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 437E113F.9070202@nmr.mgh.harvard.edu Doug Greve greve@nmr.mgh.harvard.edu 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 437CD31F.4040700@nmr.mgh.harvard.edu Doug Greve greve@nmr.mgh.harvard.edu 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422