These are generic image analysis scripts that I have written, collected, and otherwise given cobbled-together life to through much trial and error during my time at MUSC in the BRIDGE Lab. Versions of these scripts can be found in various studies' "STUDY_code" BIDS folders. These are here as a log/reference do the most basic, generic forms of these scripts, not modified for any particular study's analysis pipeline.

www.bridge-lab.org
www.bridgelab.info

Script Documentation

Preprocessing

Standard PyDesigner processing:

/path/to/pyd_preproc.sh --base /path/to/BIDS_folder

ViSTa processing:

python /path/tovista.py \
    /path/to/vista.nii /path/to/reference.nii /path/to/output/

Registration

Integrated DTI-TK and TBSS with optional ROI Analysis:

# 1_DTI-TK.sh
   /path/to/1_DTI-TK.sh \
      --input /path/to/dki_pydesigner \
      --output /path/to/dti-tk \
      --subjects sub-101 sub-104 sub-110 \
      --bet-thr 0.25

# 2_TBSS.sh
   /path/to//2_TBSS.sh \
      --input /path/to/derivatives/dti-tk \
      --output /path/to/derivatives/tbss \
      --subjects sub-101 sub-104 sub-110 \
      --wmmets    

# 3_Stats.sh
   /path/to//3_StatsS.sh \
      coming soon!    

Segmentation

Freesurfer recon-all -all Segmentation:

    /path/to/freesurfer-reconall.sh \
       --input /path/to/T1s \
       --output /path/to/freesurfer_output \
       --subjects A001 A002 A003

NOMIS Normalization:

    /path/to/FS_NOMIS.sh \
       --base /base/derivatives/freesurfer \
       --csv /path/to/PUMA_norms.csv \
       --nomis /path/to/NOMIS.py \
       --output /base/derivatives/nomis \
       --env [name of nomis conda env]

Lesion Segmentation Tool:

    /path/to/run_lst.sh /path/to/raw_data_ /path/to/Outputs 

Native Space Analysis

TractSeg:

Requires manual script edits at the moment; automation coming soon.

Gross White Matter Estimation:

    /path/to/gross_wm_thr.sh /path/to/base_dir /path/to/out_dir /path/to/output.csv 

PET and MRS

Centiloid Processing:

MRS T1 Mask Conversion:

    python MRS_T1_Mask.py mrs_complex_nifti t1_nifti output_mask>

Miscellaneous

Converting a complex NiFTi to a FLOAT23 NiFTi:

    python convert_complex_to_float.py input.nii output.nii