Hi Julia, I don't think it looks terrible (unfortunately:). You might try increasing the smoothing level (maybe 10 fwhm). doug

On 12/12/2012 08:02 AM, Julia Foecker wrote:

Hey Doug,

thanks for your reply. I tried now the polar angle mapping for the left hemisphere and I got the figure attached.

It is difficult to see the typical polar maps in that figure and I am wondering how to change the settings so that I will receive a typical polar angle map. I had a 180 deg. wedge. One cycle took 38.4 sec. There were 8 cycles. The first 5 volumes had to be deleted. I did the follwing analysis.

mkanalysis-sess analysis rtopy.self.lh -surface self lh -TR 1.2 -retnotopy 38.4 -fsd bold -fwhm 5 -paradigm rtopy.par -tpef tp-exclude.txt

Do you have any advices what to change so that it looks more like polar angle maps?

Thanks so much for any further advices,

best Julia

On Mon, 10 Dec 2012 12:27:13 -0500 Douglas N Greve greve@nmr.mgh.harvard.eduwrote

...

Hi Julia, that command is fine. It will not use the fieldsign or eccen. doug

On 12/10/2012 10:17 AM, Julia Foecker wrote:

...

Dear Doug,

I tried version 5 with the commands suggested on the webside and this is working

(http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis)

...

...

. >

However, I have only polar angle runs and I am not sure if the rtview commands is only referring to polar angle maps (because the field signs are included and I think that they consist of eccentricity maps as well which do not have a meaning in my analysis). How do I have to change the command below so that it is just referring to polar maps?

rtview --s VGP01 --lh --polar --real polar/real.nii.gz --imag polar/imag.nii.gz --fsig polar/fsig.nii.gz

Many thanks for further suggestions, Julia

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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