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