first submission

bids/README

@@ -0,0 +1,5 @@
+A free form text ( README ) describing the dataset in more details that SHOULD be provided
+
+The raw BIDS data was created using BIDScoin 2.3
+All provenance information and settings can be found in ./code/bidscoin
+For more information see: https://github.com/Donders-Institute/bidscoin

bids/code/bidscoin/bidscoiner.log

@@ -0,0 +1,6 @@
+2020-02-23 11:31:26 - bidscoin - INFO 
+2020-02-23 11:31:26 - bidscoin - INFO -------------- START BIDScoiner 2.3: BIDS 1.2.1 ------------
+2020-02-23 11:31:26 - bidscoin - INFO >>> bidscoiner sourcefolder=/data/raw bidsfolder=/data/bids subjects=None force=True participants=False bidsmap=bidsmap.yaml subprefix=sub- sesprefix=ses-
+2020-02-23 11:31:26 - bidscoin - INFO Creating dataset description file: /data/bids/dataset_description.json
+2020-02-23 11:31:26 - bidscoin - INFO Creating README file: /data/bids/README
+2020-02-23 11:31:26 - bidscoin - INFO No bidsmap file found: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap.yaml

bids/code/sbatch_step1a.sh

@@ -16,7 +16,7 @@ module load singularity
 ##### run container commands
 
 # create samples under bids/code/bidscoiner
-singularity run --bind /scratch/psyc5171/NETID/bidscoiner:/data \
+singularity run --bind /scratch/amw17004/hw2:/data \
 	/scratch/psyc5171/containers/birc-bids_latest.sif \
 	bidstrainer.py /data/bids
 

bids/code/sbatch_step1b.sh

@@ -17,7 +17,7 @@ module load singularity
 
 
 # reorganize the files
-singularity run --bind /scratch/psyc5171/NETID/bidscoiner:/data \
+singularity run --bind /scratch/amw17004/hw2:/data \
 	/scratch/psyc5171/containers/birc-bids_latest.sif \
 	/data/bids/code/reorganize.sh
 

bids/code/sbatch_step2.sh

@@ -15,13 +15,13 @@ module load singularity
 ##### run container commands
 
 # training on the sample data
-singularity run --bind /scratch/psyc5171/roh17004/bidscoiner:/data \
+singularity run --bind /scratch/psyc5171/amw17004/bidscoiner:/data \
 	/scratch/psyc5171/containers/birc-bids_latest.sif \
 	bidstrainer.py /data/bids
 
 
 # Create the bidsmap
-singularity run --bind /scratch/psyc5171/roh17004/bidscoiner:/data \
+singularity run --bind /scratch/psyc5171/amw17004/hw2:/data \
 	/scratch/psyc5171/containers/birc-bids_latest.sif \
 	bidsmapper.py -t /data/bids/code/bidscoin/bidsmap_sample.yaml \
 	-i 0 /data/raw  /data/bids

bids/code/sbatch_step3.sh

@@ -15,7 +15,7 @@ module load singularity
 ##### run container commands
 
 # Run bidscoiner to convert the raw data to BIDSa
-singularity run --bind /scratch/psyc5171/roh17004/bidscoiner:/data \
+singularity run --bind /scratch/amw17004/hw2:/data \
 	/scratch/psyc5171/containers/birc-bids_latest.sif \
 	bidscoiner.py -f /data/raw  /data/bids
 

bids/code/slurm-3092069.out

@@ -0,0 +1 @@
+ls: cannot access /data/raw/sub-*: No such file or directory

bids/code/step1a_error_3092133_4294967294.log

@@ -0,0 +1,6 @@
+WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.

bids/code/step1a_output_3092133_4294967294.log

@@ -0,0 +1,2 @@
+Creating an empty samples directory tree: /data/bids/code/bidscoin/samples
+Fill the directory tree with example DICOM files and re-run bidstrainer.py

bids/code/step1b_error_3092135_4294967294.log

@@ -0,0 +1,36 @@
+WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+/data/bids/code/reorganize.sh: line 9: m: command not found

bids/code/step1b_output_3092135_4294967294.log

@@ -0,0 +1,28 @@
+>> Processing: /data/raw/sub-TD902TD/1 (128 files)
+   Creating:  /data/raw/sub-TD902TD/1/001-AAHead_Scout
+>> Processing: /data/raw/sub-TD902TD/10 (13 files)
+   Creating:  /data/raw/sub-TD902TD/10/010-task-prosody
+>> Processing: /data/raw/sub-TD902TD/11 (1 files)
+   Creating:  /data/raw/sub-TD902TD/11/011-task-prosody_PhysioLog
+>> Processing: /data/raw/sub-TD902TD/12 (1 files)
+   Creating:  /data/raw/sub-TD902TD/12/012-task-prosody_SBRef
+>> Processing: /data/raw/sub-TD902TD/13 (336 files)
+   Creating:  /data/raw/sub-TD902TD/13/013-task-prosody
+>> Processing: /data/raw/sub-TD902TD/14 (1 files)
+   Creating:  /data/raw/sub-TD902TD/14/014-task-prosody_PhysioLog
+>> Processing: /data/raw/sub-TD902TD/2 (5 files)
+   Creating:  /data/raw/sub-TD902TD/2/002-AAHead_Scout_MPR_sag
+>> Processing: /data/raw/sub-TD902TD/3 (3 files)
+   Creating:  /data/raw/sub-TD902TD/3/003-AAHead_Scout_MPR_cor
+>> Processing: /data/raw/sub-TD902TD/4 (3 files)
+   Creating:  /data/raw/sub-TD902TD/4/004-AAHead_Scout_MPR_tra
+>> Processing: /data/raw/sub-TD902TD/5 (176 files)
+   Creating:  /data/raw/sub-TD902TD/5/005-T1w
+>> Processing: /data/raw/sub-TD902TD/6 (1 files)
+   Creating:  /data/raw/sub-TD902TD/6/006-task-music_SBRef
+>> Processing: /data/raw/sub-TD902TD/7 (287 files)
+   Creating:  /data/raw/sub-TD902TD/7/007-task-music
+>> Processing: /data/raw/sub-TD902TD/8 (1 files)
+   Creating:  /data/raw/sub-TD902TD/8/008-task-music_PhysioLog
+>> Processing: /data/raw/sub-TD902TD/9 (1 files)
+   Creating:  /data/raw/sub-TD902TD/9/009-task-prosody_SBRef

bids/code/step2_error_3096308_4294967294.log

@@ -0,0 +1,12 @@
+WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+2020-02-23 11:27:33 - bidscoin - INFO ------------ START BIDStrainer ------------
+2020-02-23 11:27:33 - bidscoin - INFO Reading: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap_template.yaml
+2020-02-23 11:27:33 - bidscoin - INFO Writing bidsmap to: /data/bids/code/bidscoin/bidsmap_sample.yaml
+2020-02-23 11:27:33 - bidscoin - INFO ------------ FINISHED! ------------
+WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts
+FATAL:   container creation failed: mount /scratch/psyc5171/amw17004/hw2->/data error: while mounting /scratch/psyc5171/amw17004/hw2: mount source /scratch/psyc5171/amw17004/hw2 doesn't exist

bids/code/step3_error_3096318_4294967294.log

@@ -0,0 +1,24 @@
+WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+2020-02-23 11:31:26 - bidscoin - INFO 
+2020-02-23 11:31:26 - bidscoin - INFO -------------- START BIDScoiner 2.3: BIDS 1.2.1 ------------
+2020-02-23 11:31:26 - bidscoin - INFO >>> bidscoiner sourcefolder=/data/raw bidsfolder=/data/bids subjects=None force=True participants=False bidsmap=bidsmap.yaml subprefix=sub- sesprefix=ses-
+2020-02-23 11:31:26 - bidscoin - INFO Creating dataset description file: /data/bids/dataset_description.json
+2020-02-23 11:31:26 - bidscoin - INFO Creating README file: /data/bids/README
+2020-02-23 11:31:26 - bidscoin - INFO No bidsmap file found: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap.yaml
+Traceback (most recent call last):
+  File "/usr/local/miniconda/bin/bidscoiner.py", line 4, in <module>
+    __import__('pkg_resources').run_script('bidscoin==2.3', 'bidscoiner.py')
+  File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
+    self.require(requires)[0].run_script(script_name, ns)
+  File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
+    exec(code, namespace, namespace)
+  File "/usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/EGG-INFO/scripts/bidscoiner.py", line 569, in <module>
+    sesprefix    = args.sesprefix)
+  File "/usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/EGG-INFO/scripts/bidscoiner.py", line 436, in bidscoiner
+    bidsignore_items = [item.strip() for item in bidsmap['Options']['bidscoin']['bidsignore'].split(';')]
+KeyError: 'Options'

bidscoiner/bids/code/reorganize.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+# rename DICOM folders to help bidsmap
+SUBJECT=$1
+for d in /data/raw/sub-${SUBJECT}/*; do
+	dicomsort.py -r -e .dcm $d
+done
+
+mv /data/raw/sub-${SUBJECT}/*/* /data/raw/sub-${SUBJECT}
+rm -rf /data/raw/sub-${SUBJECT}/[1-9]*

bidscoiner/bids/code/sbatch_step1.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+##### Job definition
+# TODO: Edit email address below
+#SBATCH --nodes=1					# OpenMP requires a single node
+#SBATCH --ntasks=1					# Run a single serial task
+#SBATCH --time=00:10:00				# Time limit hh:mm:ss
+#SBATCH -e step1_error_%A_%a.log			# Standard error
+#SBATCH -o step1_output_%A_%a.log			# Standard output
+#SBATCH --job-name=bidssetup			# Descriptive job name
+#SBATCH --partition=serial
+
+##### load required modules
+
+module load singularity
+
+##### run container commands
+
+# create samples under bids/code/bidscoiner
+singularity run --bind /scratch/psyc5171/NETID/bidscoiner:/data \
+	/scratch/psyc5171/containers/birc-bids_latest.sif \
+	bidstrainer.py /data/bids
+
+
+# reorganize the files
+singularity run --bind /scratch/psyc5171/NETID/bidscoiner:/data \
+	/scratch/psyc5171/containers/birc-bids_latest.sif \
+	/data/bids/code/reorganize.sh IBRAIN002
+
+

bidscoiner/bids/code/sbatch_step2.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+##### Job definition
+#SBATCH --nodes=1					# OpenMP requires a single node
+#SBATCH --ntasks=1					# Run a single serial task
+#SBATCH --time=00:10:00				# Time limit hh:mm:ss
+#SBATCH -e step2_error_%A_%a.log			# Standard error
+#SBATCH -o step2_output_%A_%a.log			# Standard output
+#SBATCH --job-name=bidstrain			# Descriptive job name
+#SBATCH --partition=serial
+
+##### load required modules
+
+module load singularity
+
+##### run container commands
+
+# training on the sample data
+singularity run --bind /scratch/psyc5171/roh17004/bidscoiner:/data \
+	/scratch/psyc5171/containers/birc-bids_latest.sif \
+	bidstrainer.py /data/bids
+
+
+# Create the bidsmap
+singularity run --bind /scratch/psyc5171/roh17004/bidscoiner:/data \
+	/scratch/psyc5171/containers/birc-bids_latest.sif \
+	bidsmapper.py -t /data/bids/code/bidscoin/bidsmap_sample.yaml \
+	-i 0 /data/raw  /data/bids
+
+

bidscoiner/bids/code/sbatch_step3.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+##### Job definition
+#SBATCH --nodes=1					# OpenMP requires a single node
+#SBATCH --ntasks=1					# Run a single serial task
+#SBATCH --time=00:10:00				# Time limit hh:mm:ss
+#SBATCH -e step3_error_%A_%a.log			# Standard error
+#SBATCH -o step3_output_%A_%a.log			# Standard output
+#SBATCH --job-name=bidscoin			# Descriptive job name
+#SBATCH --partition=serial
+
+##### load required modules
+
+module load singularity
+
+##### run container commands
+
+# Run bidscoiner to convert the raw data to BIDSa
+singularity run --bind /scratch/psyc5171/roh17004/bidscoiner:/data \
+	/scratch/psyc5171/containers/birc-bids_latest.sif \
+	bidscoiner.py -f /data/raw  /data/bids
+
+

step1a_error_3091907_4294967294.log

@@ -0,0 +1,6 @@
+WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.

step1a_error_3091921_4294967294.log

@@ -0,0 +1,10 @@
+WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+2020-02-20 08:05:21 - bidscoin - INFO ------------ START BIDStrainer ------------
+2020-02-20 08:05:21 - bidscoin - INFO Reading: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap_template.yaml
+2020-02-20 08:05:21 - bidscoin - INFO Writing bidsmap to: /data/bids/code/bidscoin/bidsmap_sample.yaml
+2020-02-20 08:05:21 - bidscoin - INFO ------------ FINISHED! ------------

step1a_error_3092046_4294967294.log

@@ -0,0 +1,10 @@
+WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+ERROR: ld.so: object 'libcr_run.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
+2020-02-20 10:55:36 - bidscoin - INFO ------------ START BIDStrainer ------------
+2020-02-20 10:55:36 - bidscoin - INFO Reading: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap_template.yaml
+2020-02-20 10:55:36 - bidscoin - INFO Writing bidsmap to: /data/bids/code/bidscoin/bidsmap_sample.yaml
+2020-02-20 10:55:37 - bidscoin - INFO ------------ FINISHED! ------------

step1a_output_3091907_4294967294.log

@@ -0,0 +1,2 @@
+Creating an empty samples directory tree: /data/bids/code/bidscoin/samples
+Fill the directory tree with example DICOM files and re-run bidstrainer.py