one bug for nipype.workflows.smri.freesurfer.autorecon1.py

[anbai106]

Hello, nipype experts:
I have found a bug(at least i thought, if i am wrong, correct me please)
I know that recently, you implemented the reconall workflow for FreeSurfer, that was great and I am also working on that, from the code here:
https://github.com/nipy/nipype/blob/master/nipype/workflows/smri/freesurfer/autorecon1.py
I have 3 questions:

1. When you check out every image's number of voxel of three dimensions, you constrain that it should be the same, but in the condition(in my case) that every subjects(lets say 10) just have one T1 image, so they may have different FOVs, so I think this is too strict, maybe.
   shape = nib.load(T1_files[0]).shape
for t1 in T1_files[1:]:
if nib.load(t1).shape != shape:
print("ERROR: T1s not the same size. Cannot process {0} and {1} "
"together".format(T1_files[0], t1))
sys.exit(-1)

2. When you deal with the FOV, i think you made a mistaken, I am not doctor of MRI, maybe some one work on MRI will be more reliable,
   here is your code:
   # check if cw256 is set to crop the images if size is larger than 256
if not cw256 and any(dim > 256 for dim in shape):
print("Setting MRI Convert to crop images to 256 FOV")
cw256 = True`` basically, we have a lot of tools to get these info, in nibabel, we can get them: f = nib.load(t1) voxel_size = f.header.get_zooms()# this is the dimension of voxels t1_size = f.header.get_data_shape()# this is the number of voxels for 3 dimensions`

In my case, for example, I have 50 T1, they have the same number of voxels, and the same dimension of voxels, ,and my shape(number of voxels) is (256, 256, 208), and the dimension of voxel is (1.10156, 1.10156, 1.1), so the FOV is not 256, otherwise its 282.000, which is bigger than
256, so we should use -cw256, and indeed, I run it without -cw256, I got some error, i will attach the reconall.log file. But with your code, it will not use this flag, which is a bug...

I would suggest this to be more precise(for every subject):
if voxel_size[0] * t1_size[0] > 256 or voxel_size[1] * t1_size[1] or voxel_size[2] * t1_size[2]:
print("Setting MRI Convert to crop images to 256 FOV")
output_flags.append('-cw256')

3. Also, for the reconall interface, not the workflow http://nipy.org/nipype/interfaces/generated/nipype.interfaces.freesurfer.preprocess.html#reconall, what is the reconall.inputs.args and reconall.inputs.flags, it seems that both of them are used to add additional parameters, but it seems a little redundent if there is no differences between them... If i want to give '-qcache' and '-cw256' to reconall.inputs.args, how should it look like??? like this '-qcache -cw256', or some other format??

Hope to hear from you soon, thanks for your work:)
Cordialement

Obviouly, you dont support .log file, ill just paste it here:

Thu Nov 10 15:30:58 CET 2016
/aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0
/aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/recon-all
-all -i /aramis/dataARAMIS/users/CLINICA/CLINICA_datasets/BIDS/PREVDEMALS_BIDS/GENFI/sub-PREVDEMALS0010001BE/ses-M0/anat/sub-PREVDEMALS0010001BE_ses-M0_T1w.nii.gz -qcache -subjid PREVDEMALS0010001BE_M0 -sd /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional
subjid PREVDEMALS0010001BE_M0
setenv SUBJECTS_DIR /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional
FREESURFER_HOME /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos
Actual FREESURFER_HOME /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Linux DELLEED1 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 63924
maxlocks unlimited
maxsignal 63924
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 16386724 11700512 4686212 80760 274868 7518292
-/+ buffers/cache: 3907352 12479372
Swap: 7999484 112 7999372
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:30:58-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:30:58-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:30:59-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:30:59-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:30:59-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:30:59-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:00-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:00-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:00-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:00-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:00-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:00-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:01-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:01-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:01-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:01-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:01-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:01-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $

ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $

ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:05-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/11/10-14:31:05-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: wen Machine: DELLEED1 Platform: Linux PlatformVersion: 4.2.0-42-generic CompilerName: GCC CompilerVersion: 30400
#######################################
GCADIR /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0

mri_convert /aramis/dataARAMIS/users/CLINICA/CLINICA_datasets/BIDS/PREVDEMALS_BIDS/GENFI/sub-PREVDEMALS0010001BE/ses-M0/anat/sub-PREVDEMALS0010001BE_ses-M0_T1w.nii.gz /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0/mri/orig/001.mgz

mri_convert /aramis/dataARAMIS/users/CLINICA/CLINICA_datasets/BIDS/PREVDEMALS_BIDS/GENFI/sub-PREVDEMALS0010001BE/ses-M0/anat/sub-PREVDEMALS0010001BE_ses-M0_T1w.nii.gz /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/dataARAMIS/users/CLINICA/CLINICA_datasets/BIDS/PREVDEMALS_BIDS/GENFI/sub-PREVDEMALS0010001BE/ses-M0/anat/sub-PREVDEMALS0010001BE_ses-M0_T1w.nii.gz...
TR=2200.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
writing to /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu Nov 10 15:31:13 CET 2016
Found 1 runs
/aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

cp /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0/mri/orig/001.mgz /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0/mri/rawavg.mgz

/aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0

mri_convert /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0/mri/rawavg.mgz /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0/mri/orig.mgz --conform

mri_convert /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0/mri/rawavg.mgz /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0/mri/orig.mgz --conform
WARNING ==================++++++++++++++++++++++++=======================================
The physical sizes are (282.00 mm, 282.00 mm, 228.80 mm), which cannot fit in 256^3 mm^3 volume.
The resulting volume will have 282 slices.
If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).
==================================================++++++++++++++++++++++++===============

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0/mri/rawavg.mgz...
TR=2200.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
Original Data has (1.10156, 1.10156, 1.1) mm size and (256, 256, 208) voxels.
Data is conformed to 1 mm size and 282 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /aramis/home/wen/test/test-reconall-lab/GENFI_CAPS/analysis-series-default/subjects/sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/PREVDEMALS0010001BE_M0/mri/orig.mgz...

---

ERROR! FOV=282.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.

---

Linux DELLEED1 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s PREVDEMALS0010001BE_M0 exited with ERRORS at Thu Nov 10 15:31:26 CET 2016

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Hao

[satra]

@ellisdg - could you take a look at this?

[ellisdg]

@anbai106

1. The workflow interface is designed to work in a similar way to calling the ReconAll interface where the "T1_files" input takes in one of two things:
   a) a single T1 file.
   b) a list of T1 files from the same session. The list ["file1.nii.gz", "file2.nii.gz"] would be equivalent to running the following command:
   recon-all -i file1.nii.gz -i file2.nii.gz
   Note that this is not the same thing as running recon-all multiple times. The function checking the FOVs mandates that they be identical. recon-all likewise requires that all inputs for a single call to recon-all have identical FOVs. You can try running:
   recon-all -i file1.nii.gz -i file2.nii.gz
   where "file1.nii.gz" and file2.nii.gz have different FOVs and you should get a an error.
   Does that answer your question?
2. I think you are right that the checking of FOVs should include the voxel dimensions. Would you mind making a pull request that fixes this issue?
3. Looking at the inputs to ReconAll, only the 'flags' input is mentioned:
   https://github.com/nipy/nipype/blob/master/nipype/interfaces/freesurfer/preprocess.py#L627
   The flags input is what you should use for setting setting additional options on ReconAll. It requires that the input be a string, so the input "-qcache -cw256" would work just fine. If PR ENH: Allows ReconAll.inputs.flags to take in a list of flags #1702 get accepted, it would allow you to input either a string or a list of flags like ['qcache', '-cw256'].

[anbai106]

@ellisdg
Hello, sorry to reply you in delay.
1)Thanks for your reply, I got it, So i guess it is not our case, in our case, we use mapnode to run multiple reconall, so they can come from different session, i totally agree with your explanation with one recon-alll for more than one T1 files in the same session.

2)For the second point, I tried to fork nipype into my githup, and changed it locally, and make a pull request, So if i did it correctly, I guess you can see my change now, It is my first time to use git in this way, if it did not work, please tell me:)

3)I think you forgot update the recon-all nipype interface document, there, you still have the args flag, but in the source of reconallinputspec, you remove it now.

Thanks for your responds.

BTW, the neurostar.org seems does not work in my network, did the server corrupt recently???

Thanks for your good work for nipype:)
Good day