[Freesurfer] mris_preproc - srcsubjreg
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" 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 >> >> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_preproc - srcsubjreg
Hi Doug, still wondering about this - thanks! From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara Johanna [smakar...@mgh.harvard.edu] Sent: Tuesday, May 24, 2016 16:23 To: Freesurfer support list Subject: [Freesurfer] mris_preproc - srcsubjreg 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" 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 >> >> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_preproc - srcsubjreg
I'm actually curious about this as well! Best, Panos > Hi Doug, still wondering about this - thanks! > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara > Johanna [smakar...@mgh.harvard.edu] > Sent: Tuesday, May 24, 2016 16:23 > To: Freesurfer support list > Subject: [Freesurfer] mris_preproc - srcsubjreg > > 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" 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 >>> >>> >>> >>> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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" 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 >>> >>> >>> >>> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_preproc - srcsubjreg
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@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" 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 >>> -
Re: [Freesurfer] mris_preproc - srcsubjreg
I would not expect the glm to change much, but the activation might shift around a little depending upon your new target. On 6/1/16 11:18 AM, Makaretz, Sara Johanna wrote: > 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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@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" 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 >&g
