Conversion

Load the following modules:

module use ${root_dir}/server/modulefiles
module load bashHelperKennedyRodrigue
module load containers/r/4.2.1-quarto
module load study-pams/convert_mri/latest

For more details or updates, check the github page.

Data Entry

Enter BP measurements to the Cognitive Data Sheet, and file subject’s receipts into the receipt bin.
```
${root_dir}/study-pams/Demographic_and_Task_Data/Cognitive_Data_MCI.xlsx
```

Copy physiological measures to the server and rename the files using the following template:

${root_dir}/study-pams/sourcedata/physio/KENROD_PAMS_20230101_0001_1/sub-0001_ses-01.puls
${root_dir}/study-pams/sourcedata/physio/KENROD_PAMS_20230101_0001_1/sub-0001_ses-01.resp

Copy the exam card to the server using the following template:

${root_dir}/study-pams/sourcedata/exam_cards/KENROD_PAMS_20230101_0001_1.pdf

Convert

After receiving the BHIC Data Transfer email, run the following script to unzip data:

dcm_unzip.sh --data_ref abcdefgh-12345678 --sub 0001 --ses 1 --date 20230101

After the files have been unzipped, convert the DICOM images to NIFTI with the following script:
```
dcm2niix_wrapper.sh --sub 0001 --ses 1 --date 20230101
```

QC Parameters

QC the data and check for any images that have bad quality or were cut off.
- Create a scanner_reconstruction directory for the reconstructed files (acq. 11,13,15,18,19 for ref.).
- Create a bad directory within the subject directory for bad scans if necessary.

After QC, run the QC uber script:

qc_uber.sh --sub 0001 --ses 1 --date 20230101

Combine the QC logs together with the following script:
```
qc_combine_all_sub.sh
```
Then run the following script locally (via RStudio)
```
qc_render.sh --study pams --overwrite 1
```