Problems with .csv in xcpEngine

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

best regards
Raul

Hi,

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.

Best,
Steven

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

In that case, we would need more info to help you debug:

  1. What is your XCPEngine command?
  2. What does your cohort file look like?
  3. Are you sure your data ran through fMRIPrep without errors?

Best,
Steven

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]

Best regards
Raul

Hi,

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?

Best,
Steven

Hi Steve, thanks for your time. Some of my problems are because I used window
Here, a print of dir in the cmd
Directorio de F:\Others_proyects\test

08/09/2022 10:37 .
08/09/2022 10:37 …
07/09/2022 10:14 aaa
28/08/2022 20:40 3.592 anat-antsct.dsn
01/09/2022 10:25 2.467 anat-antsct2.dsn
08/09/2022 09:45 bbb
08/09/2022 10:45 ccc
08/09/2022 10:52 cohort
07/09/2022 10:12 108 cohort.csv
07/09/2022 10:14 ddd
08/09/2022 10:37 design
07/09/2022 10:14 eee
19/04/2022 10:28 54 license.txt
28/08/2022 20:44 9.769 Nuevo Hoja de cálculo de Microsoft Office Excel.xlsx
01/09/2022 09:48 69 www-sin.csv
08/09/2022 08:47 108 www-sin1.csv
01/09/2022 09:47 108 www.csv
06/09/2022 12:59 108 www1.csv
9 archivos 16.383 bytes
9 dirs 4.622.501.449.728 bytes libres
I am fixed the cohort file to
id0,img
sub-130S6319,sub-130S6319/anat/sub-130S6319_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
Yet, the problem persist. The same is happen when I use docker run.

Windows is tricky. Can you try using a Cygwin terminal instead? https://www.cygwin.com/

What is your docker run command? Is it the same error?

Best,
Steven