Hi!
We are processing images using
recon-all -all -3T -mprage -qcache -hippocampal-subfields-T1
-brainstem-structures
We've encountered an issue when we're trying to use multiple inputs (acquired
at the same timepoint and with comparable quality). The issue is due to the two
images having slightly different voxel sizes:
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) = 1.05469, 1.05469, 1.2
MultiRegistration::loadMovables: voxel size is different
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002.mgz.
which we can see confirm from the DICOMs in the PixelSpacing tag.
So, we have three questions:
1. In general, should using multiple images jointly for processing yield better
results?
2. If so, what would you suggest for our case with images of two different
protocols? Any flags that could help? Or perform coregistration pre-run?
3. Let's say we have a cohort where all subjects have two T1-images but where
some subjects have two images acquired with slightly different protocols (e.g.
different voxel sizes) and jointly processing can't be done. Do you think it is
better to combine images in as many cases we can (and use only a single image
for the remaining cases) or only use one image per case for all cases? In other
words, we are wondering if it could bias our data set if the subset of that has
been multi-image processed is "better" than those processed with only a single
image.
We're running on FS6 (freesurfer-Linux-centos6_x86_
64-stable-pub-v6.0.0-2beb96c) and I've attached a log file from one of the
failing cases.
Thank you for your help!
Best regards,
--
Gustav Mårtensson | PhD student
Division of Clinical Geriatrics
Department of Neurobiology, Care Sciences and Society
Karolinska Institutet
___________________________________
Karolinska Institutet – a medical university
######## Preparing run #########
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /tmp/adni/freesurfer/6.0.0
Actual FREESURFER_HOME /usr/local/freesurfer-6.0.0
Linux av03 3.19.0-51-generic #57~14.04.1-Ubuntu SMP Fri Feb 19 14:36:55 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux
'/usr/local/freesurfer-6.0.0/bin/recon-all' ->
'/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/scripts/recon-all.local-copy'
-cw256 option is now persistent (remove with -clean-cw256)
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1
mri_convert
/tmp/adni/freesurfer/6.0.0/5fb413df-a275-42f6-9c58-d03179ad2c79/ADNI_002_S_0413_MR_MPRAGE_SENSE2__br_raw_20151203142649292_1_S322083_I569631.dcm
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/001.mgz
mri_convert.bin
/tmp/adni/freesurfer/6.0.0/5fb413df-a275-42f6-9c58-d03179ad2c79/ADNI_002_S_0413_MR_MPRAGE_SENSE2__br_raw_20151203142649292_1_S322083_I569631.dcm
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/tmp/adni/freesurfer/6.0.0/5fb413df-a275-42f6-9c58-d03179ad2c79/ADNI_002_S_0413_MR_MPRAGE_SENSE2__br_raw_20151203142649292_1_S322083_I569631.dcm...
Starting DICOMRead2()
dcmfile =
/tmp/adni/freesurfer/6.0.0/5fb413df-a275-42f6-9c58-d03179ad2c79/ADNI_002_S_0413_MR_MPRAGE_SENSE2__br_raw_20151203142649292_1_S322083_I569631.dcm
dcmdir = /tmp/adni/freesurfer/6.0.0/5fb413df-a275-42f6-9c58-d03179ad2c79
Ref Series No = 401
Found 172 files, checking for dicoms
Found 170 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -1.2 0 0
Vs: -1 0 0
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 170
ndcmfiles = 170
PE Dir = ROW (dicom read)
Loading pixel data
TR=6.76, TE=3.11, TI=0.00, flip angle=9.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (1, -0, 0)
writing to
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/001.mgz...
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1
mri_convert
/tmp/adni/freesurfer/6.0.0/5303bac8-bbb6-42e8-9971-ae92aab53290/ADNI_002_S_0413_MR_MPRAGE_br_raw_20151203142643500_1_S322084_I569632.dcm
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002.mgz
mri_convert.bin
/tmp/adni/freesurfer/6.0.0/5303bac8-bbb6-42e8-9971-ae92aab53290/ADNI_002_S_0413_MR_MPRAGE_br_raw_20151203142643500_1_S322084_I569632.dcm
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/tmp/adni/freesurfer/6.0.0/5303bac8-bbb6-42e8-9971-ae92aab53290/ADNI_002_S_0413_MR_MPRAGE_br_raw_20151203142643500_1_S322084_I569632.dcm...
Starting DICOMRead2()
dcmfile =
/tmp/adni/freesurfer/6.0.0/5303bac8-bbb6-42e8-9971-ae92aab53290/ADNI_002_S_0413_MR_MPRAGE_br_raw_20151203142643500_1_S322084_I569632.dcm
dcmdir = /tmp/adni/freesurfer/6.0.0/5303bac8-bbb6-42e8-9971-ae92aab53290
Ref Series No = 301
Found 172 files, checking for dicoms
Found 170 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -1.2 0 0
Vs: -1 0 0
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 170
ndcmfiles = 170
PE Dir = ROW (dicom read)
Loading pixel data
TR=6.81, TE=3.16, TI=0.00, flip angle=9.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (1, -0, 0)
writing to
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002.mgz...
#--------------------------------------------
#@# MotionCor Wed Aug 16 19:57:59 EDT 2017
Found 2 runs
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/001.mgz
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002.mgz
Checking for (invalid) multi-frame inputs...
Checking for (invalid) multi-frame inputs...
#-----------------------------------------------
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1
mri_robust_template --mov
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/001.mgz
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002.mgz
--average 1 --template
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/rawavg.mgz
--satit --inittp 1 --fixtp --noit --iscale --iscaleout
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/001-iscale.txt
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002-iscale.txt
--subsample 200 --lta
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/001.lta
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002.lta
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
--mov: Using
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/001.mgz
as movable/source volume.
--mov: Using
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002.mgz
as movable/source volume.
Total: 2 input volumes
--average: Using method 1 for template computation.
--template: Using
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/rawavg.mgz
as template output volume.
--satit: Will estimate SAT iteratively!
--inittp: Using TP 1 as target for initialization
--fixtp: Will map everything to init TP!
--noit: Will output only first template (no iterations)!
--iscale: Enableing intensity scaling!
--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
Setting iscale ...
reading source
'/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/001.mgz'...
converting source
'/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/001.mgz'
to bspline ...
MRItoBSpline degree 3
reading source
'/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002.mgz'...
converting source
'/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002.mgz'
to bspline ...
MRItoBSpline degree 3
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) = 1.05469, 1.05469, 1.2
MultiRegistration::loadMovables: voxel size is different
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/mri/orig/002.mgz.
No such file or directory
Linux av03 3.19.0-51-generic #57~14.04.1-Ubuntu SMP Fri Feb 19 14:36:55 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 0a9cfea9-7668-4a2c-927c-378ff5109fe1 exited with ERRORS at Wed Aug
16 19:58:02 EDT 2017
For more details, see the log file
/tmp/adni/freesurfer/6.0.0/0a9cfea9-7668-4a2c-927c-378ff5109fe1/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Something went wrong. Cleaning up output dir:
0a9cfea9-7668-4a2c-927c-378ff5109fe1
_______________________________________________
Freesurfer mailing list
[email protected]
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.
