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