Quick test¶
Download datasets¶
$ cd /path/to/data
$ curl https://amubox.univ-amu.fr/public.php/dav/files/KJ2L5j6L6orPXxM --output macapype_CI.zip
$ unzip -o macapype_CI.zip -d macapype_CI
Testing depending on the installation¶
Testing from Singularity image¶
$ singularity run -B /path/to/data:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI/marmo-marmobrain -out /data/macapype_CI/marmo-marmobrain/results -soft ANTS_test -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2
$ singularity run -B /path/to/data:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI/marmo-marmobrain -out /data/macapype_CI/marmo-marmobrain/results -soft ANTS_prep -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2
$ singularity run -B /path/to/data:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI/marmo-marmobrain -out /data/macapype_CI/marmo-marmobrain/results -soft ANTS_noseg -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2
$ singularity run -B /path/to/data:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI/marmo-marmobrain -out /data/macapype_CI/marmo-marmobrain/results -soft ANTS -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2
The 4 commands earlier corresponds to brain segmentation performed on an example of marmoset (Percy) . The 4 steps corresponds to incremental processings, and can performed in the given order. It is possible to test directly the last command (with -soft ANTS), but the caching system of nipype should work and the previous steps will not be performed again.
The first one (-soft ANTS_test) is to test the workflow graph. If it works, the representation graph of the pipeline is available as:
/path/to/data/macapype_CI/marmo-marmobrain/results/macapype_crop_aladin_ants_t1/graph.png
The second one (-soft ANTS_prep) is to run data preparation pipeline (corresponding to preprocessing). If it works, you should be able to see the data after automated croping and alignement in the template space:
/path/to/data/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/sub-Percy/ses-01/anat/sub-Percy_ses-01_space-stereo_T1w.nii.gz
The third one (-soft ANTS_noseg) will perform brain extraction and stop afterward. This is normally the longest step (ranging from 45min to a few hours depending on the image resolution. If it works, you should be able to see the brain mask as :
/path/to/data/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/sub-Percy/ses-01/anat/sub-Percy_ses-01_space-stereo_desc-brain_mask.nii.gz
The fourth and last one (-soft ANTS) will perform brain segmentation and mesh. If it works, you should be able to see the brain segmented mask and brain mesh as :
/path/to/data/macapype_CI/marmo-marmobrain/results/derivatives/macapype_crop_aladin_ants_t1/sub-Percy/ses-01/anat/sub-Percy_ses-01_space-stereo_desc-brain_desc-desg_mask.nii.gz
Testing from docker image¶
For testing the docker installation, the beginning of the commands should be replaced by docker run -v /path/to/data:/data macatools/macapype:v0.3.1, e.g.
$ docker run -v /path/to/data:/data macatools/macapype:v0.5 segment_pnh -data /data/macapype_CI/marmo-marmobrain -out /data/macapype_CI/marmo-marmobrain/results -soft ANTS -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2
Testing from python package install¶
From pip install¶
$ segment_pnh -data /path/to/data/macapype_CI/marmo-marmobrain -out /path/to/data/macapype_CI/marmo-marmobrain/results -soft ANTS -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2
From github install¶
$ python workflows/segment_pnh.py -data /path/to/data/macapype_CI/marmo-marmobrain -out /path/to/data/macapype_CI/marmo-marmobrain/results -soft ANTS -species marmo -sub Percy -ses 01 -deriv -pad -dt T1 T2
Note the /path/to/data instead of /data (as in the container install) in the arguments
Testing the macaque and baboon datasets¶
Two other dataset, corresponding to one macaque and one baboon, are available in the test dataset. Please not that due to higher image resolution, the preprocessing will take a longer time.
$ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI/baboon-cerimed-adrien -out /data/macapype_CI/baboon-cerimed-adrien/results -soft ANTS -species baboon -sub Fidji -ses 01 -deriv -pad -dt T1
$ singularity run -B /path/to/data/:/data /path/to/containers/macapype_v0.5.sif segment_pnh -data /data/macapype_CI/baboon-cerimed-adrien -out /data/macapype_CI/baboon-cerimed-adrien/results -soft ANTS -species baboon -sub Fidji -ses 01 -deriv -pad -dt T1
Testing different pipelines and options¶
It is possible to run the pipeline with only T1w available with -dt T1 (instead of -dt T1 T2 previously). Please see Commands for further information on the parameters available for command line