I went to the shell script and changed the input for aparc+aseg and aseg. and managed to make it work.
My other question is that now that I have it running, after it is done I would like to run a vertex wise analysis. Is there a tutorial/help or command that I should apply to do asymmetry analysis. I was looking at the group analysis and setting GLM for thickness and age. How could I do that with the results of xhemi for asymmetry in left and right hemisphere? Thank you for you help! > On Nov 4, 2016, at 10:31 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote: > > Try adding --zilles --reg > > It is a hack, but it might just work > > > On 11/04/2016 07:34 AM, daianapu...@gmail.com <mailto:daianapu...@gmail.com> > wrote: >> >> 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" >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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 >> <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 >> <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 >> <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 >> <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 <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 > > > >> 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 > >> 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 > > > >>>>> _______________________________________________ > 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 >> >> >> >> _______________________________________________ >> 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 > Fax: 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>
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