Hi, When i try running make_folding_atlas I get
xhemireg Trout2016 Wed Nov 2 13:11:23 EDT 2016 #@# xhemireg --s Trout2016 pbsubmit: Command not found. Launched 9 xhemireg processes #%# Waiting for 9 xhemireg processes Wed Nov 2 13:11:33 EDT 2016 #%# Waiting for 9 xhemireg processes Wed Nov 2 13:12:33 EDT 2016 I do not have access to a cluster. is there any way to bypass this? Thank you, Daiana On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > I've written a script that will come out with version 6, but I've put it > here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas > > I think it should work in 5.3, but I'm not sure. If not, you can > download the dev version and make the atlas using that. Run it with > --help to get info on how to run it. > > > > On 10/28/2016 05:10 PM, Daya P wrote: > > Hi Doug, > > > > I needed to make a registration template and an cortical atlas because > > I am trying to measure cortical thickness, GM and surface area on cat > > brains. > > > > What would be the necessary changes? > > Would it be possible (and appropriate) to use just > > mris_left_right_register instead? > > > > Daiana > > > > On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > A difference of 10 out of 500 or 1000 does not both me at all. Why > > do you need to create your own atlas? It is doable for the cross > > hemi stuff, it is just difficult. > > > > > > On 10/26/16 10:16 AM, Daya P wrote: > >> > >> Thank you for your help! > >> > >> I created a registration template and atlas from scratch could I > >> input that in the interhemispheric registration analysis? > >> > >> The ROIs for the diffrerent regions per hemisphere are 50-100 > >> vertices > >> > >> On Oct 24, 2016 5:03 PM, "Douglas N Greve" > >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > wrote: > >> > >> It would depend on how big the ROI is to begin with. Do you > >> know that we > >> have our own interhemispheric analysis that might be better > >> for this? > >> Check out > >> > >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> > >> > >> > >> On 10/24/2016 12:33 PM, Daya P wrote: > >> > Hi Bruce, > >> > > >> > I drew ROIs on an initial subject and then after > >> registering all other > >> > subjects to the initial one, used mri_label2label to map > >> the ROIs from > >> > the initial subject to subsequent ones. > >> > I am interested in looking at asymmetry between left and > >> right regions. > >> > > >> > I had two concerns, one that the ROIs have different # > >> vertices on > >> > different subjects, but as you mentioned the nonlinear > >> process makes > >> > sense, since each subject does not have the exact same > >> brain size and > >> > curvature. > >> > > >> > Another concern was that the ROIs on the left and right > >> hemisphere in > >> > a subject do not have the exact same number of vertices. > >> Would a > >> > difference of 10 vertices max bias results? > >> > > >> > Thank you for your help, > >> > > >> > Daiana R. Pur > >> > Research Assistant > >> > Canadian Surgical Technologies & Advanced Robotics > >> > Brain and Mind Institute > >> > Western University > >> > London, ON, N6A 5B7 > >> > Canada > >> > > >> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl > >> > <fis...@nmr.mgh.harvard.edu > >> <mailto:fis...@nmr.mgh.harvard.edu> > >> <mailto:fis...@nmr.mgh.harvard.edu > >> <mailto:fis...@nmr.mgh.harvard.edu>>> wrote: > >> > > >> > Hi Daiana > >> > > >> > yes, that is to be expected given the nonlinear nature > >> of the > >> > cross-subject registration. It shouldn't bias things, > >> although > >> > you'll need to give us more details if you want a more > >> definitive > >> > answer. > >> > > >> > cheers > >> > Bruce > >> > > >> > > >> > > >> > On Mon, 24 Oct 2016, Daya P wrote: > >> > > >> > Hi All, > >> > > >> > My question is about using mri_label2label. When > >> mapping the > >> > labels from one > >> > subject to another the number of vertices of each > >> ROI is > >> > different. Is that > >> > something to be expected? > >> > > >> > How much of a difference does a number of vertices > >> of 50 > >> > compare to 40 have > >> > on measures like thickness, grey matter and surface > >> area? > >> > > >> > I would really appreciate some help > >> > > >> > Thank you, > >> > > >> > Daiana R. Pur > >> > Research Assistant > >> > Canadian Surgical Technologies & Advanced Robotics > >> > Brain and Mind Institute > >> > Western University > >> > London, ON, N6A 5B7 > >> > Canada > >> > > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >> > > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> <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 > >> <http://www.partners.org/complianceline> > >> > <http://www.partners.org/complianceline > >> <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. > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > >> Phone Number: 617-724-2358 <tel:617-724-2358> > >> Fax: 617-726-7422 <tel:617-726-7422> > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> <https://gate.nmr.mgh.harvard.edu/filedrop2> > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> Outgoing: > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > _______________________________________________ Freesurfer mailing > > list Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <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. > > > > _______________________________________________ > > 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 >
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