search

edickie / ciftify

The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets
https://edickie.github.io/ciftify/
MIT License
111 stars 156 forks source link

config load issue - yaml.load is deprecated #120

Open oricon opened 4 years ago

oricon commented 4 years ago

I'm having a problem with msm in ciftify_recon_all that I think has to do with an issue with loading the msm configuration file. I have double-checked that the msm binary is at the front of my path but I'm still getting the 'running version of MSM does not match config'. Please let me know if that yaml.load error isn't the issue.

[joseph.orr@c0124 bin$ ciftify_recon_all --ciftify-work-dir /fdata/scratch/joseph.orr/t3/cifti --fs-subjects-dir /fdata/scratch/joseph.orr/t3/preproc/freesurfer --fs-license ./license.txt --no-symlinks sub-1037 /apps/psyc/anaconda3/lib/python3.7/site-packages/ciftify/utils.py:274: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. config = yaml.load(yaml_stream) Running version of MSM does not match config /apps/psyc/anaconda3/lib/python3.7/site-packages/ciftify/data/hcp_config/MSMSulcStrainFinalconf [joseph.orr@c0124 bin$ which msm /apps/psyc/msm_hocr/msm

edickie commented 4 years ago

The yaml issue is just a warning and shouldn't be an issue.

What version of msm do you have installed?

oricon commented 4 years ago

I have the v.1 release of msm_centos (renamed to msm) from https://github.com/ecr05/MSM_HOCR/releases that has worked for me with the HCP Pipeline Scripts. I tried to run ciftify_recon_all using 'singularity exec' but got an error that ciftify_recon_all couldn't be found.

-- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A&M Institute for Neuroscience Texas A&M University College Station, TX

On Fri, Jul 26, 2019 at 3:22 PM Erin W Dickie notifications@github.com wrote:

The yaml issue is just a warning and shouldn't be an issue.

What version of msm do you have installed?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_edickie_ciftify_issues_120-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DACBNSLYGGWPEISSK5WJVRBTQBNMJRA5CNFSM4IHGVJQ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD25T3XA-23issuecomment-2D515587548&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=r5Mpc3mGXfHYvMphItda23EYv_4RBAqWoRqiqZo1OLo&m=qZvUg5xdsTqeJR7DMV64jlGJNdimGPZVp7gUNlTvuRU&s=H0C-nlEfpCH7sOsgJi_d6okiLDxAmNT3YfVGdxzclq8&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ACBNSL4OGVS6Q3HCSTLC6T3QBNMJRANCNFSM4IHGVJQQ&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=r5Mpc3mGXfHYvMphItda23EYv_4RBAqWoRqiqZo1OLo&m=qZvUg5xdsTqeJR7DMV64jlGJNdimGPZVp7gUNlTvuRU&s=as0d3xxk_5MZ1qXxcaxteEXb6kejF11vezgvc5VW-lw&e= .

edickie commented 4 years ago

That is odd. Can you type the full singularity exec command?

oricon commented 4 years ago

Sure - I'm running the following: [joseph.orr@login01 1.3.2-2.3.2$ singularity exec --cleanenv /apps/psyc/containers/fmriprep_ciftify/1.3.2-2.3.2 ciftify_recon_all --ciftify-work-dir /fdata/scratch/joseph.orr/t3/cifti --fs-subjects-dir /fdata/scratch/joseph.orr/t3/preproc/freesurfer --fs-license $PWD/license.txt --no-symlinks sub-1037 WARNING: Non existent 'bind path' source: '/cms' /.singularity.d/actions/exec: 9: exec: ciftify_recon_all: not found

The container was created with singularity build with the latest dockerhub tag. My cluster requires that container images are unsquashed. The /cms bind path issue is odd since its definitely in the folder so should be bound, and it works like that with fmriprep proper. I ran all my data through fmriprep 1.4.0 so I just want to run recon-all and ciftify_fmri separately. It looks like the scripts are in the image because if I run a find they seem to be there: [joseph.orr@login01 1.3.2-2.3.2$ find . -iname ciftify* ./home/code/ciftify ./home/code/ciftify/ciftify ./home/code/ciftify/ciftify/bin/ciftify_seed_corr ./home/code/ciftify/ciftify/bin/ciftify_peaktable.py ./home/code/ciftify/ciftify/bin/ciftify_groupmask ./home/code/ciftify/ciftify/bin/ciftify_PINT_vertices.py ./home/code/ciftify/ciftify/bin/ciftify_peaktable ./home/code/ciftify/ciftify/bin/ciftify_postPINT2_sub2sub ./home/code/ciftify/ciftify/bin/ciftify_postPINT1_concat ./home/code/ciftify/ciftify/bin/ciftify_subject_fmri.py ./home/code/ciftify/ciftify/bin/ciftify_clean_img ./home/code/ciftify/ciftify/bin/ciftify_groupmask.py ./home/code/ciftify/ciftify/bin/ciftify_subject_fmri ./home/code/ciftify/ciftify/bin/ciftify_atlas_report.py ./home/code/ciftify/ciftify/bin/ciftify_surface_rois.py ./home/code/ciftify/ciftify/bin/ciftify_statclust_report.py ./home/code/ciftify/ciftify/bin/ciftify_meants ./home/code/ciftify/ciftify/bin/ciftify_PINT_vertices ./home/code/ciftify/ciftify/bin/ciftify_statclust_report ./home/code/ciftify/ciftify/bin/ciftify_surface_rois ./home/code/ciftify/ciftify/bin/ciftify_postPINT1_concat.py ./home/code/ciftify/ciftify/bin/ciftify_postPINT2_sub2sub.py ./home/code/ciftify/ciftify/bin/ciftify_clean_img.py ./home/code/ciftify/ciftify/bin/ciftify_vol_result.py ./home/code/ciftify/ciftify/bin/ciftify_atlas_report ./home/code/ciftify/ciftify/bin/ciftify_vol_result ./home/code/ciftify/ciftify/bin/ciftify_falff ./home/code/ciftify/ciftify/bin/ciftify_meants.py ./home/code/ciftify/ciftify/bin/ciftify_falff.py ./home/code/ciftify/ciftify/bin/ciftify_recon_all.py ./home/code/ciftify/ciftify/bin/ciftify_seed_corr.py ./home/code/ciftify/ciftify/bin/ciftify_recon_all

I'll try using docker2singularity instead of singularity build to see if that fixes things.

Joseph M. Orr, Ph.D., FPsyS Assistant Professor Department of Psychological and Brain Sciences Texas A&M Institute for Neuroscience Texas A&M University College Station, TX

On Tue, Jul 30, 2019 at 3:07 PM Erin W Dickie notifications@github.com wrote:

That is odd. Can you type the full singularity exec command?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_edickie_ciftify_issues_120-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DACBNSL7VBJNLJIFPQZ6G2GTQCCNO3A5CNFSM4IHGVJQ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3FFC2Y-23issuecomment-2D516575595&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=r5Mpc3mGXfHYvMphItda23EYv_4RBAqWoRqiqZo1OLo&m=a0RwZPs8q1mHaMr-Ju8I1_aa59pl6B3WhRjq5yNBYC0&s=7QKhnNdfJJn9B5LgTUL8Cssg1gonL2I1W07o6HNjzas&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ACBNSL43FKBN677IDARAQJ3QCCNO3ANCNFSM4IHGVJQQ&d=DwMCaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=r5Mpc3mGXfHYvMphItda23EYv_4RBAqWoRqiqZo1OLo&m=a0RwZPs8q1mHaMr-Ju8I1_aa59pl6B3WhRjq5yNBYC0&s=moG7eZeXVNrD3geewfpE6tnyPVtOpuiWI9b2xNpLKUU&e= .