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 greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@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" <greve@nmr.mgh.harvard.edu <mailto:greve@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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@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. 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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