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nichols/ukb_unconfound_v2:Update_bash_scripts into master
Open Tom Nichols requested to merge nichols/ukb_unconfound_v2:Update_bash_scripts into master
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README.md
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@@ -21,8 +21,9 @@ These html files are also generated with the scripts in `confound_processing`.
* Activate [bb_python](https://git.fmrib.ox.ac.uk/falmagro/UK_biobank_pipeline_v_1/blob/master/bb_python/python_installation/install_bb_python.sh) virtual env.
* Adapt the script [init_vars](https://git.fmrib.ox.ac.uk/falmagro/UK_biobank_pipeline_v_1/blob/master/init_vars) to your system configuration and source it.
* Add `sh_utils` directory to `$PATH`
* Change `$subjDir` with the absolute path to the directory of all UKB subjects (a file `subj.txt` is needed as an index in that directory).
* Set `$subjDir` to the absolute path to the directory of all UKB subjects (a file `subj.txt` is needed as an index in that directory).
* Each subject in `$subjDir` needs to be in UKB directory format. A DICOM directory is needed for each subject with the `*.txt` and `*.dcm` generated by FBP
* Set `$SUBJECTS_DIR` to the absolute path to the directory of all UKB subjects Freesurfer results (a file `subj.txt` is needed as an index in that directory).
* Change $MATLAB_BIN to the appropriate Matlab binary
# Dependencies