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vmrspmcoreg [2010/06/22 21:58] (current)
jochen created
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 +====== vmrspmcoreg ======
 +===== Motivation =====
 +The main motivation for this function is to cross-check BrainVoyager'​s registration quality with that of SPM (once again cross-checked with manual inspection, of course).
 +===== Requirements =====
 +For this function to work, either SPM5 or SPM8 must be available on the path. For SPM8, it is important that all required subfolders (e.g. matlabbatch,​ etc.) are already on the path. If in doubt, use ''​spm fmri''​ prior to calling this function (this call adds all required sub-folders of SPM to the path).
 +Also, Matlab must have write access to the temporary folder (on Unix-ish systems, that usually is ''/​tmp''​) to write out the VMRs as Analyze files.
 +W.r.t. to the VMRs, you must have two objects loaded which you want to bring into the same space (whereas the reference/​secondary VMR is the stationary one!)
 +===== Function reference ('help vmrspmcoreg'​) =====
 +<​file> ​ vmrspmcoreg ​ - apply SPM's coregistration to two VMRs
 +  FORMAT: ​      ​vmrtrf = vmrspmcoreg(srcvmr,​ refvmr)
 +  Input fields:
 +        srcvmr ​     VMR to coregister (primary VMR)
 +        refvmr ​     reference (stationary/​secondary VMR)
 +  Output fields:
 +        vmrtrf ​     BV compatible TRF object</​file>​
 +===== Notes =====
 +These are the steps taken by vmrspmcoreg:​
 +  * load the required batch/job file for the available SPM version
 +  * write both VMRs as Analyze files (using the [[vmr.WriteAnalyzeVol]] method)
 +  * putting the two filenames into the job
 +  * passing control to SPM's job manager
 +  * read back the Analyze file headers
 +  * delete the temporary Analyze files
 +  * determine the required transformation (incl. taking care of origin difference)
 +  * create TRF object and settings all required fields
 +===== Example =====
 +For an example, check the reference page of [[vmr.ApplyTRF]],​ which also explains how to then apply the obtained TRF object to actually re-sample the source VMR into the target space.
vmrspmcoreg.txt ยท Last modified: 2010/06/22 21:58 by jochen