Dear Freesurfers, I've been troubleshooting my bizarre looking fieldsign data. I ran bbregister for my polar and eccentricity images, then re-ran the retinotopy analysis. The data still look the same. The fieldsign image is still a mass of blue and red speckles.
Any tips on how I should proceed?
Thanks. Michelle
Hi Michelle, to troubleshoot these kind of things, it's best to start at the early parts of the stream and work your way forward. Eg, is there a lot motion in any of the functional runs? What does the map look like when you view it in the volume instead of on the surface? Also, it is very helpful to know what commands you ran.
doug
On 8/2/11 8:52 PM, Michelle Umali wrote:
Dear Freesurfers, I've been troubleshooting my bizarre looking fieldsign data. I ran bbregister for my polar and eccentricity images, then re-ran the retinotopy analysis. The data still look the same. The fieldsign image is still a mass of blue and red speckles.
Any tips on how I should proceed?
Thanks. Michelle _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Freesurfers, I'm troubleshooting my retinotopy data and am still having issues with wonky fieldsign data. The registration looked ok, so now I am trying to look at the retinotopy results using rtview. I got an error message saying it can't find the register.dof6.dat file. So, now I am stepping back to the beginning. Below are the commands I used for the analysis.
-Does one need to specify starting position of wedge/size of wedge?
Any help would be greatly appreciated. Michelle _____________ Here are the commands I used:
recon-all -all ld09
tksurfer sj09 lh inflated and then for rh. Then I cut occipital patches.
Then I registered the eccen and polar f.nii files: bbregister --s ld09 --mov f.nii --init-fsl --reg register.dat tkregister2 --mov f.nii --reg register.dat --surf mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj09 -force selxavg3-sess -a rtopy.self.lh -s sj09 selxavg3-sess -a rtopy.self.rh -s sj09 fieldsign-sess -a rtopy.self.lh -occip -s sj09 fieldsign-sess -a rtopy.self.rh -occip -s sj09
How do the eccen and polar look by themselves? You can look at them with tksurfer-sess doug
Michelle Umali wrote:
Hi Freesurfers, I'm troubleshooting my retinotopy data and am still having issues with wonky fieldsign data. The registration looked ok, so now I am trying to look at the retinotopy results using rtview. I got an error message saying it can't find the register.dof6.dat file. So, now I am stepping back to the beginning. Below are the commands I used for the analysis.
-Does one need to specify starting position of wedge/size of wedge?
Any help would be greatly appreciated. Michelle _____________ Here are the commands I used:
recon-all -all ld09
tksurfer sj09 lh inflated and then for rh. Then I cut occipital patches.
Then I registered the eccen and polar f.nii files: bbregister --s ld09 --mov f.nii --init-fsl --reg register.dat tkregister2 --mov f.nii --reg register.dat --surf mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj09 -force selxavg3-sess -a rtopy.self.lh -s sj09 selxavg3-sess -a rtopy.self.rh -s sj09 fieldsign-sess -a rtopy.self.lh -occip -s sj09 fieldsign-sess -a rtopy.self.rh -occip -s sj09
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So when viewing with tksurfer I am assuming that -map angle shows the polar data. It looks ok. There's a lot of yellow and red, which I am assuming is the overall significance and not significance by position yes?
tksurfer-sess -a rtopy.self.lh -s sj09 -map angle
To view eccen data, is it -map eccen?
thanks. michelle
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
How do the eccen and polar look by themselves? You can look at them with tksurfer-sess doug
Michelle Umali wrote:
Hi Freesurfers, I'm troubleshooting my retinotopy data and am still having issues with wonky fieldsign data. The registration looked ok, so now I am trying to look at the retinotopy results using rtview. I got an error message saying it can't find the register.dof6.dat file. So, now I am stepping back to the beginning. Below are the commands I used for the analysis.
-Does one need to specify starting position of wedge/size of wedge?
Any help would be greatly appreciated. Michelle _____________ Here are the commands I used:
recon-all -all ld09
tksurfer sj09 lh inflated and then for rh. Then I cut occipital patches.
Then I registered the eccen and polar f.nii files: bbregister --s ld09 --mov f.nii --init-fsl --reg register.dat tkregister2 --mov f.nii --reg register.dat --surf mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj09 -force selxavg3-sess -a rtopy.self.lh -s sj09 selxavg3-sess -a rtopy.self.rh -s sj09 fieldsign-sess -a rtopy.self.lh -occip -s sj09 fieldsign-sess -a rtopy.self.rh -occip -s sj09
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