Thank you! Does this mean that an older glm would have still used fsaverage for the "common surf" but then the output is mapped to the target? Outputs from older glms load no problem on the targets, and look "as expected"
Aka would you expect a major difference in glmfit outputs with old mris_preproc reg vs new mris_preproc reg?
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, May 31, 2016 12:47 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc - srcsubjreg
Sorry for the delay. This is because sphere.reg only applies to fsaverage. Previously, the specification of a different target would only influence smoothing done as part of mris_preproc; the registration would still be done to fsaverage. This is probably not the intent of people who are specifying a target, so I changed mris_preproc to require a targets-specific registration. You can generate this with
surfreg --s subject --t target
then run mris_preproc specifying the given target doug
On 05/24/2016 04:23 PM, Makaretz, Sara Johanna wrote:
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
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