multiscalebrainparcellator Error in freesurfer

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Ellen van Maren

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Mar 25, 2021, 10:10:35 AMMar 25
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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

I skip the BIDS validation, because there would be an error otherwise. however, if I check my folder online, it is validated correctly (https://bids-standard.github.io/bids-validator/)
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

Sebastien Tourbier

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Mar 25, 2021, 10:59:25 AMMar 25
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Hi Ellen!

I wonder if you might not have enough memory and this could in turn trigger the recon-all process to get killed.
Using Docker on Mac, it uses 2GB by default but can be adjusted in Preferences -> Resources.

Hope this helps!
Best,
Sebastien

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Ellen van Maren

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Mar 26, 2021, 3:24:59 AMMar 26
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Hi Sebastien

Thank you very much. This solved the problem!

 

Best, Ellen

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