Merge pull request #102 from sebastientourbier/enh/generate_png_motio…

…nindex_v2.0.2-dev ENH: Generate png image for motionindex (Part of #40)
Medical-Image-Analysis-Laboratory · Jul 16, 2021 · fd8c74d · fd8c74d
2 parents 0350d81 + 39ab3fc
commit fd8c74d
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Showing 17 changed files with 1,023 additions and 585 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -117,7 +117,7 @@ jobs:
       - singularity/install-go:
           go-version: '1.13'
       - singularity/debian-install-3:
-          singularity-version: 3.5.1
+          singularity-version: 3.7.3
       - run:
           name: "Building Singularity image from Docker image"
           command: |
@@ -212,7 +212,6 @@ jobs:
             # Get all files in derivatives except the _*.json interface hash generated by nipype (find)
             # remove the full path of the derivatives (sed) / sort the files and write it to a text file
             sudo find /tmp/src/mialsuperresolutiontoolkit/data/derivatives \
-                -path */figures -prune -o \
                 -not -name "_*.json" \
                 -not -name "*.proc*" \
                 -type f -print | \
@@ -259,7 +258,6 @@ jobs:
             # Get all files in derivatives except the _*.json interface hash generated by nipype (find)
             # remove the full path of the derivatives (sed) / sort the files and write it to a text file
             sudo find /tmp/src/mialsuperresolutiontoolkit/data/derivatives \
-                -path */figures -prune -o \
                 -not -name "_*.json" \
                 -not -name "*.proc*" \
                 -type f -print | \
@@ -328,7 +326,7 @@ jobs:
       - singularity/install-go:
           go-version: '1.13'
       - singularity/debian-install-3:
-          singularity-version: 3.5.1
+          singularity-version: 3.7.3
       - run:
           name: "Create the data/test and data/singularity-derivatives folders"
           no_output_timeout: 1h
@@ -363,7 +361,6 @@ jobs:
             # Get all files in derivatives except the _*.json interface hash generated by nipype (find)
             # remove the full path of the derivatives (sed) / sort the files and write it to a text file
             sudo find /tmp/src/mialsuperresolutiontoolkit/data/singularity-derivatives \
-                -path */figures -prune -o \
                 -not -name "_*.json" \
                 -not -name "*.proc*" \
                 -type f -print | \
@@ -402,7 +399,6 @@ jobs:
             # Get all files in derivatives except the _*.json interface hash generated by nipype (find)
             # remove the full path of the derivatives (sed) / sort the files and write it to a text file
             sudo find /tmp/src/mialsuperresolutiontoolkit/data/singularity-derivatives \
-                -path */figures -prune -o \
                 -not -name "_*.json" \
                 -not -name "*.proc*" \
                 -type f -print | \

diff --git a/.circleci/test-01_outputs.txt b/.circleci/test-01_outputs.txt
@@ -404,7 +404,10 @@ nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_report/report.rst
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/result_srtkTVSuperResolution.pklz
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_6V_rad1.json
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_6V_rad1.nii.gz
+nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_6V_rad1.png
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/_inputs.pklz
+nipype/sub-01/rec-1/srr_pipeline/stackOrdering/motion_index_QC.png
+nipype/sub-01/rec-1/srr_pipeline/stackOrdering/motion_index_QC.tsv
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/_node.pklz
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/_report/report.rst
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/result_stackOrdering.pklz
@@ -419,7 +422,8 @@ pymialsrtk-2.0.2-dev/sub-01/anat/_srtkMaskImage013/sub-01_run-4_id-1_desc-prepro
 pymialsrtk-2.0.2-dev/sub-01/anat/_srtkMaskImage014/sub-01_run-5_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/_srtkMaskImage015/sub-01_run-6_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SDI_id-1_T2w.nii.gz
-pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_T2w_desc-brain_mask.nii.gz
+pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_desc-motion_stats.tsv
+pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_mod-T2w_desc-brain_mask.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_T2w.json
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-1_id-1_desc-preprocSR_T2w.nii.gz
@@ -434,9 +438,11 @@ pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-5_id-1_desc-preprocSR_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-5_T2w_desc-brain_mask.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-6_id-1_desc-preprocSR_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-6_T2w_desc-brain_mask.nii.gz
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-1_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-2_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-3_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-4_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-5_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-6_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/figures/sub-01_rec-SR_id-1_desc-motion_stats.png
+pymialsrtk-2.0.2-dev/sub-01/figures/sub-01_rec-SR_id-1_T2w.png
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-1_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-2_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-3_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-4_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-5_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-6_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
diff --git a/.circleci/test-02_outputs.txt b/.circleci/test-02_outputs.txt
@@ -269,7 +269,10 @@ nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_report/report.rst
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/result_srtkTVSuperResolution.pklz
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_3V_rad1.json
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_3V_rad1.nii.gz
+nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_3V_rad1.png
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/_inputs.pklz
+nipype/sub-01/rec-1/srr_pipeline/stackOrdering/motion_index_QC.png
+nipype/sub-01/rec-1/srr_pipeline/stackOrdering/motion_index_QC.tsv
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/_node.pklz
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/_report/report.rst
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/result_stackOrdering.pklz
@@ -288,12 +291,15 @@ pymialsrtk-2.0.2-dev/sub-01/anat/_srtkMaskImage010/sub-01_run-1_id-1_desc-prepro
 pymialsrtk-2.0.2-dev/sub-01/anat/_srtkMaskImage011/sub-01_run-3_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/_srtkMaskImage012/sub-01_run-6_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SDI_id-1_T2w.nii.gz
-pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_T2w_desc-brain_mask.nii.gz
+pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_desc-motion_stats.tsv
+pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_mod-T2w_desc-brain_mask.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_T2w.json
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-1_id-1_desc-preprocSR_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-3_id-1_desc-preprocSR_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-6_id-1_desc-preprocSR_T2w.nii.gz
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-1_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-3_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-6_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/figures/sub-01_rec-SR_id-1_desc-motion_stats.png
+pymialsrtk-2.0.2-dev/sub-01/figures/sub-01_rec-SR_id-1_T2w.png
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-1_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-3_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-6_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
diff --git a/.circleci/test-03_outputs.txt b/.circleci/test-03_outputs.txt
@@ -404,7 +404,10 @@ nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_report/report.rst
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/result_srtkTVSuperResolution.pklz
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_6V_rad1.json
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_6V_rad1.nii.gz
+nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_6V_rad1.png
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/_inputs.pklz
+nipype/sub-01/rec-1/srr_pipeline/stackOrdering/motion_index_QC.png
+nipype/sub-01/rec-1/srr_pipeline/stackOrdering/motion_index_QC.tsv
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/_node.pklz
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/_report/report.rst
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/result_stackOrdering.pklz
@@ -419,7 +422,8 @@ pymialsrtk-2.0.2-dev/sub-01/anat/_srtkMaskImage013/sub-01_run-4_id-1_desc-prepro
 pymialsrtk-2.0.2-dev/sub-01/anat/_srtkMaskImage014/sub-01_run-5_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/_srtkMaskImage015/sub-01_run-6_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SDI_id-1_T2w.nii.gz
-pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_T2w_desc-brain_mask.nii.gz
+pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_desc-motion_stats.tsv
+pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_mod-T2w_desc-brain_mask.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_T2w.json
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-1_id-1_desc-preprocSR_T2w.nii.gz
@@ -434,9 +438,11 @@ pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-5_id-1_desc-preprocSR_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-5_T2w_desc-brain_mask.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-6_id-1_desc-preprocSR_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-6_T2w_desc-brain_mask.nii.gz
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-1_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-2_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-3_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-4_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-5_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-6_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/figures/sub-01_rec-SR_id-1_desc-motion_stats.png
+pymialsrtk-2.0.2-dev/sub-01/figures/sub-01_rec-SR_id-1_T2w.png
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-1_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-2_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-3_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-4_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-5_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-6_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
diff --git a/.circleci/test-04_outputs.txt b/.circleci/test-04_outputs.txt
@@ -269,7 +269,10 @@ nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_report/report.rst
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/result_srtkTVSuperResolution.pklz
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_3V_rad1.json
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_3V_rad1.nii.gz
+nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_3V_rad1.png
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/_inputs.pklz
+nipype/sub-01/rec-1/srr_pipeline/stackOrdering/motion_index_QC.png
+nipype/sub-01/rec-1/srr_pipeline/stackOrdering/motion_index_QC.tsv
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/_node.pklz
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/_report/report.rst
 nipype/sub-01/rec-1/srr_pipeline/stackOrdering/result_stackOrdering.pklz
@@ -288,12 +291,15 @@ pymialsrtk-2.0.2-dev/sub-01/anat/_srtkMaskImage010/sub-01_run-1_id-1_desc-prepro
 pymialsrtk-2.0.2-dev/sub-01/anat/_srtkMaskImage011/sub-01_run-3_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/_srtkMaskImage012/sub-01_run-6_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SDI_id-1_T2w.nii.gz
-pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_T2w_desc-brain_mask.nii.gz
+pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_desc-motion_stats.tsv
+pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_mod-T2w_desc-brain_mask.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_T2w.json
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_rec-SR_id-1_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-1_id-1_desc-preprocSR_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-3_id-1_desc-preprocSR_T2w.nii.gz
 pymialsrtk-2.0.2-dev/sub-01/anat/sub-01_run-6_id-1_desc-preprocSR_T2w.nii.gz
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-1_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-3_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
-pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-6_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/figures/sub-01_rec-SR_id-1_desc-motion_stats.png
+pymialsrtk-2.0.2-dev/sub-01/figures/sub-01_rec-SR_id-1_T2w.png
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-1_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-3_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
+pymialsrtk-2.0.2-dev/sub-01/xfm/sub-01_run-6_id-1_mod-T2w_from-origin_to-SDI_mode-image_xfm.txt
diff --git a/build_bidsapp.sh b/build_bidsapp.sh
@@ -1,4 +1,4 @@
-#! /bin/sh
+#!/bin/sh
 CMP_BUILD_DATE="$(date -u +\"%Y-%m-%dT%H:%M:%SZ\")"
 echo "$CMP_BUILD_DATE"
 

diff --git a/docker/bidsapp/environment.yml b/docker/bidsapp/environment.yml
@@ -15,6 +15,7 @@ dependencies:
 - nilearn=0.7.1
 - pydotplus=2.0.2
 - pandoc=2.11.0.1
+- seaborn=0.11.1
 
 - pip:
     - coverage==5.1
@@ -36,3 +37,4 @@ dependencies:
     - sphinx-argparse==0.2.5
     - nbsphinx==0.7.1
     - recommonmark==0.5.0
+    - matplotlib==3.4
diff --git a/docker/bidsapp/run.py b/docker/bidsapp/run.py
@@ -86,55 +86,49 @@ def check_and_return_valid_nb_of_cores(openmp_nb_of_cores, nipype_nb_of_cores, o
         nipype_nb_of_cores = 1
     else:
         if openmp_nb_of_cores == 0 and nipype_nb_of_cores == 0:
-
             openmp_nb_of_cores, nipype_nb_of_cores = return_default_nb_of_cores(nb_of_cores, openmp_proportion)
 
         elif openmp_nb_of_cores > 0 and nipype_nb_of_cores == 0:
-
-            if openmp_nb_of_cores >= nb_of_cores:
-                if openmp_nb_of_cores > nb_of_cores:
-                    print(f'WARNING: Value of {openmp_nb_of_cores} set by "--openmp_nb_of_cores" is bigger than'
-                          f'the number of cores available ({nb_of_cores}) and will be reset.')
+            if openmp_nb_of_cores > nb_of_cores:
+                print(f'WARNING: Value of {openmp_nb_of_cores} set by "--openmp_nb_of_cores" is bigger than'
+                      f'the number of cores available ({nb_of_cores}) and will be reset.')
                 openmp_nb_of_cores = nb_of_cores
                 nipype_nb_of_cores = 1
             else:
               openmp_nb_of_cores = openmp_nb_of_cores
               nipype_nb_of_cores = nb_of_cores // openmp_nb_of_cores
 
         elif openmp_nb_of_cores == 0 and nipype_nb_of_cores > 0:
-
-            if nipype_nb_of_cores >= nb_of_cores:
-                if nipype_nb_of_cores > nb_of_cores:
-                    print(f'WARNING: Value of {nipype_nb_of_cores} set by "--nipype_nb_of_cores" is bigger than'
-                          f'the number of cores available ({nb_of_cores}) and will be reset.')
+            if nipype_nb_of_cores > nb_of_cores:
+                print(f'WARNING: Value of {nipype_nb_of_cores} set by "--nipype_nb_of_cores" is bigger than'
+                      f'the number of cores available ({nb_of_cores}) and will be reset.')
                 nipype_nb_of_cores = nb_of_cores
                 openmp_nb_of_cores = 1
             else:
               nipype_nb_of_cores = nipype_nb_of_cores
               openmp_nb_of_cores = nb_of_cores // nipype_nb_of_cores
 
         elif openmp_nb_of_cores > 0 and nipype_nb_of_cores > 0:
-
-            if nipype_nb_of_cores >= nb_of_cores:
-                if openmp_nb_of_cores >= nb_of_cores:
-                    print(f'WARNING: Value of {nipype_nb_of_cores} and {openmp_nb_of_cores} set by "--nipype_nb_of_cores" and'
-                          f'"--nipype_nb_of_cores" when multiplied are bigger than the number of cores available ({nb_of_cores})'
+            if nipype_nb_of_cores > nb_of_cores:
+                if openmp_nb_of_cores > nb_of_cores:
+                    print(f'WARNING: Value of {nipype_nb_of_cores} and {openmp_nb_of_cores} set by "--openmp_nb_of_cores" and'
+                          f'"--nipype_nb_of_cores" are both bigger than the number of cores available ({nb_of_cores})'
                           'and will be reset.')
                     openmp_nb_of_cores, nipype_nb_of_cores = return_default_nb_of_cores(nb_of_cores, openmp_proportion)
                 else:
                     if (openmp_nb_of_cores * nipype_nb_of_cores) > nb_of_cores:
                         print(f'WARNING: Multiplication of {nipype_nb_of_cores} and {openmp_nb_of_cores} set by "--nipype_nb_of_cores" and'
-                              f'"--nipype_nb_of_cores" are bigger than the number of cores available ({nb_of_cores}) and will be reset.')
+                              f'"--nipype_nb_of_cores" is bigger than the number of cores available ({nb_of_cores}) and will be reset.')
                         openmp_nb_of_cores, nipype_nb_of_cores = return_default_nb_of_cores(nb_of_cores, openmp_proportion)
             else:
-                if openmp_nb_of_cores >= nb_of_cores:
-                    print(f'WARNING: Value of {openmp_nb_of_cores} set by "--nipype_nb_of_cores" are bigger'
+                if openmp_nb_of_cores > nb_of_cores:
+                    print(f'WARNING: Value of {openmp_nb_of_cores} set by "--openmp_nb_of_cores" is bigger'
                           f'than the number of cores available ({nb_of_cores}) and will be reset.')
                     openmp_nb_of_cores, nipype_nb_of_cores = return_default_nb_of_cores(nb_of_cores, openmp_proportion)
                 else:
                     if (openmp_nb_of_cores * nipype_nb_of_cores) > nb_of_cores:
                         print(f'WARNING: Multiplication of {nipype_nb_of_cores} and {openmp_nb_of_cores} set by "--nipype_nb_of_cores" and'
-                              f'"--nipype_nb_of_cores" are bigger than the number of cores available ({nb_of_cores}) and will be reset.')
+                              f'"--nipype_nb_of_cores" is bigger than the number of cores available ({nb_of_cores}) and will be reset.')
                         openmp_nb_of_cores, nipype_nb_of_cores = return_default_nb_of_cores(nb_of_cores, openmp_proportion)
 
     return openmp_nb_of_cores, nipype_nb_of_cores

diff --git a/docker/jupyter/environment.yml b/docker/jupyter/environment.yml
@@ -43,3 +43,4 @@ dependencies:
     - recommonmark==0.5.0
     - jupyter_contrib_nbextensions #==0.5.1
 #    - pybids==0.9.1
+    - matplotlib==3.4