MRI

Please check the ROOT and directories match your current structure. It requires the file ntag.txt that contains the padded subject numbers (ADNIDOD)

The order of the scripts for freesurfer are:

Each script will need to be moved into your legion directory (scp or ftp) and THEN made into an executable file.

syntax is

chmod a+x SCRIPTNAME

The script is then ran by ./SCRIPTNAME

This check to make sure that the correct subject directories exist.

This moves the files over to a defined directory and moves them from sagital to axial in the process.

This makes the freesurfer directory and then copies over the structural scan over and then it's ready for recon-all.

Name		Name	Last commit message	Last commit date
Latest commit History 14 Commits
README.md		README.md
base_make_subject_directories.sh		base_make_subject_directories.sh
dti_CHECK_prep_legion.sh		dti_CHECK_prep_legion.sh
dti_pre_prep_legion.sh		dti_pre_prep_legion.sh
dti_tidyup.sh		dti_tidyup.sh
ntag.txt		ntag.txt
push2github_local.sh		push2github_local.sh
struc_CHECK_pre_prep_legion_ADNIDOD.sh		struc_CHECK_pre_prep_legion_ADNIDOD.sh
struc_CHECK_pre_prep_legion_FTD.sh		struc_CHECK_pre_prep_legion_FTD.sh
struc_freesurfer2fsl_reg_legion.sh		struc_freesurfer2fsl_reg_legion.sh
struc_freesurfer2fsl_roi_legion.sh		struc_freesurfer2fsl_roi_legion.sh
struc_freesurfer_ADNI_DOD_directory_prep.sh		struc_freesurfer_ADNI_DOD_directory_prep.sh
struc_freesurfer_FTD_directory_prep.sh		struc_freesurfer_FTD_directory_prep.sh
struc_freesurfer_directory_prep.sh		struc_freesurfer_directory_prep.sh
struc_pre_prep_legion.sh		struc_pre_prep_legion.sh
struc_pre_prep_legion_ADNIDOD.sh		struc_pre_prep_legion_ADNIDOD.sh
struc_pre_prep_legion_FTD.sh		struc_pre_prep_legion_FTD.sh
struc_precheck_prep_legion.sh		struc_precheck_prep_legion.sh
struc_removeneck.sh		struc_removeneck.sh
struc_tidy_pre_prep_legion.sh		struc_tidy_pre_prep_legion.sh

TheSharmalab/MRI