Thanks. My colours don't seem to correspond very well though - ie i see red in
dorsal occipital cortex when it should be blue, reversing doesn't help. (And btw
if freesurfer only uses 3 colours for polar presumably there will be no
difference for right and left hemispheres?).
Could the creation of 'polar' be going wrong because the fieldsign creation
didn't work? I have made an occipital patch so that can't be the problem. when i
run:
tksurfer -dorothy rh inflated -tcl mk-fieldsign.tcl
i get errors like '% can't read "name": no such variable% and 'can't read
"env(MRI_DIR)": no such variable%
i have previously run 'source Setupfreesurfer so i don't know why this is
happening.
thanks for your help
Jane
Re: [Freesurfer] retinotopy and FsFast
Stephanie McMains
Thu, 24 Nov 2005 11:51:14 -0800
The eccen should go fovea=red, parafoveal=blue, and periphery = green. If they
aren't going in that order, reverse the overlay.
the polar angle should be, blue for horizontal meridian, green for lower visual
field and red for upper visual field.
Making the fs map will also fail if you don't have a occipital patch made.
Thought that might be your trouble.....
Stephanie McMains
On Nov 24, 2005, at 12:09 PM, Jane Aspell wrote:
hi again
I have been proceeding with the retinotopy analysis using FsFast, following
the
instructions at:
https://surfer.nmr.mgh.harvard.edu/fswiki/
FsFastIndividualRetinotopyAnalysis and i believe i have successfully overlaid
the results on my surfaces and now
have two questions:
i wasn't able to create the fieldsign with 'paint-sess' because it couldn't
find tksurfer.new. when i run 'surf-sess' i use the flag -old which forces it
to use
tksurfer.old but this doesn't work in the former case. how can i make
'paint-sess' use tksurfer.old and thus create the fieldsign?
there are no instructions on how to relate the colours seen when viewing
eccen and polar to the location of the ring and wedge. is there a map somewhere
that can be loaded that tells me what order the colours run from fovea to
periphery
and from vertical to horizontal meridian etc.?
thanks again for your help!
jane
In message <[EMAIL PROTECTED]> Doug Greve
<[EMAIL PROTECTED]> writes:
>
> you should be running everything fromt the study dir. Often, your study
> dir is also the parent to the sessions. When it is not, then you need to
> supply a -d sesspar or -df sessparfile
>
> doug
>
>
> Jane Aspell wrote:
>
> >Ok, thanks.
> >It seems that the problem with finding the session came about because I was
> >running 'sfa-sess' from the 'MYSTUDY' study directory when it seems i should
> >have run it from the 'session parent' directory.
> >cheers,
> >Jane
> >
> >
> >In message <[EMAIL PROTECTED]> Doug Greve
> ><[EMAIL PROTECTED]> writes:
> >
> >
> >>that's a bug in the wiki, "-s avdk" should not appear there. Rather, it
> >>should be "-s yoursession" or "-sf sessidfile". If it cannot find the
> >>sessions, then something is not set up correctly. Can you double check
> >>that the sessions in the sessidfile are in the current directory?
> >>
> >>
> >>Jane Aspell wrote:
> >>
> >>
> >>
> >>>Hi
> >>>
> >>>Thanks for all your previous help with freesurfer.
> >>>
> >>>I am trying to use FsFast to do retinotopy analysis and have been
> >>>following the
> >>>instructions at:
> >>>https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
> >>>
> >>>I come undone at the stage of running the actual analysis, where the
> >>>command
> >>>should be:
> >>>
> >>>
> >>>
> >>>
> >>>>sfa-sess -s avdk -a rtopy
> >>>>
> >>>>
> >>>>
> >>>>
> >>>what does 'avdk' refer to? when i run it i get: ERROR: could not find
> >>>session
> >>>
> >>>
> >avdk
> >
> >
> >>>when i try it with the arguments:
> >>>
> >>>
> >>>
> >>>
> >>>>sfa-sess -analysis rtopy -sf sessid
> >>>>
> >>>>
> >>>>
> >>>>
> >>>which is similar to the arguments needed for 'selxavg-sess' i get a similar
> >>>error of not been able to find my (particular subject's) session. i
> >>>believe i
> >>>have set up the all the directory structures etc correctly for the sessions
> >>>format as previous steps worked fine.
> >>>
> >>>any ideas what's going wrong?
> >>>
> >>>thanks
> >>>
> >>>Jane Aspell
> >>>
> >>>
> >>>
> >>>_______________________________________________
> >>>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
> >>[EMAIL PROTECTED]
> >>Phone Number: 617-724-2358
> >>Fax: 617-726-7422
> >>
> >>
> >>
> >
> >
> >
> >
> >
> >
>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [EMAIL PROTECTED]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
--
Dr Jane Aspell
Department of Experimental Psychology, University of Oxford,
South Parks Road, Oxford, OX1 3UD
tel: +44 (0)1865-281606
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