Thanks, that worked. Just running into a different issue now. I upgraded to version 20.1.3 of fmriprep and freesurfer 6.0.0. I get the following standar error:
Traceback (most recent call last):
File “/gs/gsfs0/users/yifeman/.conda/envs/my-conda-env/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/gs/gsfs0/users/yifeman/.conda/envs/my-conda-env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 516, in run
result = self._run_interface(execute=True)
File “/gs/gsfs0/users/yifeman/.conda/envs/my-conda-env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_interface
return self._run_command(execute)
File “/gs/gsfs0/users/yifeman/.conda/envs/my-conda-env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 741, in _run_command
result = self._interface.run(cwd=outdir)
File “/gs/gsfs0/users/yifeman/.conda/envs/my-conda-env/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 397, in run
runtime = self._run_interface(runtime)
File “/gs/gsfs0/users/yifeman/.conda/envs/my-conda-env/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 792, in _run_interface
self.raise_exception(runtime)
File “/gs/gsfs0/users/yifeman/.conda/envs/my-conda-env/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 723, in raise_exception
).format(**runtime.dictcopy())
RuntimeError: Command:
recon-all -autorecon1 -noskullstrip -hires -openmp 7 -subjid sub-A006 -sd /home/users/yifeman/BIDS_walkthrough/freesurfer -xopts-use -nomotioncor
Standard output:
INFO: hi-res volumes are conformed to the min voxel size
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 /gs/gsfs0/users/yifeman/BIDS_walkthrough/freesurfer
Actual FREESURFER_HOME /gs/gsfs0/hpc01/apps/freesurfer/6.0.0
-rwx------ 1 yifeman res_com_domain_users 22553 Sep 24 10:59 /gs/gsfs0/users/yifeman/BIDS_walkthrough/freesurfer/sub-A006/scripts/recon-all.log
Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
/gs/gsfs0/hpc01/apps/freesurfer/6.0.0/bin/recon-all' -> /gs/gsfs0/users/yifeman/BIDS_walkthrough/freesurfer/sub-A006/scripts/recon-all.local-copy’
#--------------------------------------------
#@# Talairach Thu Sep 24 12:28:47 EDT 2020
/gs/gsfs0/users/yifeman/BIDS_walkthrough/freesurfer/sub-A006/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/gs/gsfs0/users/yifeman/BIDS_walkthrough/freesurfer/sub-A006/mri
/public/apps/freesurfer/6.0.0/bin/mri_nu_correct.mni
–no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp
Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Thu Sep 24 12:28:47 EDT 2020
Can’t locate MNI/Startup.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /public/apps/freesurfer/6.0.0/mni/bin/nu_correct line 37.
BEGIN failed–compilation aborted at /public/apps/freesurfer/6.0.0/mni/bin/nu_correct line 37.
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.22941
/gs/gsfs0/users/yifeman/BIDS_walkthrough/freesurfer/sub-A006/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.22941/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.22941/nu0.mnc -odt float
Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp
reading from orig.mgz…
TR=9.86, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 4.47035e-09, -4.47035e-09)
j_ras = (-4.47035e-09, -8.9407e-09, -1)
k_ras = (1.11759e-09, 1, -8.9407e-09)
changing data type from uchar to float (noscale = 0)…
writing to ./tmp.mri_nu_correct.mni.22941/nu0.mnc…
Outputting Volume: …
Iteration 1 Thu Sep 24 12:29:05 EDT 2020
nu_correct -clobber ./tmp.mri_nu_correct.mni.22941/nu0.mnc ./tmp.mri_nu_correct.mni.22941/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.22941/0/ -iterations 1000 -distance 50
Can’t locate MNI/Startup.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /public/apps/freesurfer/6.0.0/mni/bin/nu_correct line 37.
BEGIN failed–compilation aborted at /public/apps/freesurfer/6.0.0/mni/bin/nu_correct line 37.
ERROR: nu_correct
Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-A006 exited with ERRORS at Thu Sep 24 12:29:05 EDT 2020
For more details, see the log file /gs/gsfs0/users/yifeman/BIDS_walkthrough/freesurfer/sub-A006/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Standard error:
Can’t locate MNI/Startup.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /public/apps/freesurfer/6.0.0/mni/bin/nu_correct line 37.
BEGIN failed–compilation aborted at /public/apps/freesurfer/6.0.0/mni/bin/nu_correct line 37.
Return code: 1
I found my MNI/Startup.pm script in “/public/apps/freesurfer/6.0.0/mni/lib/perl5/5.8.5/MNI/Startup.pm” so I’m not sure why freesurfer is not finding this as well. This path is saved with the variable $MNI_PERL5LIB. Thanks for your help!