Hi, FS experts:
I run the reconAlll command with two nii file, and I got some error here, can
you help me to check it out, cuz I think I use the command correctly...
here is the info for the error:
I think the problem is for the mri_convert command, I checked thr orig folder,
there is no T1.mgz file! can you tell me why?
crash-20160624-204118-guest-_recon_all0.pklz
File: crash-20160624-204118-guest-_recon_all0.pklz
Node: _recon_all0
Working directory:
/tmp/tmpzZyfB0/reconall_workflow/recon_all/mapflow/_recon_all0
Node inputs:
T1_files =
['/home/guest/HAO/Clinica/clinica/examples/data/Recon-all/example2/struct.nii']
T2_file = <undefined>
args = -qcache
directive = all
environ = {}
flags = <undefined>
hemi = <undefined>
ignore_exception = False
openmp = <undefined>
subject_id = example2
subjects_dir = /tmp/tmpzZyfB0
terminal_output = stream
Traceback:
Traceback (most recent call last):
File
"/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py",
line 18, in run_node
result['result'] = node.run(updatehash=updatehash)
File
"/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/pipeline/engine.py",
line 1428, in run
self._run_interface()
File
"/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/pipeline/engine.py",
line 1538, in _run_interface
self._result = self._run_command(execute)
File
"/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/pipeline/engine.py",
line 1664, in _run_command
result = self._interface.run()
File
"/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/interfaces/base.py",
line 1033, in run
runtime = self._run_wrapper(runtime)
File
"/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/interfaces/base.py",
line 1457, in _run_wrapper
runtime = self._run_interface(runtime)
File
"/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/interfaces/base.py",
line 1491, in _run_interface
self.raise_exception(runtime)
File
"/home/guest/Downloads/ENTER/lib/python2.7/site-packages/nipype/interfaces/base.py",
line 1415, in raise_exception
raise RuntimeError(message)
RuntimeError: Command:
recon-all -all -i
/home/guest/HAO/Clinica/clinica/examples/data/Recon-all/example2/struct.nii
-qcache -subjid example2 -sd /tmp/tmpzZyfB0
Standard output:
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /tmp/tmpzZyfB0
Actual FREESURFER_HOME /usr/local/freesurfer
Linux guest-Latitude-E6220 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22
11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
/tmp/tmpzZyfB0/example2
mri_convert
/home/guest/HAO/Clinica/clinica/examples/data/Recon-all/example2/struct.nii
/tmp/tmpzZyfB0/example2/mri/orig/001.mgz
Linux guest-Latitude-E6220 3.19.0-49-generic #55~14.04.1-Ubuntu SMP Fri Jan 22
11:24:31 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s example2 exited with ERRORS at vendredi 24 juin 2016, 20:40:29
(UTC+0200)
For more details, see the log file /tmp/tmpzZyfB0/example2/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Standard error:
Return code: 1
Interface ReconAll failed to run.
Thanks in advance
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