adding scripts for dcm2bids

DownloadData/0.1_dcm2bids_SLURM.sh

+#!/bin/bash
+#SBATCH --mail-user=mcnabbc1@cardiff.ac.uk
+#SBATCH --mail-type=END
+#SBATCH --job-name=SW2_dcm2bids
+#SBATCH --partition=cubric-centos7
+#SBATCH -o /home/sapcm15/sbatch_reports/SW2_dcm2bids_%j.out
+#SBATCH -e /home/sapcm15/sbatch_reports/SW2_dcm2bids_%j.err
+#SBATCH --array=1-1
+
+
+export PATH=$PATH:/home/sapcm15/gitlab/brainandgenomicshub/DownloadData
+
+
+# use the SLURM_ARRAY_TASK_ID to define the subject ID (sub) from the subject_list.txt file
+sub=$(sed -n ${SLURM_ARRAY_TASK_ID}p /home/sapcm15/gitlab/brainandgenomicshub/DownloadData/subject_list.txt)
+
+# run the analysis - note that the first argument is the participant ID - they will get their own SLURM job
+batch_dcm2bids.sh ${sub}
+

DownloadData/README.md

+# Analysis scripts for downloading data and storing in BIDS format
+**Carolyn McNabb**</br>
+Last updated: September 2024
+
+
+## Downloading MRI data from XNAT
+First, you'll need to download the MRI data from XNAT. 
+
+## DICOM to dicomBIDS conversion
+Once data are downloaded, you can convert the DICOM files to NifTI format and arrange these according to the Brain Imaging Data Structure ([BIDS](https://bids-specification.readthedocs.io/en/stable/)). 
+
+#### Initial environment setup
+To use dcm2bids, you need to be in a python environment. First you'll need to set this up and then you can download dcm2bids.
+
+
+2.1. Set up environment for dcm2bids 
+```
+gedit environment.yml 
+```
+Paste in the following:
+```
+name: dcm2bids
+channels:
+    - conda-forge
+dependencies:
+    - dcm2niix
+    - dcm2bids
+    - pip
+```
+
+
+Create conda environment and activate:
+```
+conda env create -f environment.yml --prefix ~/dcm2bids_env
+
+source activate ~/dcm2bids_env
+
+cd /cubric/scratch/sapcm15/BioBank_forCarolyn/sourcedata
+```
+
+
+2.2. Install dcm2bids
+In terminal, type:
+```
+pip install dcm2bids
+```
+#### If environment has already been setup
+
+2.2. activate environment
+```
+source activate ~/dcm2bids_env
+
+cd /cubric/scratch/sapcm15/BioBank_forCarolyn/sourcedata
+```
+
+
+2.3. Convert raw data to BIDS format with dcm2bids
+First, test that dcm2bids is working by typing
+```
+dcm2bids --help
+```
+Use the dcm2bids helper function to look at your json files (associated with each of your nifti files - these will be in the tmp_dcm2bids folder).
+```
+dcm2bids_helper -d /cubric/scratch/sapcm15/BioBank_forCarolyn/scans
+```
+
+### Run dcm2bids 
+To run dcm2bids, you need to have a configuration file set up. For the SW2 project, this is stored in `~/gitlab/UKBiobank_CUBRIC/DownloadData/dcm2bids_config.SW2.json`
+
+You'll also need a subject list of all the subjects you want to convert from DICOM to NifTI. This should be stored in the brainandgenomicshub gitlab folder and called `subject_list.txt`. 
+
+Now, open `0.1_dcm2bids_SLURM.sh` and update the `#SBATCH --array=1-1` line to include all the subjects in your list that you want to convert, e.g. `#SBATCH --array=3-15`. You'll also need to update the paths in `batch_dcm2bids` to match the paths where you've downloaded the data from XNAT and the path where you keep this gitlab repository.
+
+You should now be ready to run dcm2bids. In the linux terminal, type:
+```
+sbatch 0.1_dcm2bids_SLURM.sh
+```
+This will send the command to the cluster and each subject will get it's own job id. You can check the progress of the jobs by typing:
+```
+squeue -u <youruserid>
+```
+You can cancel all the jobs you just sent by typing:
+```
+scancel -u <youuserid>
+```
+You can cancel individual jobs too, by typing:
+```
+scancel <jobid>
+```
+
+Once the job has finished, you can check whether there were any errors by looking in the reports folder you specified in `0.1_dcm2bids_SLURM.sh`. The job will create two files, one ending `.err` and one ending `.out`. You will need to check both of them to make sure the job ran okay.
\ No newline at end of file

DownloadData/batch_dcm2bids.sh

+# Carolyn McNabb - dcm2bids script for WAND data
+#!/bin/bash
+
+#Define subject - $1 represents the first input argument from the SLURM file (in this case, the subject ID)
+# id=$1
+# sub=${id//$"314_"/}
+sub=$1
+
+#Set up paths
+bids_dir=/cubric/scratch/sapcm15/BioBank_forCarolyn/sourcedata
+home_dir=/home/sapcm15
+dicom_dir=/cubric/scratch/sapcm15/BioBank_forCarolyn/XNATDownloads
+json_dir=${home_dir}/gitlab/brainandgenomicshub/DownloadData
+
+echo "running dcm2bids for ${sub}"
+
+#use dcm2bids environment
+source activate ${home_dir}/dcm2bids_env
+
+#run dcm2bids analysis
+dcm2bids -d ${dicom_dir}/${sub}/scans -p ${sub} -s 01 -c ${json_dir}/dcm2bids_config_SW2.json -o ${bids_dir} #for collab bids
\ No newline at end of file

DownloadData/dcm2bids_config_SW2.json

+{
+    "dcm2niixOptions": "-b y -ba y -z y -f '%n_%3s_%f_%p'",
+    "descriptions": [
+        {
+        "dataType": "anat",
+        "modalityLabel": "T1w",
+        "criteria": {
+            "ImageType":  ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"],
+            "SeriesDescription": "T1_p2_1mm_fov256_sag_TI_880"
+                    }
+        },
+        {
+        "dataType": "func",
+        "modalityLabel": "sbref",   
+        "criteria": {
+            "ImageType":  ["ORIGINAL", "PRIMARY", "M", "ND", "MOSAIC"],
+            "SeriesDescription": "MB8_FMRI_fov210_2.4mm_resting_SBRef" 
+                    }
+        },
+        {
+        "dataType": "func",
+        "modalityLabel": "bold",
+        "criteria": {
+            "ImageType": ["ORIGINAL", "PRIMARY", "M", "MB", "ND", "MOSAIC"],
+            "SeriesDescription": "MB8_FMRI_fov210_2.4mm_resting"
+                    },
+            "sidecarChanges": {
+                "TaskName": "rest"
+            }
+        },
+        {
+        "dataType": "anat",
+        "modalityLabel": "FLAIR",
+        "criteria": {
+            "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"],
+            "SeriesDescription": "t2_flair_sag_p2_1mm_FS_ellip_pf78"
+                    }
+        },
+        {
+        "dataType": "dwi",
+        "modalityLabel": "dwi",
+        "customLabels": "dir-PA_part-mag",
+        "criteria": {
+        "ImageType": ["ORIGINAL", "PRIMARY", "DIFFUSION", "NONE", "MB", "ND"],
+            "SeriesDescription": "diff_PA_MPopt_MB3_3b0_lowflip",
+            "PhaseEncodingDirection": "j"
+            }
+        },
+        {
+        "dataType": "dwi",
+        "modalityLabel": "dwi",
+        "customLabels": "dir-AP_part-mag",
+        "criteria": {
+        "ImageType": ["ORIGINAL", "PRIMARY", "DIFFUSION", "NONE", "MB", "ND", "MOSAIC"],
+            "SeriesDescription": "diff_AP_MPopt_MB3_50b1000_50b2000_8b0_lowflip",
+            "PhaseEncodingDirection": "j-"
+            }
+        }, 
+        {
+        "dataType": "swi",
+        "modalityLabel": "GRE",
+        "customLabels": "echo-1",
+        "criteria": {
+            "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM", "FM", "FIL"],
+            "SeriesDescription": "SWI_3mm_Updated_v1.1",
+            "EchoNumber": 1
+                    }
+        },
+        {
+        "dataType": "swi",
+        "modalityLabel": "GRE",
+        "customLabels": "echo-2",
+        "criteria": {
+            "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM", "FM", "FIL"],
+            "SeriesDescription": "SWI_3mm_Updated_v1.1",
+            "EchoNumber": 2
+                    }
+        }
+    ]
+}
+

DownloadData/subject_list.txt

+sub-01
\ No newline at end of file