Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as the default srcsurfreg when the target is not fsaverage - see below
Thanks for any info! (not urgent)
On 2016-5-24, 11:30, "Z K" zkaufman@nmr.mgh.harvard.edu wrote:
Good question, and I dont know the answer. mris_preproc is Dougs baby so I suggest just posting this question to the list with "mris_preproc" in the subject, and I bet he will give you the answer.
-Zeke
On 05/23/2016 10:31 PM, Makaretz, Sara Johanna wrote:
Hi Zeke,
I am running some surface glms where targ is a patient surface. The help says --target TargetSubject (requires ?h.TargetSubject.sphere.reg), and I was getting errors because dev-default mris_preproc wanted mri_surf2surf to have srcsurfreg = $SUBJECTS_DIR/$srcsubject/surf/$h.$TARGSUBJ.sphere.reg
But mris_preproc in 5.3 let me do target = patient surface with no extra surf reg files or extra flags to get mri_surf2surf to use srcsurfreg = $SUBJECTS_DIR/$srcsubject/surf/$h.sphere.reg
I had been running this with 5.3: mris_preproc \ --target $TARGSUBJ \ --hemi lh \ --meas thickness \ --fsgd file.fsgd \ --out lh.output.mgh
And I was about to email freesurfer@nmr but "for fun" tried adding --surfreg sphere.reg which got mris_surf2surf to use the right reg files. So now I'm selfishly trying to figure this out - do you know what prompted the switch from sphere.reg "opt-out" to sphere.reg "opt-in"? Aka why sphere.reg is non-default when the target is non-fsaverage? Did that make sense? I know there must be some reason, so I really want to know a bit more so I can stay sane when old scripts break.
Thanks for any info! Sorry to bother you! Sara
Outputs from the FS-dev one:
$Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $ .... Src lh $TARGSUBJ.sphere.reg Trg lh sphere.reg .... mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg $TARGSUBJ.sphere.reg --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg sphere.reg --etcetcetc .... ERROR can't find $SUBJECTS_DIR/$SRCSUBJ/surf/$TARGSUBJ.sphere.reg because I never made it
Outputs from the FS-dev one with fsaverage as the targ subj:
$Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $ .... Src lh sphere.reg Trg lh sphere.reg .... mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --etcetcetc .... mris_preproc finds everything, runs no problem
Outputs from the FS-5.3 one:
$Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ .... Src lh sphere.reg Trg lh sphere.reg .... mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg sphere.reg --etcetcetc .... mris_preproc exits with no errors because everything exists