resolve BIDS validation errors

Author: Monika_Utrosa_Skerjanec

README.md

@@ -20,7 +20,7 @@ All scripts ran by main_xxx.sh are located in .../scripts except for fMRIprep pr
 	--> These folders are untouched by next steps to ensure replicable pipeline.
 2. Check that data is complete and correctly named.
 3. Run pre_import.py to create sidecar files, needed for config file.
-4. Set up the config file for BIDSifying MRI data with `dcm2bids`. The configuration doesn't have to include the headscouts and the phoenix ZIP report.
+4. Set up the config file for BIDSifying MRI data with `dcm2bids`. The configuration doesn't have to include the headscouts and the phoenix ZIP report. Validate the config.json file: https://jsonlint.com/.
 5. Add "dataset_description.json" file to data_MRI/sourcedata/raw
 6. Remove any duplicate data.
 7. Run [BIDS Validator](http://bids.neuroimaging.io/tools/validator.html) on the dataset to ensure compliance to [the BIDS specification](https://bids-specification.readthedocs.io/en/stable/).

import_localizer.sh

@@ -10,12 +10,12 @@ source activate localizer_fMRI
 
 # Subject-specific parameters
 subID=1
-sesID=1
+sesID=3
 project="SubCort_HighRes"
 task="localizer"
-homePath='/home/mutrosa/Documents/projects/select_fMRI'
-acq_list=("DresdenNoFat" "DresdenWFat" "ME1TR880" "ME3TR1600" "ME3TR1100" "ME3TR850" "ME3TR700")
-# acq_list=("DresdenNoFat175" "DresdenWFat175" "ME1TR780" "ME3TR1180" "ME3TR770" "ME3TR680")
+homePath="/home/mutrosa/Documents/projects/select_fMRI"
+# acq_list=("DresdenNoFat" "DresdenWFat" "ME1TR880" "ME3TR1600" "ME3TR1100" "ME3TR850" "ME3TR700")
+acq_list=("DresdenNoFat175" "DresdenWFat175" "ME1TR780" "ME3TR1180" "ME3TR770" "ME3TR680")
 
 # STEP 0
 ## Generate sidecar files to set up the configuration files.

pre_import.py

@@ -5,8 +5,8 @@
 
 # 1. Adjust parameters for your subject/session
 # Activate the correct conda environment: conda activate dcm2bids
-subID    = 2
-sesID    = 2
+subID    = 1
+sesID    = 1
 project  = "SubCort_HighRes"
 homePath = '/home/mutrosa/Documents/projects/select_fMRI/data_MRI/'