5. PyHRF commands¶

5.1. fMRI data analysis¶

5.1.1. pyhrf_jde_vem_analysis¶

5.1.1.1. Usage:¶

pyhrf_jde_vem_analysis [options] TR parcels_file onsets_file [bold_data_run1 [bold_data_run2 ...]]

5.1.1.2. Description:¶

Run an fMRI analysis using the JDE-VEM framework. All arguments (even positional ones) are optional and default values are defined in the beginning of the script.

5.1.1.3. Options:¶

positional arguments:
  tr                    Repetition time of the fMRI data
  parcels_file          Nifti integer file which define the parcels
  onsets_file           CSV onsets file
  bold_data_file        4D-Nifti file of BOLD data

optional arguments:
  -h, --help            show this help message and exit
  -c DEF_CONTRASTS_FILE, --def_contrasts_file DEF_CONTRASTS_FILE
                        JSON file defining the contrasts
  -d DT, --dt DT        time resolution of the HRF (if not defined here or in
                        the script, it is automatically computed)
  -l HRF_DURATION, --hrf-duration HRF_DURATION
                        time lenght of the HRF (in seconds, default: 25.0)
  -o OUTPUT_DIR, --output OUTPUT_DIR
                        output directory (created if needed, default:
                        /home/tperret/code/pyhrf)
  --nb-iter-min NB_ITER_MIN
                        minimum number of iterations of the VEM algorithm
                        (default: 5)
  --nb-iter-max NB_ITER_MAX
                        maximum number of iterations of the VEM algorithm
                        (default: 100)
  --beta BETA           (default: 1.0)
  --hrf-hyperprior HRF_HYPERPRIOR
                        (default: 1000)
  --sigma-h SIGMA_H     (default: 0.1)
  --estimate-hrf        (default: True)
  --no-estimate-hrf     explicitly disable HRFs estimation
  --zero-constraint     (default: True)
  --no-zero-constraint  explicitly disable zero constraint (default enabled)
  --drifts-type DRIFTS_TYPE
                        set the drifts type, can be 'poly' or 'cos' (default:
                        poly)
  -v {DEBUG,10,INFO,20,WARNING,30,ERROR,40,CRITICAL,50}, --log-level {DEBUG,10,INFO,20,WARNING,30,ERROR,40,CRITICAL,50}
                        (default: WARNING)
  -p, --parallel        (default: True)
  --no-parallel         explicitly disable parallel computation
  --save-processing     (default: True)
  --no-save-processing

5.2. Parcellation tools¶

5.2.1. pyhrf_parcellate_glm¶

5.2.2. pyhrf_parcellate_spatial¶

5.2.3. pyhrf_parcellation_extract¶

5.2.3.1. Usage:¶

pyhrf_parcellation_extract [options] PARCELLATION_FILE PARCEL_ID1 [PARCEL_ID2 ...]

5.2.3.2. Description:¶

Extract a sub parcellation comprising only PARCEL_ID1, PARCEL_ID2, ... from the input parcellation PARCELLATION_FILE.

5.2.3.3. Options:¶

-h, --help            show this help message and exit
-v VERBOSELEVEL, --verbose=VERBOSELEVEL
                    { 0 :    'no verbose' 1 :    'minimal verbose' 2 :
                    'main steps' 3 :    'main function calls' 4 :    'main
                    variable values' 5 :    'detailled variable values' 6
                    :    'debug (everything)' }
-o FILE, --output=FILE
                    Output parcellation file. Default is
                    <input_file>_<PARCEL_IDS>.(nii|gii)
-c, --contiguous      Make output parcel ids be contiguous

5.2.3.4. Example¶

The input parcellation parcellation.nii looks like:

../_images/pyhrf_parcellation_extract_input.png

pyhrf_parcellation_extract parcellation.nii 36 136 -o parcellation_sub.nii

The output parcellation parcellation_sub.nii will look like:

../_images/pyhrf_parcellation_extract_output.png

5.3. Misc tools¶

5.3.1. pyhrf_list_datafiles¶

5.3.1.1. Usage:¶

pyhrf_list_datafiles [options]

5.3.1.2. Description:¶

This command lists all data files included in the package.

5.3.1.3. Options¶

-h, --help       show this help message and exit
-b, --base-name  Display only basenames

5.3.1.4. Examples:¶

pyhrf_list_datafiles

/home/user/software/pyhrf/python/pyhrf/datafiles/SPM_v12.mat.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/SPM_v5.mat.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/SPM_v8.mat.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/cortex_occipital_hrf_territories_3mm.nii
/home/user/software/pyhrf/python/pyhrf/datafiles/cortex_occipital_hrf_territories_convex_hull.tgz
/home/user/software/pyhrf/python/pyhrf/datafiles/cortex_occipital_right_GWmask_3mm.nii.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/cortex_occipital_white_surf.gii.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/dummySmallBOLD.nii.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/dummySmallMask.nii.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/paradigm_V4.csv
/home/user/software/pyhrf/python/pyhrf/datafiles/paradigm_loc.csv
/home/user/software/pyhrf/python/pyhrf/datafiles/paradigm_loc_a.csv
/home/user/software/pyhrf/python/pyhrf/datafiles/paradigm_loc_av.csv
/home/user/software/pyhrf/python/pyhrf/datafiles/paradigm_loc_av_comma.csv
/home/user/software/pyhrf/python/pyhrf/datafiles/paradigm_loc_av_d.csv
/home/user/software/pyhrf/python/pyhrf/datafiles/paradigm_loc_c_only.csv
/home/user/software/pyhrf/python/pyhrf/datafiles/paradigm_loc_cp_only.csv
/home/user/software/pyhrf/python/pyhrf/datafiles/paradigm_loc_cpcd.csv
/home/user/software/pyhrf/python/pyhrf/datafiles/real_data_surf_tiny_bold.gii
/home/user/software/pyhrf/python/pyhrf/datafiles/real_data_surf_tiny_mesh.gii
/home/user/software/pyhrf/python/pyhrf/datafiles/real_data_surf_tiny_parcellation.gii
/home/user/software/pyhrf/python/pyhrf/datafiles/real_data_vol_4_regions_BOLD.nii.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/real_data_vol_4_regions_anatomy.nii.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/real_data_vol_4_regions_mask.nii.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/simu.pck
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_hrf_3_territories.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_hrf_3_territories_8x8.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_hrf_4_territories.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_activated.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_ghost.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_house_sun.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_icassp13.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_invader.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_pacman.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_small_spots_1.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_small_spots_2.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_stretched_1.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_template.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_tiny_1.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_tiny_2.png
/home/user/software/pyhrf/python/pyhrf/datafiles/simu_labels_tiny_3.png
/home/user/software/pyhrf/python/pyhrf/datafiles/stanford_willard_parcellation_3x3x3mm.nii.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/subj0_anatomy.nii.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/subj0_bold_session0.nii.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/subj0_parcellation.nii.gz
/home/user/software/pyhrf/python/pyhrf/datafiles/subj0_single_roi.nii.gz

pyhrf_list_datafiles -b

SPM_v12.mat.gz
SPM_v5.mat.gz
SPM_v8.mat.gz
cortex_occipital_hrf_territories_3mm.nii
cortex_occipital_hrf_territories_convex_hull.tgz
cortex_occipital_right_GWmask_3mm.nii.gz
cortex_occipital_white_surf.gii.gz
dummySmallBOLD.nii.gz
dummySmallMask.nii.gz
paradigm_V4.csv
paradigm_loc.csv
paradigm_loc_a.csv
paradigm_loc_av.csv
paradigm_loc_av_comma.csv
paradigm_loc_av_d.csv
paradigm_loc_c_only.csv
paradigm_loc_cp_only.csv
paradigm_loc_cpcd.csv
real_data_surf_tiny_bold.gii
real_data_surf_tiny_mesh.gii
real_data_surf_tiny_parcellation.gii
real_data_vol_4_regions_BOLD.nii.gz
real_data_vol_4_regions_anatomy.nii.gz
real_data_vol_4_regions_mask.nii.gz
simu.pck
simu_hrf_3_territories.png
simu_hrf_3_territories_8x8.png
simu_hrf_4_territories.png
simu_labels_activated.png
simu_labels_ghost.png
simu_labels_house_sun.png
simu_labels_icassp13.png
simu_labels_invader.png
simu_labels_pacman.png
simu_labels_small_spots_1.png
simu_labels_small_spots_2.png
simu_labels_stretched_1.png
simu_labels_template.png
simu_labels_tiny_1.png
simu_labels_tiny_2.png
simu_labels_tiny_3.png
stanford_willard_parcellation_3x3x3mm.nii.gz
subj0_anatomy.nii.gz
subj0_bold_session0.nii.gz
subj0_parcellation.nii.gz
subj0_single_roi.nii.gz