for the same participant have different resolutions? (i don't have a dataset to test, but trying to debug some issues another group has been having).
cheers,
satra
thank you doug, martin, and bruce.
martin: i believe she was doing this for motion correction
i've attached the error this person observed below. so it does seem that mri_robust_template at present doesn't do any resampling.
bruce: we can definitely see ways in which this could be done outside recon-all and then sent to recon-all as a single image. but i just wanted to verify that the error we were observing was expected behavior at present.
cheers,
satra
RuntimeError: Command: mri_robust_template --satit --average 1 --fixtp --mov /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep0/001.mgz /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/002.mgz /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep2/003.mgz /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep3/004.mgz /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4/005.mgz --inittp 1 --iscale --noit --template rawavg.mgz --iscaleout 001-iscale.txt 002-iscale.txt 003-iscale.txt 004-iscale.txt 005-iscale.txt --subsample 200 --lta 001.lta 002.lta 003.lta 004.lta 005.lta Standard output: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--satit: Will estimate SAT iteratively! --average: Using method 1 for template computation. --fixtp: Will map everything to init TP! --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep0/001.mgz as movable/source volume. --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/002.mgz as movable/source volume. --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep2/003.mgz as movable/source volume. --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep3/004.mgz as movable/source volume. --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4/005.mgz as movable/source volume. Total: 5 input volumes --inittp: Using TP 1 as target for initialization --iscale: Enableing intensity scaling! --noit: Will output only first template (no iterations)! --template: Using rawavg.mgz as template output volume. --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep0/001.mgz'... converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep0/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/002.mgz'... converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/002.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep2/003.mgz'... converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep2/003.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep3/004.mgz'... converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep3/004.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4/005.mgz'... converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4/005.mgz' to bspline ... MRItoBSpline degree 3 Standard error: ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 1, 1, 1.2 size(0) = 1, 1, 1 MultiRegistration::loadMovables: voxel size is different /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/002.mgz.
Return code: 251 Interface RobustTemplate failed to run.
On Tue, May 31, 2016 at 2:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Satra
it will probably reject this by default, which you can get around be reslicing one of them to be like the other. Or "conforming" both of them.
cheers Bruce On Tue, 31 May 2016, Satrajit Ghosh wrote:
hi folks, does recon-all work if the input T1s for the same participant have
different
resolutions? (i don't have a dataset to test, but trying to debug some issues another group has been having).
cheers,
satra
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.
yes, typically it is a mistake that we want to catch
cheers Bruce On Tue, 31 May 2016, Satrajit Ghosh wrote:
thank you doug, martin, and bruce. martin: i believe she was doing this for motion correction
i've attached the error this person observed below. so it does seem that mri_robust_template at present doesn't do any resampling.
bruce: we can definitely see ways in which this could be done outside recon-all and then sent to recon-all as a single image. but i just wanted to verify that the error we were observing was expected behavior at present.
cheers,
satra
RuntimeError: Command: mri_robust_template --satit --average 1 --fixtp --mov /Volumes/LaCie/RaquelA lmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_ 006_S_4150/T1_prep/mapflow/_T1_prep0/001.mgz /Volumes/LaCie/RaquelAlmeida/wo rkflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_415 0/T1_prep/mapflow/_T1_prep1/002.mgz /Volumes/LaCie/RaquelAlmeida/workflow_di r/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep /mapflow/_T1_prep2/003.mgz /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflo w_dir/l1workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/ _T1_prep3/004.mgz /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1w orkflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4 /005.mgz --inittp 1 --iscale --noit --template rawavg.mgz --iscaleout 001-is cale.txt 002-iscale.txt 003-iscale.txt 004-iscale.txt 005-iscale.txt --subsa mple 200 --lta 001.lta 002.lta 003.lta 004.lta 005.lta Standard output: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--satit: Will estimate SAT iteratively! --average: Using method 1 for template computation. --fixtp: Will map everything to init TP! --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workfl ow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep0/001. mgz as movable/source volume. --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workfl ow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/002. mgz as movable/source volume. --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workfl ow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep2/003. mgz as movable/source volume. --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workfl ow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep3/004. mgz as movable/source volume. --mov: Using /Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1workfl ow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4/005. mgz as movable/source volume. Total: 5 input volumes --inittp: Using TP 1 as target for initialization --iscale: Enableing intensity scaling! --noit: Will output only first template (no iterations)! --template: Using rawavg.mgz as template output volume. --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1wor kflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep0/0 01.mgz'... converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1 workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep 0/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1wor kflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep1/0 02.mgz'... converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1 workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep 1/002.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1wor kflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep2/0 03.mgz'... converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1 workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep 2/003.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1wor kflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep3/0 04.mgz'... converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1 workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep 3/004.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1wor kflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep4/0 05.mgz'... converting source '/Volumes/LaCie/RaquelAlmeida/workflow_dir/workflow_dir/l1 workflow/ReconAll/AutoRecon1/_subject_id_006_S_4150/T1_prep/mapflow/_T1_prep 4/005.mgz' to bspline ... MRItoBSpline degree 3 Standard error: ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 1, 1, 1.2 size(0) = 1, 1, 1 MultiRegistration::loadMovables: voxel size is different /Volumes/LaCie/Raqu elAlmeida/workflow_dir/workflow_dir/l1workflow/ReconAll/AutoRecon1/_subject_ id_006_S_4150/T1_prep/mapflow/_T1_prep1/002.mgz.
Return code: 251 Interface RobustTemplate failed to run. On Tue, May 31, 2016 at 2:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Satra
it will probably reject this by default, which you can get around be reslicing one of them to be like the other. Or "conforming" both of them. cheers Bruce On Tue, 31 May 2016, Satrajit Ghosh wrote: > hi folks, > does recon-all work if the input T1s for the same participant have different > resolutions? (i don't have a dataset to test, but trying to debug some > issues another group has been having). > > cheers, > > satra > > >
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.
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Martin Reuter -
Satrajit Ghosh