'$' - indicates shell commands

'dir' - refers to the directory where the study data is found (ex. /jet/aguirre/CrossModal)

'new subject' - the subject you are currently analyzing (ex. X111111X)

'old subject' - a subject that has been analyzed previously (ex. X000000X)

Follow steps found on Preprocessing wiki

Use /jet/aguirre/CrossModal/PrepScripts/VBPs/'old subject'.vbp & /jet/aguirre/CrossModal/PrepScripts/VBPs/Stock_CMP_Prep_new.vbp/

[Or else, use vb2tes [folder name for images] [folder name.tes] wto manually create a .tes file for the perfusion scan and the reference perfusion scan

$cd 'dir'/'new subject'/Perf

$idl

$@vs

$@ /home/jwang/idl/perf

$ .run /home/jwang/idl/trio_perfms_nomoco_psc

  T1b = (default is 1650ms): 1650
  pls input imaging time for each slice (ms) : 60
  Enter the post tagging delay in ms : 1200
  Enter the tagging duration in ms : 1500

• The older script was:

$ .run /home/jwang/idl/trio_pasl_moco

When asked to select the "perf .tes file" choose lower numbered ms.tes scan (non-motion corrected) in the right side window
When asked to select the "M0.cub file" choose lower numbered M0.tes file in the right side of the window

$ Enter the post tagging delay in ms: 1200 (may be diff. for diff. study) This will take approx. 2 minutes to finish

$ exit

Output images will appear during the above process and will resemble the images shown below:

$cd 'dir'/'new subject'/Perf $vb2imgs *pf.tes cbf

This creates the following files within a CBF directory:

• cbf000.hdr & cbf000.img - raw perfusion (reference subtracted)
• cbf001.hdr & cbf001.img - quantitative cbf (units ml/min/100g)
• cbf002.hdr & cbf002.img - t1 image
• cbf003.hdr & cbf003.img - raw perfusion (reference unsubtracted)

$cd 'dir/PrepScripts/CoRegCBF_Scripts

$cp “old subject”_CoRegNorm_CBF.vbp “new subject”_CoRegNorm_CBF.vbp

$emacs “newsubject”_CoRegAll.vbp

• replace string: “previous subject” with “new subject”
• check line 34 — .tes file should have the name of the *ms.tes file that remains in the Perf folder

$vbprep “newsubject”_CoRegAll.vbp

Output will be:

1) 4 hdr & img files in 'dir'/'new subject'/Perf/cbf/
2) “nQuantCBF_CoReg.cub" in Anatomy/ 
3) 6 RawPerf files, Functional.hdr, & Functional.img in 'dir'/'new subject'/Perf 

To view "nQuantCBF_CoReg.cub" load as you would for functional data and use a threshold of ~95.0