[Freesurfer] cannot configure overlay in tksurfer
Hi all,
I'm trying to overlay some cortical thickness correlation maps onto
a freesurfer surface, and when I select configure->overlay from the
toolbar, an error message pops up stating:
bad window path name ".wwConfigOverlayDisplayDlog.fwFlags.cbwReverse"
bad window path name ".wwConfigOverlayDisplayDlog.fwFlags.cbwReverse"
while executing
"grid $cbwReverse -column 2 -row 1 -stick w"
(procedure "DoConfigOverlayDisplayDlog" line 126)
invoked from within
"DoConfigOverlayDisplayDlog"
invoked from within
".w.fwMenuBar.mbwView.mw.cmw5 invoke active"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke active]"
(procedure "tk::MenuInvoke" line 47)
invoked from within
"tk::MenuInvoke .w.fwMenuBar.mbwView.mw.cmw5 1"
(command bound to event)
I'm using banzai and am working in the dev environment. If anyone can
help me out, that would be great, thanks!
-Eric
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Re: [Freesurfer] FS-FAST registration across sessions
You can try putting all the runs into a single bold directory. The motion correction will (do it's best to) align them. doug Jane Aspell wrote: Hi My question was asked last year by Tommi Raij (see email pasted below) but I couldn't find a reply to it in the archives. I am analysing retinotopy data that was collected over several sessions but I cannot see how to register scans from multiple sessions together, and to the subject's anatomical scan. Although Fs-Fast appears to combine the data from multiple sessions during the retinotopy analysis it only seems to be possible to use one registration file (register.dat) when overlaying the results onto the anatomical. I would have thought that registering scans from multiple sessions together would be a feature that many people would require. Is there anyway to do it? Tommi gives some possible methods in his email below. When I do try and overlay my data onto a surface I see 'gaps' in the blue/yellow colouring of the fieldsign map overlaid onto the cortical surface. I wonder if this could be due to the inaccuracy of the registration given that I only used the register.dat from the registration of the first session. hope that makes sense! i'd be grateful for any help with this! Jane -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] notes on Jan 2006 release
Dear all, In the notes on the Jan 2006 release it was mentioned that the subcortical atlas is built from the Siemens scans, and thus might not be reliable for GE scans. How might this subcortical atlas handle data aqcuired on a Philips scanner? thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] notes on Jan 2006 release
Hi Sasha, in the newest version of the aseg we've made a lot of progress on this front, and labeling across different platforms is pretty much comparable to labeling on the same platform. cheers, Bruce On Mon, 23 Jan 2006, Sasha Wolosin wrote: Dear all, In the notes on the Jan 2006 release it was mentioned that the subcortical atlas is built from the Siemens scans, and thus might not be reliable for GE scans. How might this subcortical atlas handle data aqcuired on a Philips scanner? thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ 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
Re: [Freesurfer] notes on Jan 2006 release
Can the aseg from the current dev release (Oct 3rd, 2005) be used to get subcortical measurements from data acquired on Philips scanner? Or is the new aseg only available in the upcoming release? Thanks, Sasha >>> Bruce Fischl <[EMAIL PROTECTED]> 1/23/2006 2:42 pm >>> Hi Sasha, in the newest version of the aseg we've made a lot of progress on this front, and labeling across different platforms is pretty much comparable to labeling on the same platform. cheers, Bruce On Mon, 23 Jan 2006, Sasha Wolosin wrote: > Dear all, > > In the notes on the Jan 2006 release it was mentioned that the > subcortical atlas is built from the Siemens scans, and thus might not be > reliable for GE scans. How might this subcortical atlas handle data > aqcuired on a Philips scanner? > > thanks, > Sasha > > > > Disclaimer: > The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. > ___ > 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
Re: [Freesurfer] notes on Jan 2006 release
it can be, but the new one will be more accurate On Mon, 23 Jan 2006, Sasha Wolosin wrote: Can the aseg from the current dev release (Oct 3rd, 2005) be used to get subcortical measurements from data acquired on Philips scanner? Or is the new aseg only available in the upcoming release? Thanks, Sasha Bruce Fischl <[EMAIL PROTECTED]> 1/23/2006 2:42 pm >>> Hi Sasha, in the newest version of the aseg we've made a lot of progress on this front, and labeling across different platforms is pretty much comparable to labeling on the same platform. cheers, Bruce On Mon, 23 Jan 2006, Sasha Wolosin wrote: Dear all, In the notes on the Jan 2006 release it was mentioned that the subcortical atlas is built from the Siemens scans, and thus might not be reliable for GE scans. How might this subcortical atlas handle data aqcuired on a Philips scanner? thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ 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
FW: [Freesurfer] overlay thickness maps
-Original Message- From: Kirk, Gregory Sent: Monday, January 23, 2006 4:25 PM To: 'Kevin Teich' Subject: RE: [Freesurfer] overlay thickness maps Yes Kevin, im still a dum dum sometimes, as your comment I Looked it in shell window, and saw all was not well. In response to Load-Overlay-> load lh.thickness from the subject surf/ Directory get errors % surfer: needs at least 2 marked vertices % surfer: needs at least 2 marked vertices % surfer: needs at least 2 marked vertices % mri_read(): couldn't determine type of file /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/THORNTONH/sur f/lh.thickness surfer: couldn't load /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/THORNTONH/sur f/lh.thickness sclv_read_from_volume: error in MRIreadInfo. The overlays that are loaded in the buckner are .mgz files and it does not seem happy with these Doug Greve is the winner in our best suggestion category with Another method is to use mri_surf2surf to to convert the curv file into an mgh file (run it with --help to see how to use it). Then just load the mgh file as an overlay (with "compute identity"). Which when applied with- and the output is- [EMAIL PROTECTED] surf]$ mri_surf2surf --hemi lh --srcsubject MASONO --srcsurfval thickness --src_type curv --trgsubject MASONO --trgsurfval lh.thickness.mgz --trg_type mgz srcsubject = MASONO srcval = thickness srctype= curv trgsubject = MASONO trgval = lh.thickness.mgz trgtype= mgz surfreg= sphere.reg hemi = lh frame = 0 fwhm-in= 0 fwhm-out = 0 Reading source surface reg /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/MASONO/surf/l h.sphere.reg Loading source data Reading curvature file /home/gkirk/freesurfer-new/freesurfer/subjects/sickle_cell/MASONO/surf/l h.thickness INFO: trgsubject = srcsubject Saving target data Reshaping 2 (nvertices = 107662) Gives .mgz files that surfer is happy to use as an overlay, and produces what looks like good Thickness maps. Thanks all Greg. -Original Message- From: Kevin Teich [mailto:[EMAIL PROTECTED] Sent: Friday, December 23, 2005 5:33 PM To: Kirk, Gregory Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] overlay thickness maps There are a couple things that could be wrong. Make sure that calculating an identity registration is the proper thing to be doing here. Doug can probably tell you more about this. Next, is the file actually loading? Make sure that the output to the shell doesn't have any errors, and that there's a new line in the label/value area with the overlay's name on it. Make sure that there are actually values in that line as you move the mouse aroudn over the surface. If there are, do View->Configure->Overlay and see if you can set the threshold so that it encompasses the values, as the default threshold might be incorrect. On Fri, Dec 23, 2005 at 03:42:31PM -0500, Kirk, Gregory wrote: > > I would like to overlay lh.thickness, rh.thickness on inflated for > single subject, not the glm results, how to do that is well documented > from the tutorial/tutorial group study > > > tried tksurfer subject lh inflated - got the gray surface > > next file->load overlay -> $SUBJECTS_DIR/subject/surf choose > lh.thickness > * calculate identity map > > it redraws the surface but there is no colormap of the thickness -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
