4 Nov
2016
4 Nov
'16
7:34 a.m.
Hi,
Thank you for your reply, when I run xhemireg I get an error for cannot find aseg. is there any way to avoid that? in the way there is a noaseg flag for other commmands. I built a cortical Atlas and dont have subcortical labels
Thank you ,
Daiana
Daiana Pur
On Wed, Nov 2, 2016 at 2:48 PM -0400, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
oh, sorry, it does assume that you have pbsubmit, I had forgotten that. You can actually follow the instructions for building your own atlas at the bottom of the xhemi web page
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
This does the same thing as make_folding_atlas. It takes a long time if you don't have a computational cluster to submit it to, which is why I wrote make_folding_atlas
doug
On 11/02/2016 01:15 PM, Daya P wrote:
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
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 > >> 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" >> >> 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 >> > >> >> >> 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 >> > >> > >> >> >>> 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 >> > >> >> >> >> > >> 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. >> > >> > >> > >> > >> > _______________________________________________ >> > 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 >> greve@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 >> > >> >> >> >> _______________________________________________ >> 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. > > _______________________________________________ > 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 greve@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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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/
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