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
>
>
>
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