twolevel_dbm.py and 1level

[weimath]

for 'python twolevel_dbm.py 1level t1.csv

-----------------------------------------------------------
twolevel_dbm.py: Running Second-Level Modelbuild

--------------------------------------------------------------------------------------
 Creating template output/secondlevel/secondlevel_template0.nii.gz from a population average image from the inputs.
 /mnt/hgfs/data_chen/data_3DT1/BD_003_tanbowen/coTanBowen12.niiii
--------------------------------------------------------------------------------------
/opt/ANTs/bin//antsMultivariateTemplateConstruction2.sh: line 272:  8928 Segmentation fault      (core dumped) ${ANTSPATH}/AverageImages $dim $output 1 ${images[*]}
Your initial template : output/secondlevel/secondlevel_template0.nii.gz[0 ] was not created.  This indicates trouble!  You may want to check correctness of your input parameters. exiting.

Subprocess Error on command antsMultivariateTemplateConstruction2.sh -d 3 -o output/secondlevel/secondlevel_ -r 1 -l 1 -y 0 -c 0 -a 1 -e 1 -g 0.25 -i 4 -n 0 -m CC[4] -t SyN -u 20:00:00 -v 8gb -q 100x100x70x20 -f 6x4x2x1 -s 3x2x1x0 t1.csv  && echo DONE > output/secondlevel/COMPLETE

[gdevenyi]

In order to provide any support, you will need to provide

1. How you installed ANTs
2. The type of files you are inputting
3. The exact command you're using

[gdevenyi]

This looks wrong:

 /mnt/hgfs/data_chen/data_3DT1/BD_003_tanbowen/coTanBowen12.niiii

I'm pretty sure there's not that many "i" in nii

[weimath]

In order to provide any support, you will need to provide

1. How you installed ANTs
2. The type of files you are inputting
3. The exact command you're using

1, installed ANTs by https://github.com/ANTsX/ANTs/wiki/Compiling-ANTs-on-Linux-and-Mac-OS 2, like this:

/mnt/hgfs/data_chen/data_3DT1/s_002/s002.nii.gz /mnt/hgfs/data_chen/data_3DT1/s_003/s003.nii.gz

in .csv file 3, python twolevel_dbm.py 1level t1.csv
I use this command, and error is :

Segmentation fault (core dumped)

Subprocess Error on command PrintHeader /mnt/hgfs/data_chen/data_3DT1/s_002/s002.nii.gz 1

[weimath]

when run 2level, 2 hours has past, but at 0%.

please, thkans!

[gdevenyi]

This is a crash of the ANTs tools and has nothing to do with twolevel_dbm.py.

Subprocess Error on command PrintHeader /mnt/hgfs/data_chen/data_3DT1/s_002/s002.nii.gz 1

I cannot assist with a broken ANTs install.

when run 2level, 2 hours has past, but at 0%.

1. You did not share "t2.csv" contents.
2. antsMultivariateTemplateConstruction2.sh is computationally expensive and with your current configuration you are running a serial subject-wise run based on the output. The output will update when a subject-wise model build completes.

[weimath]

Thanks for your reply.

[weimath]

Dear Prof, Ps: for "t_dbm.py", I just change name from "twolevel_dbm.py" but “antsMultivariateTemplateConstruction2.sh” could run normally

[weimath]

Dear Prof, Could you share me your a result file about jacobians files, Please, thank you very much.

[gdevenyi]

Something is wrong with your CSV file:

Guesses

1. Non-ascii characters
2. Non Unix line endings
3. Not actually a plain text csv file

Dear Prof, Could you share me your a result file about jacobians files, Please, thank you very much.

I don't understand the question.

[weimath]

2. Non Unix line endings

I got it! thank you very much!

[weimath]

result like this *_absolute_smooth0.8493218002880191.nii.gz

I'm not sure if it's right? It looks weird

[gdevenyi]

The outputs a smoothed jacobians. Please see the documentation here: https://github.com/CoBrALab/twolevel_ants_dbm#outputs