Designate directory to store intermediate, temporary files?

[geowk]

Hello,

Is there a way to assign a directory other than /tmp/ to store intermediate, temporary files during preprocessing, etc.? Similar to fmriprep's work directory?

Thanks.

-g

[geowk]

Just added in the line:

-B /data/rabies_dir/name_of_temp_file_directory_location:/tmp/

That worked. Now the temp files from the minctoolkit commands are dumped into the designated directory: /data/rabies_dir/name_of_temp_file_directory_location/ directory instead of the default /tmp/ directory.

-g

[Gab-D-G]

Thanks for the input @geowk !

[gdevenyi]

You didn't specify if you're using singularity or docker. There is a standard singularity solution for this, the --workdir option, which is intended exactly for handling temporary dirs in containers.

[Gab-D-G]

Even better.

[geowk]

Hello,

Thank you both for the feedback.

I was using the singularity container, rabies version 0.5.1. Didn't see the --workdir option, just the positional arguments for bids_dir and output_dir.

Will try the --workdir option.

-g

% singularity run rabies.sif preprocess --help
usage: rabies preprocess [-h] [--bids_filter BIDS_FILTER] [--bold_only] [--anat_autobox] [--bold_autobox] [--oblique2card {none,affine,3dWarp}] [--apply_despiking]
                         [--HMC_option {intraSubjectBOLD,0,1,2,3,optim}] [--isotropic_HMC] [--voxelwise_motion] [--apply_slice_mc] [--detect_dummy]
                         [--data_type {int16,int32,float32,float64}] [--anat_inho_cor ANAT_INHO_COR] [--anat_robust_inho_cor ANAT_ROBUST_INHO_COR] [--bold_inho_cor BOLD_INHO_COR]
                         [--bold_robust_inho_cor BOLD_ROBUST_INHO_COR] [--commonspace_reg COMMONSPACE_REG] [--inherit_unbiased_template INHERIT_UNBIASED_TEMPLATE]
                         [--bold2anat_coreg BOLD2ANAT_COREG] [--nativespace_resampling NATIVESPACE_RESAMPLING] [--commonspace_resampling COMMONSPACE_RESAMPLING]
                         [--anatomical_resampling ANATOMICAL_RESAMPLING] [--apply_STC] [--TR TR] [--tpattern {alt-z,alt-z2,seq-z,alt+z,alt+z2,seq+z}] [--stc_axis {X,Y,Z}]
                         [--interp_method {linear,cubic,quintic,heptic,wsinc5,wsinc9,fourier}] [--anat_template ANAT_TEMPLATE] [--brain_mask BRAIN_MASK] [--WM_mask WM_MASK]
                         [--CSF_mask CSF_MASK] [--vascular_mask VASCULAR_MASK] [--labels LABELS]
                         bids_dir output_dir

positional arguments:
  bids_dir              The root folder of the BIDS-formated input data directory.
                        
  output_dir            the output path to drop outputs from major preprocessing steps.
                        

optional arguments:
  -h, --help            show this help message and exit
  --bids_filter BIDS_FILTER
                        Allows to provide additional BIDS specifications (found within the input BIDS directory) 
                        for selected a subset of functional and/or anatomical images. Takes as input a JSON file 
                        containing the set of parameters for functional image under 'func' and under 'anat' for the 
                        anatomical image. See online documentation for an example. 
                        (default: {'func': {'suffix': ['bold', 'cbv']}, 'anat': {'suffix': ['T1w', 'T2w']}})
                        
  --bold_only           Apply preprocessing with only EPI scans. Commonspace registration is executed directly using
                        the corrected EPI 3D reference images. The commonspace registration simultaneously applies
                        distortion correction, this option will produce only commonspace outputs.
                        (default: False)
                        
  --anat_autobox        Crops out extra space around the brain on the structural image using AFNI's 3dAutobox
                        https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dAutobox.html.
                        (default: False)
                        
  --bold_autobox        Crops out extra space around the brain on the EPI image using AFNI's 3dAutobox
                        https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dAutobox.html.
                        (default: False)
                        
  --oblique2card {none,affine,3dWarp}
                        Correct for oblique coordinates on all structural and functional data. 
                           WARNING: these corrections are suboptimal, and may alter the data. Only apply if necessary. 
                        
                        affine: only the affine matrix is changed to cardinal axes. 
                        
                        3dWarp: Applies AFNI's 3dWarp -oblique2card. This involves resampling the 
                        data on a new isotropic grid.
                        (default: none)
                        
  --apply_despiking     Applies AFNI's 3dDespike https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dDespike.html.
                        (default: False)
                        
  --HMC_option {intraSubjectBOLD,0,1,2,3,optim}
                        Select a pre-built option for registration during head motion realignment. 'optim' was customized
                        as documented in https://github.com/CoBrALab/RABIES/discussions/259. Other options were taken from 
                        https://github.com/ANTsX/ANTsR/blob/master/R/ants_motion_estimation.R.
                        (default: optim)
                        
  --isotropic_HMC       Whether to resample the EPI to isotropic resolution (taking the size of the axis with highest 
                        resolution) for the estimation of motion parameters. This should greatly mitigating registration 
                        'noise' which arise from partial volume effects, or poor image resolution (see online post on 
                        this topic https://github.com/CoBrALab/RABIES/discussions/288). This option will increase 
                        computational time, given the higher image resolution. 
                        (default: False)
                        
  --voxelwise_motion    Whether to output estimates of absolute displacement and framewise displacement at each voxel. 
                        This will generate 4D nifti files representing motion timeseries derived from the 6 motion  
                        parameters. This is handled by antsMotionCorrStats. 
                        (default: False)
                        
  --apply_slice_mc      Whether to apply a slice-specific motion correction after initial volumetric HMC. This can 
                        correct for interslice misalignment resulting from within-TR motion. With this option, 
                        motion corrections and the subsequent resampling from registration are applied sequentially
                        since the 2D slice registrations cannot be concatenate with 3D transforms. 
                        (default: False)
                        
  --detect_dummy        Detect and remove initial dummy volumes from the EPI, and generate a reference EPI based on
                        these volumes if detected. Dummy volumes will be removed from the output preprocessed EPI.
                        (default: False)
                        
  --data_type {int16,int32,float32,float64}
                        Specify data format outputs to control for file size.
                        (default: float32)
                        
...

[Gab-D-G]

This would be found with singularity run --workdir, it is part of Singularity, not RABIES.

[geowk]

Thanks. Good to know.

Thanks again to both of you.

-g