Merge branch 'master' of github.com:ajoshiusc/USCCleveland

process_script/README.md

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+# README
+
+`brainsuite_process_all.exe` is a script written for automating the workflow for Cleveland clinic. 
+To run the workflow, make sure that the following three files are in the same directory.
+* brainsuite_process_all.exe
+* config_brainsuite.ini
+* t1list.txt
+
+A sample of these three files can be downloaded with the release.
+[Release_V1](https://github.com/ajoshiusc/USCCleveland/releases/tag/brainsuite_process_v1)
+
+
+once all three files are in a directory, simply execute the `brainsuite_process_all.exe`. The executable will do the following for each T1 file:
+1. read list of T1 images from  `t1list.txt`
+2. read path of brainsuite from `config_brainsuite.ini`
+3. Resample T1 images to 1mm cubic voxels are rename them to MRI_1mm.nii.gz
+4. If the T1 files are not on `C:`, copy them to a temp directory, execute the entire brainsuite sequence, copy back the files to original location and delete the temp dir.
+5. Run BrainSuite cortical extraction sequence
+6. Run SVReg sequence using USCBrain atlas
+
+
+The entire sequence takes about 1.5 hrs per subject, so please be patient.
+
+If you have any questions, please email me Anand Joshi ([email protected]).