External Email - Use Caution
Dear Yujing,
Thank you for the quick reply. When I enter umask in my terminal I already get
0002 as output so I think this is not the issue. Is there anything else I could
do?
Kind regards,
Jari Gool | MD-PhD candidate
Department of Anatomy & Neurosciences, Amsterdam UMC Location VUmc
________________________________
Van: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> namens Huang, Yujing
<yhuan...@mgh.harvard.edu>
Verzonden: vrijdag 24 november 2023 13:59
Aan: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Onderwerp: Re: [Freesurfer] Automatic prompt reply for freesurfer
subsegmentations
It looks like “imageDump.mgz” is copied to the directory during segmentation.
Can you check your ‘umask’?
>umask
I think “mode 0444 (r--r--r--)” is caused by the umask setting to 0222. Try to
change your umask to 0002 in .bashrc or .profile – add a line ‘umask 0002’.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Gool, J.K. (Jari)
Sent: Thursday, November 23, 2023 6:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Automatic prompt reply for freesurfer subsegmentations
External Email - Use Caution
Dear,
I would like to run the different available Freesurfer subsegmentations
(brainstem, amygdala/hippocampus, thalamus, hypothalamus and ScLimbic) on a
large sample of 150 subjects (code below). I want to run multiple subjects in
parallel using the sbatch command on the linux server I am working on. Because
of previous recon-all processing in 7.3.2 I would like to also perform the
subsegmentations in this version and ScLimbic in 7.4.0. The problem is that the
“segmentBS.sh”, “segmentThalamicNuclei.sh” and “segmentHA_T1.sh” halfway
prompts for user input: “mv: replace 'imageDump.mgz', overriding mode 0444
(r--r--r--)?”. The imageDump.mgz file is made within this same subsegmentation
script and I have no problem with replacing this file. When I run the code
interactively I just reply with “y” and the subsegmentation finishes without
any errors. When I want to submit my script as a job and in batch, I am unable
to provide this user input and the subsegmentation gets stuck at the prompt. I
have tried to change my code of the subsegmentations with yes and echo (such as
“yes | segmentBS.sh ${subj}_ses-EEGfMRI1
/home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/” or
“echo “y” | segmentBS.sh ${subj}_ses-EEGfMRI1
/home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/”) but
the script still gets stuck on the prompt. Do you know how I can fix this? We
would also like to perform these subsegmentations in a large consortium and
hope to be able to automate this problem so sites will not have to manually
provide the user input every time.
Thank you in advance for your help, it is much appreciated.
Kind regards,
Jari Gool | MD-PhD candidate
Department of Anatomy & Neurosciences, Amsterdam UMC Location VUmc
#!/bin/bash
#SBATCH --job-name=subsegmentations_ams
#SBATCH --mem=16G
#SBATCH --partition=luna-cpu-long
#SBATCH --qos=anw-cpu
#SBATCH --cpus-per-task=1
#SBATCH --time=03-00:00:00
#SBATCH --nice=2000
#SBATCH --array=1-37%3
#SBATCH --output=slurm-%A.%a.out
module load FreeSurfer/7.3.2-centos8_x86_64
#make list of subjects
SUBJECTS_DIR=/scratch/anw/jkgool/freesurfer_rick/input/
cd ${SUBJECTS_DIR}
ls -d sub-* > subjects.txt
subj=$(sed "${SLURM_ARRAY_TASK_ID}q;d" subjects.txt)
#1 hypothalamus (doc:
https://secure-web.cisco.com/1zzIXIXnWRnq-g2GJqUYLNUzu2SHP68ScMqA9PP1C5yj-KWHM-Zu25MaWbwe2pwIh1f-LIc3nZSdfU8of90lzMGdbaREY57MQOEFQ90jJHhEYXNQM4CYr5Kz2Cy-numPynGj1I-JD8Yz7QvM_2_L1hyHoqeH90ErRTn3acoA-Bwhrj40jBpUUoywsljj6vNSh0c7D81AdTbQxLu23yr3mf9piRNrFC6mB5f69_5PpFmO9Ux0z0lDB49RBgvcwqNzvqCIKT6_VPAEtjfCaxtgjeYC9s6MMn9DIEizyG-e0sy9zjoZanT9H8vRgW4rZTCv2It-ovA6phXlSrPz8l2xmNw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHypothalamicSubunits)
echo "running hypothalamus segmentation..."
mri_segment_hypothalamic_subunits --s ${subj}_ses-EEGfMRI1 --sd
/home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/
--write_posteriors
#2 brainstem (doc:
https://secure-web.cisco.com/1g5cOkTomD7Hpix0PgD1Lhl9ArOqLsH9E9os69e_J2cfYRl7ViXMqtJVmJkUCOh3451chs4dlYaCmveWeByX4tRsQYIxnaVfVyvFJISkNc-FULkUl7O1QH5SS0RWbq0eR6tqTOsQqN3hchveU3n-kkzTpGsSa4WAvQ5qhRwgK7TLQSz8YTDLR2Tais1NGwgLZWsAcE8mmq1_xf1JlJwdxmalm-nO-5rMGNPfM1mW0gy7AYN5t46p4Lfx9SkqT0Xi8ysdGNa2AROTSlkAcrtXf0EmM33GiLSUABkMm_KKgPWWx4zdp_qxmsKzidUEata48bEH5F0iNhtCbwhL0Q2gqUg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBrainstemSubstructures)
echo "running brainstem segmentation..."
segmentBS.sh ${subj}_ses-EEGfMRI1
/home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/
#3 thalamus (doc:
https://secure-web.cisco.com/1cUdN_ti2E_dzVkW7HDmxM2Wiau14Kv4bkqOiHnUKVx4G1PDiAPZT0M6hzpOu3iGQkvIwtSUqNJbVd7wGtn2JcvJZcSe968Rupl29TMojNShMnWWHeYpY1-4XMh_OGqjfKvq_Uc7r-zBYbtOT75Mf3l0NHoWw8dszc67TVs_uPdFEoKfjZ7ka8DD-i46DruTBREdI32keYq8C1kfvxMuMqEILqY18qJe03UsARu2AqZ2tsHH30KTVI1Eui7YlzK3wFGgCy3FFgNj7DnI8a8XmXCYqVg2DnsGe2T-ygqHMVGKBekrcjVA1XgY56Awwq6bBTS024G1YXRfVKXUrgfh9ng/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FThalamicNuclei)
echo "running thalamic nuclei segmentation..."
segmentThalamicNuclei.sh ${subj}_ses-EEGfMRI1
/home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/
#4 hippocampal subfields and amygdala (doc:
https://secure-web.cisco.com/1BpbGiTWLV_LBKMEhY-sObmXZ5eLhacZvE1VCSXyPH-8Zcqmq3E3uw1XoK5-g3gxm_EthTUnExmTjhd9UCoVFcD6RgOfXG0C9-J1y4HB226qL3FcRYv-xaSPiEFNnzJuiqcZ_CCG6mn7GFl5OkbsPFJadmkku82UQa-qmAgcqTxL3o4sckqdFDTCFbEbVMghoPkvKbImzcjVvC-ThmvwOTKW8ytD82Egg9eTnUH5mth55tvz1rgQEp7B1D3EQQiipnoDPzyOC-poZ2XzQl9ZXjqukdVCjNYX8sh0FJ1FBKHA9q3R4SQl7K_uBEuGaLxIiMLd3Lh_zJ_RFP0BaXRVdJQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala)
echo "running hippocampal subfields and amygdala segmentation..."
segmentHA_T1.sh ${subj}_ses-EEGfMRI1
/home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/
module load FreeSurfer/7.4.0-centos8_x86_64
#5 subcortical limbic structures (doc:
https://secure-web.cisco.com/1W3wBjp8FNGbGIvtzSOqAWuYqXOYZq0SiGqjzIv97TQLbG7oJ780jcEADH_ntjnPonxD58FurFvTgdC67yPwqASL5RQf14buQUb9uETTmXPaJ8sd-V86LNr86823SFBply718B4vaCmlGs6nKUSrVMR2qgs3qVo66Q8th1oEVayC049uFS7PL2oIq2UWpifubMFREMYEXp_UvbLSOWSZb_cN782uQle7M2sBkmTIF9vDgjooLbnGF-Ob0hH_oVrVqq5RJbMF79dXeLIKRBlpz27nXYKVB0d_yIv_me1Y8vW9cBNfGO0c9aB6LyOSMjYcUxoAjmZZBaGtqwcgMWEK_vg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FScLimbic)
echo "running limbic structures segmentation..."
mri_sclimbic_seg --i
/home/anw/jkgool/my-scratch/freesurfer_rick/input/${subj}/ses-EEGfMRI1/anat/
--o
/home/anw/jkgool/my-scratch/freesurfer_rick/output/test_nov23/freesurfer/${subj}_ses-EEGfMRI1/output_sclim
--write_volumes --write_qa_stats
______________________________________________________
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