CogRehab_MRI_server

Shell and R scripts used for MRI analyses on the BIC server at the Royal Ottawa Mental Health Center.

1. COGREH
   • sets environment for FreeSurfer (sets FREESURFER_HOME, FSFAST_HOME and SUBJECTS_DIR) and navigates to the scripts folder of the CogRehab study

• This requires some modification to the ~/.bashrc file. Needs to add the following to ~/.bashrc first: alias COGREH='export SUBJECTS_DIR=/group/guimond_CogReh/CogRehab/SUBJECTS_DIR; export FREESURFER_HOME=/usr/local/freesurfer-6.0; export FSFAST_HOME=$FREESURFER_HOME/fsfast; source $FREESURFER_HOME/SetUpFreeSurfer.sh; cd /group/guimond_CogReh/CogRehab/scripts'

2. setup.sh

   • reminds to set environment for FreeSurfer
   • reminds to supply subject ID as an argument
   • copies nii and E-prime txt output to /group/guimond_CogReh/CogRehab/raw_data
   • sets up data environment for the given participant (build profile with anat, bold, resting and nm in /group/guimond_CogReh/CogRehab/subjects) - Note: Anat contains T1. Bold contains fMRI scans. NM is neuromelanin- sensitivity scan. Resting is resting state. - 001 in bold is vm encoding run1 - 002 in bold is vm encoding run2 - 003 in bold is vm recognition - 004 in bold is efn run1 - 005 in bold is efn run2 - 006 in bold is fb run1 - 007 in bold is fb run2
   • creates a TMS-EEG environment for each participant (a folder for each participant with their T1 and script inside)

3. recon.sh

   • recon-all for a participant

4. normTarg.sh

   • creates coordinates for TMS-EEG

5. par.R

   • creates 7 paradigm files for each participant (for vm_encoding run1, vm_encoding run2, vm_recognition, efn run1, efn run2, fb run1, fb run2) and saves the paradigm files into /par_file in /subjects as .csv files and into each directory of /bold in /subjects as .par files.

6. preproc.sh

• preprocesses fMRI scans for the participant.

7. make_analysis.sh

   • configures analyses and contrasts for each fMRI task (defines number of conditions, names of paradigm files, run list files, etc.)

8. make_contrast.sh

   • configures contrasts for each fMRI task (e.g., condition 1 – condition 2)

9. make_selxavge.sh

   • First level analysis

10. FS_IN_ONE.sh

    • combines steps 2-7.