Hello, the Cohort.csv required for this causes me trouble when attempting to start xcpEngine with Docker. Someone can help me, and share a example of this .csv. Additionally, this is a report of the problem.
· [D][/design/design.dsn]
INFO: /root/matlab/startup.m does not exist … creating
sed: cannot rename /design/sedyyBjXX: Device or resource busy
· [C][/cohort/cohort.csv]
Error in file(file, “rt”) : cannot open the connection
Calls: read.csv → read.table → file
In addition: Warning messages:
1: In file(file, “rt”) :
‘raw = FALSE’ but ‘/cohort/cohort.csv’ is not a regular file
2: In file(file, “rt”) :
cannot open file ‘/cohort/cohort.csv’: it is a directory
Execution halted
· [O][/xcpOutput]
· [M][Executing serially]
····································································
Date: 202208312314
UUID: 5d54fccf-e0da-49bf-94b6-3eb0cf977fa0
Not a direct answer, but have you tried XCP_D? It is more actively maintained as is designed as a bids app to act directly on fMRIprep outputs. It might suit your needs better. No cohort csv file required.
Hi Steve, thanks for your reply. The problem is that I need the structural pipeline for volumetric mesuares by ROIs and it only is available on xcpEngine.
best regards
Raul
Thanks, Steve, for your help. I am sorry for the deleted answer. I need to focus on a response.
1.For commands, I used
pip install xcpengine-docker
cd in the folder to work
xcpengine-docker -d anat-antsct2.dsn -r bbb -o ccc -c ./www-sin1.csv
2.My .csv is:
id0,img
sub-130S6319,bbb/sub-130S6319/anat/sub-130S6319_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
3.Yes, fMRIPrep finishes without errors
I can understand the error but is a problem to open the .csv, with R
····································································
· [D][/design/design.dsn]
INFO: /root/matlab/startup.m does not exist … creating
sed: cannot rename /design/sedfUsxfd: Device or resource busy
· [C][/cohort/cohort.csv]
Error in file(file, “rt”) : cannot open the connection
Calls: read.csv → read.table → file
In addition: Warning messages:
1: In file(file, “rt”) :
‘raw = FALSE’ but ‘/cohort/cohort.csv’ is not a regular file
2: In file(file, “rt”) :
cannot open file ‘/cohort/cohort.csv’: it is a directory
Execution halted
· [O][/xcpOutput]
· [M][Executing serially]
What folder is this, and what is in here? Can you print the outputs of ls?
Your img item should be defined relative to the reference provided in the -r flag. So unless you have a folder called bbb inside bbb, this will have to be changed.
I have only used XCP via singularity run, so I cannot at this point say whether the error is from something related to the points above or something with the xcpengine-docker code. When testing further, can you try running through docker run?