Hi Sebastien,
I'm trying to use your multiscalebrainparcellator, which is really exciting. However, I'm always getting the same error during the freesurfer's part in a participant level analysis.
I'm using the version 1.1.1 via docker, working on a mac.
This is my input:
$docker run -it --rm -v .../my_dataset:/bids_dir -v .../my_dataset/derivatives:/output_dir sebastientourbier/multiscalebrainparcellator:v1.1.1 /bids_dir /output_dir participant --participant_label 06 --skip_bids_validator --brainstem_structures --hippocampal_subfields --thalamic_nuclei --isotropic_resolution 1.0
This is the first part of my log file:
Thu Mar 25 08:42:35 UTC 2021
/output_dir/freesurfer/sub-06
/opt/freesurfer/bin/recon-all
-all -no-isrunning -parallel -openmp 1 -subjid /output_dir/freesurfer/sub-06 -sd /output_dir/freesurfer
subjid sub-06
setenv SUBJECTS_DIR /output_dir/freesurfer
FREESURFER_HOME /opt/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Linux 6f8c0371630f 4.19.121-linuxkit #1 SMP Thu Jan 21 15:36:34 UTC 2021 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 1048576
memorylocked 64 kbytes
maxproc unlimited
maxlocks unlimited
maxsignal 7439
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 2036172 322688 1254880 7656 458604 1521528
Swap: 1048572 610392 438180
This is the last part of my log file after some hours of processing:
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.20 x + 0.0
Left_Putamen too bright - rescaling by 0.916 (from 1.085) to 92.5 (was 100.9)
Left_Pallidum too bright - rescaling by 0.972 (from 1.025) to 99.7 (was 102.5)
Right_Pallidum too bright - rescaling by 1.007 (from 1.000) to 99.7 (was 99.0)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
Killed
Linux 6f8c0371630f 4.19.121-linuxkit #1 SMP Thu Jan 21 15:36:34 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-06 exited with ERRORS at Thu Mar 25 12:11:22 UTC 2021
Do you have an idea what I'm doing wrong?
Thank you a lot for your help.
Best, Ellen