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 greve@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, daianapur94@gmail.com mailto:daianapur94@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" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto: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 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 > >> > > >> > > >> > > >> >
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