Merge remote-tracking branch 'gin/master'

.gitignore

@@ -3,3 +3,5 @@
 .RData
 .Ruserdata
 code/*/*.html
+logs
+decoding/sub-*/logs

.gitmodules

@@ -10,3 +10,7 @@
 	path = glm
 	url = https://github.com/lnnrtwttkhn/highspeed-glm.git
 	datalad-id = b7fed17e-2758-11eb-aebd-8c859041f10d
+[submodule "bids"]
+	path = bids
+	url = https://github.com/lnnrtwttkhn/highspeed-bids.git
+	datalad-id = 94ae2510-f811-11ea-a3da-00e04c10078d

bids

@@ -0,0 +1 @@
+Subproject commit fe49606245f8a3068195040ba7c7fb9734d3ca69

code/decoding/highspeed-decoding-cluster.sh

@@ -63,28 +63,28 @@ SUB_COUNT=0
 for i in {1..40}; do
 	# turn the subject id into a zero-padded number:
 	SUB=$(printf "%02d\n" ${i})
+	# start slurm job file:
+	echo "#!/bin/bash" > job
 	# name of the job
-	echo "#PBS -N decoding_sub-${SUB}" >> job
+	echo "#SBATCH --job-name highspeed-decoding-sub-${SUB}" >> job
 	# set the expected maximum running time for the job:
-	echo "#PBS -l walltime=12:00:00" >> job
+	echo "#SBATCH --time 12:00:00" >> job
 	# determine how much RAM your operation needs:
-	echo "#PBS -l mem=${MEM}" >> job
+	echo "#SBATCH --mem ${MEM}" >> job
 	# request multiple cpus:
-	echo "#PBS -l nodes=1:ppn=${N_CPUS}" >> job
+	echo "#SBATCH --cpus-per-task ${N_CPUS}" >> job
 	# write (output) log to log folder:
-	echo "#PBS -o ${PATH_LOG}" >> job
-	# write (error) log to log folder:
-	echo "#PBS -e ${PATH_LOG}" >> job
+	echo "#SBATCH --output ${PATH_LOG}/highspeed-decoding-sub-${SUB}-%j.out" >> job
 	# email notification on abort/end, use 'n' for no notification:
-	echo "#PBS -m n" >> job
+	echo "#SBATCH --mail-type NONE" >> job
 	# start in the current directory:
-	echo "#PBS -d ${PATH_CODE}" >> job
+	echo "#SBATCH --workdir ." >> job
 	# activate virtual environment on cluster:
 	echo "source /etc/bash_completion.d/virtualenvwrapper" >> job
-	echo "workon decoding" >> job
+	echo "workon highspeed-decoding" >> job
 	# define the main command:
 	echo "python3 ${PATH_SCRIPT} ${SUB}" >> job
 	# submit job to cluster queue and remove it to avoid confusion:
-	qsub job
+	sbatch job
 	rm -f job
 done

code/decoding/highspeed_decoding.py

@@ -76,7 +76,7 @@ if 'darwin' in sys.platform:
 elif 'linux' in sys.platform:
     # path to the project root:
     project_name = 'highspeed-decoding'
-    path_root = os.getcwd().split(project_name)[0] + project_name
+    path_root = os.getenv('PWD').split(project_name)[0] + project_name
     # define the path to the cluster:
     path_tardis = path_root
     # define the path to the server:
@@ -220,42 +220,42 @@ path_mask_vis_task = opj(path_masks, 'mask_visual', sub, '*', '*task-highspeed*.
 path_mask_vis_task = sorted(glob.glob(path_mask_vis_task), key=lambda f: os.path.basename(f))
 logging.info('found %d visual mask task files' % len(path_mask_vis_task))
 logging.info('paths to visual mask task files:\n%s' % pformat(path_mask_vis_task))
-dl.get(glob.glob(path_mask_vis_task))
+dl.get(path_mask_vis_task)
 
 # load the hippocampus mask task files:
 path_mask_hpc_task = opj(path_masks, 'mask_hippocampus', sub, '*', '*task-highspeed*.nii.gz')
 path_mask_hpc_task = sorted(glob.glob(path_mask_hpc_task), key=lambda f: os.path.basename(f))
 logging.info('found %d hpc mask files' % len(path_mask_hpc_task))
 logging.info('paths to hpc mask task files:\n%s' % pformat(path_mask_hpc_task))
-dl.get(glob.glob(path_mask_hpc_task))
+dl.get(path_mask_hpc_task)
 
 # load the whole brain mask files:
 path_mask_whole_task = opj(path_fmriprep, '*', 'func', '*task-highspeed*T1w*brain_mask.nii.gz')
 path_mask_whole_task = sorted(glob.glob(path_mask_whole_task), key=lambda f: os.path.basename(f))
 logging.info('found %d whole-brain masks' % len(path_mask_whole_task))
 logging.info('paths to whole-brain mask files:\n%s' % pformat(path_mask_whole_task))
-dl.get(glob.glob(path_mask_whole_task))
+dl.get(path_mask_whole_task)
 
 # load the functional mri task files:
 path_func_task = opj(path_level1, 'smooth', sub, '*', '*task-highspeed*nii.gz')
 path_func_task = sorted(glob.glob(path_func_task), key=lambda f: os.path.basename(f))
 logging.info('found %d functional mri task files' % len(path_func_task))
 logging.info('paths to functional mri task files:\n%s' % pformat(path_func_task))
-dl.get(glob.glob(path_func_task))
+dl.get(path_func_task)
 
 # define path to the functional resting state runs:
 path_rest = opj(path_tardis, 'masks', 'masks', 'smooth', sub, '*', '*task-rest*nii.gz')
 path_rest = sorted(glob.glob(path_rest), key=lambda f: os.path.basename(f))
 logging.info('found %d functional mri rest files' % len(path_rest))
 logging.info('paths to functional mri rest files:\n%s' % pformat(path_rest))
-dl.get(glob.glob(path_rest))
+dl.get(path_rest)
 
 # load the anatomical mri file:
 path_anat = opj(path_fmriprep, 'anat', '%s_desc-preproc_T1w.nii.gz' % sub)
 path_anat = sorted(glob.glob(path_anat), key=lambda f: os.path.basename(f))
 logging.info('found %d anatomical mri file' % len(path_anat))
 logging.info('paths to anatoimical mri files:\n%s' % pformat(path_anat))
-dl.get(glob.glob(path_anat))
+dl.get(path_anat)
 
 # load the confounds files:
 path_confs_task = opj(path_fmriprep, '*', 'func', '*task-highspeed*confounds_regressors.tsv')
@@ -263,21 +263,21 @@ path_confs_task = sorted(glob.glob(path_confs_task), key=lambda f: os.path.basen
 logging.info('found %d confounds files' % len(path_confs_task))
 logging.info('found %d confounds files' % len(path_confs_task))
 logging.info('paths to confounds files:\n%s' % pformat(path_confs_task))
-dl.get(glob.glob(path_confs_task))
+dl.get(path_confs_task)
 
 # load the spm.mat files:
 path_spm_mat = opj(path_level1, 'contrasts', sub, '*', 'SPM.mat')
 path_spm_mat = sorted(glob.glob(path_spm_mat), key=lambda f: os.path.dirname(f))
 logging.info('found %d spm.mat files' % len(path_spm_mat))
 logging.info('paths to spm.mat files:\n%s' % pformat(path_spm_mat))
-dl.get(glob.glob(path_spm_mat))
+dl.get(path_spm_mat)
 
 # load the t-maps of the first-level glm:
 path_tmap = opj(path_level1, 'contrasts', sub, '*', 'spmT*.nii')
 path_tmap = sorted(glob.glob(path_tmap), key=lambda f: os.path.dirname(f))
 logging.info('found %d t-maps' % len(path_tmap))
 logging.info('paths to t-maps files:\n%s' % pformat(path_tmap))
-dl.get(glob.glob(path_tmap))
+dl.get(path_tmap)
 '''
 ========================================================================
 LOAD THE MRI DATA:

code/decoding/requirements.txt

@@ -0,0 +1,59 @@
+annexremote==1.4.4
+appdirs==1.4.4
+attrs==20.3.0
+boto==2.49.0
+certifi==2020.11.8
+cffi==1.14.3
+chardet==3.0.4
+Counter==1.0.0
+cryptography==3.2.1
+cycler==0.10.0
+datalad==0.13.5
+Deprecated==1.2.10
+distro==1.5.0
+fasteners==0.15
+future==0.18.2
+humanize==3.1.0
+idna==2.10
+iniconfig==1.1.1
+iso8601==0.1.13
+jeepney==0.6.0
+joblib==0.17.0
+jsmin==2.2.2
+keyring==21.5.0
+keyrings.alt==4.0.1
+kiwisolver==1.3.1
+matplotlib==3.3.3
+monotonic==1.5
+msgpack==1.0.0
+nibabel==3.2.0
+nilearn==0.7.0
+numpy==1.19.4
+packaging==20.4
+pandas==1.1.4
+patool==1.12
+Pillow==8.0.1
+pkg-resources==0.0.0
+pluggy==0.13.1
+py==1.9.0
+pycparser==2.20
+PyGithub==1.53
+PyJWT==1.7.1
+pyparsing==2.4.7
+pytest==6.1.2
+python-dateutil==2.8.1
+pytz==2020.4
+PyYAML==5.3.1
+requests==2.25.0
+scikit-learn==0.23.2
+scipy==1.5.4
+SecretStorage==3.2.0
+simplejson==3.17.2
+six==1.15.0
+sklearn==0.0
+threadpoolctl==2.1.0
+toml==0.10.2
+tqdm==4.53.0
+urllib3==1.26.2
+Whoosh==2.7.4
+wrapt==1.12.1

decoding/sub-01/data/sub-01_decoding.csv

@@ -0,0 +1 @@
+../../../.git/annex/objects/30/Vj/MD5E-s38665809--4aae2cf9f0b62e844072dda6a64f6268.csv/MD5E-s38665809--4aae2cf9f0b62e844072dda6a64f6268.csv

decoding/sub-01/data/sub-01_thresholding.csv

@@ -0,0 +1 @@
+../../../.git/annex/objects/Mk/gW/MD5E-s263--816e6d83a01e9e526899e600d4f6a658.csv/MD5E-s263--816e6d83a01e9e526899e600d4f6a658.csv

decoding/sub-01/data/sub-01_voxel_patterns_union_cat.csv

@@ -0,0 +1 @@
+../../../.git/annex/objects/13/f2/MD5E-s9741759--92c1dea2c101c66ea149030e1fc3bece.csv/MD5E-s9741759--92c1dea2c101c66ea149030e1fc3bece.csv

decoding/sub-01/data/sub-01_voxel_patterns_union_cat.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Mw/8V/MD5E-s5349226--ac5eed9fc10e029e14b277aa37d4573a.nii.gz/MD5E-s5349226--ac5eed9fc10e029e14b277aa37d4573a.nii.gz

decoding/sub-01/data/sub-01_voxel_patterns_union_chair.csv

@@ -0,0 +1 @@
+../../../.git/annex/objects/Mj/7p/MD5E-s9634264--8bd2a6dc100ec77d36c327a0389836b5.csv/MD5E-s9634264--8bd2a6dc100ec77d36c327a0389836b5.csv

decoding/sub-01/data/sub-01_voxel_patterns_union_chair.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/3J/pV/MD5E-s5294119--c36a44b9f83fd0f5519845cfaa702d95.nii.gz/MD5E-s5294119--c36a44b9f83fd0f5519845cfaa702d95.nii.gz

decoding/sub-01/data/sub-01_voxel_patterns_union_face.csv

@@ -0,0 +1 @@
+../../../.git/annex/objects/M3/mW/MD5E-s9713054--7d48628b499fd407e6f7762718e1c316.csv/MD5E-s9713054--7d48628b499fd407e6f7762718e1c316.csv

decoding/sub-01/data/sub-01_voxel_patterns_union_face.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/k2/x8/MD5E-s5349968--31b4eafde5dba4a6bda86a6dd1910f77.nii.gz/MD5E-s5349968--31b4eafde5dba4a6bda86a6dd1910f77.nii.gz

decoding/sub-01/data/sub-01_voxel_patterns_union_house.csv

@@ -0,0 +1 @@
+../../../.git/annex/objects/Kf/M1/MD5E-s9713145--e78494374f9dbeeabc3590f1148d0dd3.csv/MD5E-s9713145--e78494374f9dbeeabc3590f1148d0dd3.csv

decoding/sub-01/data/sub-01_voxel_patterns_union_house.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/QP/Kw/MD5E-s5349773--997634942a55cba310dc54ea515897ce.nii.gz/MD5E-s5349773--997634942a55cba310dc54ea515897ce.nii.gz

decoding/sub-01/data/sub-01_voxel_patterns_union_hpc_cat.csv

@@ -0,0 +1 @@
+../../../.git/annex/objects/9q/P3/MD5E-s1105102--b0436f9bd00ca31d09ff9eb357d97ccf.csv/MD5E-s1105102--b0436f9bd00ca31d09ff9eb357d97ccf.csv

decoding/sub-01/data/sub-01_voxel_patterns_union_hpc_cat.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/63/mG/MD5E-s1207025--462e726e89078a5502a1d32f984b8ecd.nii.gz/MD5E-s1207025--462e726e89078a5502a1d32f984b8ecd.nii.gz

decoding/sub-01/data/sub-01_voxel_patterns_union_hpc_chair.csv

@@ -0,0 +1 @@
+../../../.git/annex/objects/VG/QP/MD5E-s1092762--bdc24a43b782d8517c63f6a65dda846a.csv/MD5E-s1092762--bdc24a43b782d8517c63f6a65dda846a.csv

decoding/sub-01/data/sub-01_voxel_patterns_union_hpc_chair.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Xm/xX/MD5E-s1194195--f986ce66b00c5e829d1e4f90f1a4ed60.nii.gz/MD5E-s1194195--f986ce66b00c5e829d1e4f90f1a4ed60.nii.gz

decoding/sub-01/data/sub-01_voxel_patterns_union_hpc_face.csv

@@ -0,0 +1 @@
+../../../.git/annex/objects/Vm/66/MD5E-s1104706--b4600dfc29caace159f9d17e9345815b.csv/MD5E-s1104706--b4600dfc29caace159f9d17e9345815b.csv

decoding/sub-01/data/sub-01_voxel_patterns_union_hpc_face.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/0P/71/MD5E-s1206800--5b3b874eeb4330bf004ccbb0d3bd717b.nii.gz/MD5E-s1206800--5b3b874eeb4330bf004ccbb0d3bd717b.nii.gz

decoding/sub-01/data/sub-01_voxel_patterns_union_hpc_house.csv

@@ -0,0 +1 @@
+../../../.git/annex/objects/QF/W5/MD5E-s1105106--6b2054374af9833752837fd68e2998aa.csv/MD5E-s1105106--6b2054374af9833752837fd68e2998aa.csv

decoding/sub-01/data/sub-01_voxel_patterns_union_hpc_house.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/px/FX/MD5E-s1207435--3c007cfa50e8d731e979e1f1d9c49653.nii.gz/MD5E-s1207435--3c007cfa50e8d731e979e1f1d9c49653.nii.gz

decoding/sub-01/data/sub-01_voxel_patterns_union_hpc_shoe.csv

@@ -0,0 +1 @@
+../../../.git/annex/objects/kw/v4/MD5E-s1105021--b81bbb89529e3ee1cbc6fc99b2d26e89.csv/MD5E-s1105021--b81bbb89529e3ee1cbc6fc99b2d26e89.csv

decoding/sub-01/data/sub-01_voxel_patterns_union_hpc_shoe.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/z9/84/MD5E-s1207368--ce395545cc33d9fa053ddc93bee37ce9.nii.gz/MD5E-s1207368--ce395545cc33d9fa053ddc93bee37ce9.nii.gz

decoding/sub-01/data/sub-01_voxel_patterns_union_shoe.csv

@@ -0,0 +1 @@
+../../../.git/annex/objects/QF/p0/MD5E-s9721836--5b4b0c3e6f5e3f4c0cd03cfbccda832c.csv/MD5E-s9721836--5b4b0c3e6f5e3f4c0cd03cfbccda832c.csv

decoding/sub-01/data/sub-01_voxel_patterns_union_shoe.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/K5/Q2/MD5E-s5352579--8c921422199fc97d4b49e64a16e508e6.nii.gz/MD5E-s5352579--8c921422199fc97d4b49e64a16e508e6.nii.gz

decoding/sub-01/masks/sub-01_run-01_tmap_masked.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Fv/60/MD5E-s195380--8240ccb656d04eb808163348ac667a66.nii.gz/MD5E-s195380--8240ccb656d04eb808163348ac667a66.nii.gz

decoding/sub-01/masks/sub-01_run-01_tmap_masked_thresh.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/39/WM/MD5E-s34132--72df82e1c5ce3adf6b4f35a1f05c6327.nii.gz/MD5E-s34132--72df82e1c5ce3adf6b4f35a1f05c6327.nii.gz

decoding/sub-01/masks/sub-01_run-02_tmap_masked.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/8M/j7/MD5E-s195104--67154b8fea385d5880790c30212461d0.nii.gz/MD5E-s195104--67154b8fea385d5880790c30212461d0.nii.gz

decoding/sub-01/masks/sub-01_run-02_tmap_masked_thresh.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/PQ/J4/MD5E-s34288--6db6065d67b8d719b39ec5c54bf59128.nii.gz/MD5E-s34288--6db6065d67b8d719b39ec5c54bf59128.nii.gz

decoding/sub-01/masks/sub-01_run-03_tmap_masked.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/j5/5K/MD5E-s195484--964052d7cde5aae8423646861363009e.nii.gz/MD5E-s195484--964052d7cde5aae8423646861363009e.nii.gz

decoding/sub-01/masks/sub-01_run-03_tmap_masked_thresh.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/jG/P4/MD5E-s34654--0e26be655890a05b0e908f67f6b2f651.nii.gz/MD5E-s34654--0e26be655890a05b0e908f67f6b2f651.nii.gz

decoding/sub-01/masks/sub-01_run-04_tmap_masked.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/vJ/1X/MD5E-s195702--493d43fe0c878cf9885d8a19e13b390b.nii.gz/MD5E-s195702--493d43fe0c878cf9885d8a19e13b390b.nii.gz

decoding/sub-01/masks/sub-01_run-04_tmap_masked_thresh.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/3P/K0/MD5E-s34338--815886a7231d87c68f2b33c5fb344fca.nii.gz/MD5E-s34338--815886a7231d87c68f2b33c5fb344fca.nii.gz

decoding/sub-01/masks/sub-01_run-05_tmap_masked.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/qw/Q4/MD5E-s195670--6840a23e91d1a6f1dc9649dfc9ee61f4.nii.gz/MD5E-s195670--6840a23e91d1a6f1dc9649dfc9ee61f4.nii.gz

decoding/sub-01/masks/sub-01_run-05_tmap_masked_thresh.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Xw/71/MD5E-s34088--d302a739c14653f31a8797f34d1e1b27.nii.gz/MD5E-s34088--d302a739c14653f31a8797f34d1e1b27.nii.gz

decoding/sub-01/masks/sub-01_run-06_tmap_masked.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/qP/xJ/MD5E-s194883--4d984635726746c43e34fe7ec573993a.nii.gz/MD5E-s194883--4d984635726746c43e34fe7ec573993a.nii.gz

decoding/sub-01/masks/sub-01_run-06_tmap_masked_thresh.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/JZ/G5/MD5E-s34123--df5ad69f5565741c5c0eaf03c5c2117c.nii.gz/MD5E-s34123--df5ad69f5565741c5c0eaf03c5c2117c.nii.gz

decoding/sub-01/masks/sub-01_run-07_tmap_masked.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/47/7w/MD5E-s194783--364431aa9a3405dfa7823d471cd9d865.nii.gz/MD5E-s194783--364431aa9a3405dfa7823d471cd9d865.nii.gz

decoding/sub-01/masks/sub-01_run-07_tmap_masked_thresh.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/1P/vv/MD5E-s34155--271d85dd05d27ad8b5b131c17dcf11e9.nii.gz/MD5E-s34155--271d85dd05d27ad8b5b131c17dcf11e9.nii.gz

decoding/sub-01/masks/sub-01_run-08_tmap_masked.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/2G/79/MD5E-s195608--be51f4fa5f86ed086150a411136e602f.nii.gz/MD5E-s195608--be51f4fa5f86ed086150a411136e602f.nii.gz

decoding/sub-01/masks/sub-01_run-08_tmap_masked_thresh.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Mv/fG/MD5E-s33939--6f634ae4db36aa8adbbebd982d1123ec.nii.gz/MD5E-s33939--6f634ae4db36aa8adbbebd982d1123ec.nii.gz

decoding/sub-01/masks/sub-01_task-rest_mask-union.nii.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/9j/4j/MD5E-s11390--2b00300aa7d45b3eb8f3254facaf4854.nii.gz/MD5E-s11390--2b00300aa7d45b3eb8f3254facaf4854.nii.gz

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