cat-container issueshttps://jugit.fz-juelich.de/m.wierzba/cat-container/-/issues2021-09-25T21:31:08+02:00https://jugit.fz-juelich.de/m.wierzba/cat-container/-/issues/1Initial tests of the batch files2021-09-25T21:31:08+02:00Małgorzata WierzbaInitial tests of the batch filesI have tested all example uses described in the `cat_standalone.sh` documentation and there are still some issues that need to be addressed. Please see the attached output logs for more details.
I tested all batches in their original ve...I have tested all example uses described in the `cat_standalone.sh` documentation and there are still some issues that need to be addressed. Please see the attached output logs for more details.
I tested all batches in their original version (as included with the official CAT distribution), but for the `cat_standalone_segment.txt` I also tested version that I got from Felix (`cat_standalone_segment_1590928451.log`).
The number appended to the name of each `.log` file is a unix timestamp.
[cat_standalone_segment_1590928451.log](/uploads/83e68be90d70bb49e2b6fcaa1624dd4d/cat_standalone_segment_1590928451.log)
[cat_standalone_smooth_1590928322.log](/uploads/5b3765a923112d854268a8c302a9ba33/cat_standalone_smooth_1590928322.log)
[cat_standalone_resample_1590928260.log](/uploads/9e679269c4a120377e4571bc12607698/cat_standalone_resample_1590928260.log)
[cat_standalone_simple_1590927869.log](/uploads/eaae8deed8b1e1d3b83f79f72d29c2fd/cat_standalone_simple_1590927869.log)
[cat_standalone_segment_1590926462.log](/uploads/be6ec9c9d6ee3e78d504412f629dced5/cat_standalone_segment_1590926462.log)Małgorzata WierzbaMałgorzata Wierzbahttps://jugit.fz-juelich.de/m.wierzba/cat-container/-/issues/7add new versions of CAT to the container dataset2021-09-25T21:29:17+02:00Felix Hoffstaedterf.hoffstaedter@fz-juelich.deadd new versions of CAT to the container datasetLet's add new CAT12 versions to the dataset.
I'll put all containers I have in `/data/project/ukb_vbm/CAT-versions`Let's add new CAT12 versions to the dataset.
I'll put all containers I have in `/data/project/ukb_vbm/CAT-versions`https://jugit.fz-juelich.de/m.wierzba/cat-container/-/issues/4Problem bypassing `main.sh` by calling `exec` instead of `run`2020-06-05T00:29:31+02:00Małgorzata WierzbaProblem bypassing `main.sh` by calling `exec` instead of `run`Full error message:
```
% singularity exec /mnt/build/cat.simg /code/cat_standalone.sh -b /home/mih/cat_standalone_segment.txt /home/mih/sub-01_T1w.nii
...
02-Jun-2020 11:01:04 - Failed 'CAT12: Segmentation'
Error using copyfile
Unknow...Full error message:
```
% singularity exec /mnt/build/cat.simg /code/cat_standalone.sh -b /home/mih/cat_standalone_segment.txt /home/mih/sub-01_T1w.nii
...
02-Jun-2020 11:01:04 - Failed 'CAT12: Segmentation'
Error using copyfile
Unknown shell error 32512
In file "/code/SPM/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_run_newcatch.m" (???), function "cat_run_newcatch" at line 218.
In file "/code/SPM/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_run.m" (???), function "run_job" at line 842.
In file "/code/SPM/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_run.m" (???), function "cat_run" at line 451.
The following modules did not run:
Failed: CAT12: Segmentation
Execution failed: /tmp/cat_24760.m
Bye for now...
Error using MATLABbatch system
Job execution failed. The full log of this run can be found in MATLAB command window, starting with the lines (look for the line showing the exact #job as displayed in this error message)
```The setup for the CAT processing of UKbiobankMałgorzata WierzbaMałgorzata Wierzbahttps://jugit.fz-juelich.de/m.wierzba/cat-container/-/issues/2Try to use non-NeuroDebian base for container2020-06-05T00:27:15+02:00Hanke, Michaelmichael.hanke@gmail.comTry to use non-NeuroDebian base for containerThis pulls in a potentially significant number of unnecessary dependencies. Given that this is all Matlab stuff, we can/should make it self-contained and minimalistic. Possible start with this
```
Bootstrap: docker
From: debian:buster-s...This pulls in a potentially significant number of unnecessary dependencies. Given that this is all Matlab stuff, we can/should make it self-contained and minimalistic. Possible start with this
```
Bootstrap: docker
From: debian:buster-slim
```
Worth trying, but only after things work in general.Małgorzata WierzbaMałgorzata Wierzbahttps://jugit.fz-juelich.de/m.wierzba/cat-container/-/issues/5Using batch files stored in `/batch` as defaults, unless the user specifies o...2020-06-04T23:39:23+02:00Małgorzata WierzbaUsing batch files stored in `/batch` as defaults, unless the user specifies otherwiseRight now the setup is not flexible enough: it requires the user to copy the batch file (likely in a system-wide location and identical for all), and the to-be-processed image (very custom) into the same location.
It should be possible...Right now the setup is not flexible enough: it requires the user to copy the batch file (likely in a system-wide location and identical for all), and the to-be-processed image (very custom) into the same location.
It should be possible for the user to use his own batch file, but it shouldn't be *required*.The setup for the CAT processing of UKbiobankMałgorzata WierzbaMałgorzata Wierzbahttps://jugit.fz-juelich.de/m.wierzba/cat-container/-/issues/3Accepting both .nii and .nii.gz2020-06-03T23:54:22+02:00Małgorzata WierzbaAccepting both .nii and .nii.gzTry `zrun` to do that automatically.Try `zrun` to do that automatically.The setup for the CAT processing of UKbiobankMałgorzata WierzbaMałgorzata Wierzbahttps://jugit.fz-juelich.de/m.wierzba/cat-container/-/issues/6`--containall` should not be required2020-06-03T23:51:43+02:00Małgorzata Wierzba`--containall` should not be requiredThe container should not require any specific bind mounts (that should be user-choice only).The container should not require any specific bind mounts (that should be user-choice only).The setup for the CAT processing of UKbiobankMałgorzata WierzbaMałgorzata Wierzba