Dear all, I've been having issues with my fieldsign images all I get are speckles. I did the following and did not get any errors:
1) ran recon-all -all 2) cut and saved occipital patches (rh.occip.patch.3d) from inflated surface 3) ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d rh.occip.patch.flat 4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 paradigm rtopy.par -nskip 4 fwhm 0 5) selxavg3-sess -a rtopy.self.rh -s sj09 6) fieldsign-sess -a rtopy.self.rh -occip -s sj09
When I looked at the fieldsign map using: 7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign
all I got were blue and red speckles. The polar and eccentricity maps seemed ok.
Any help would be great.
Michelle
Hi Michelle, do the eccen and polar maps look ok? Also, I would probably smooth them a little bit. The field sign calculation is basically a spatial derivative so it can be sensitive to noise. doug
Michelle Umali wrote:
Dear all, I've been having issues with my fieldsign images all I get are speckles. I did the following and did not get any errors:
- ran recon-all -all
- cut and saved occipital patches (rh.occip.patch.3d) from inflated surface
- ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d rh.occip.patch.flat
4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 paradigm rtopy.par -nskip 4 fwhm 0 5) selxavg3-sess -a rtopy.self.rh -s sj09 6) fieldsign-sess -a rtopy.self.rh -occip -s sj09
When I looked at the fieldsign map using: 7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign
all I got were blue and red speckles. The polar and eccentricity maps seemed ok.
Any help would be great.
Michelle _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, The eccen and polar maps look ok, although activation tends to be limited to the occipital poles and lateral surface not really along the calcarine.
Is it possible to find out how the colors in the eccen and polar images correspond to positions in the stimulus using rtview? There's no legend.
Thanks. Michelle
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Michelle, do the eccen and polar maps look ok? Also, I would probably smooth them a little bit. The field sign calculation is basically a spatial derivative so it can be sensitive to noise. doug
Michelle Umali wrote:
Dear all, I've been having issues with my fieldsign images all I get are speckles. I did the following and did not get any errors:
- ran recon-all -all
- cut and saved occipital patches (rh.occip.patch.3d) from inflated surface
- ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d
rh.occip.patch.flat 4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 paradigm rtopy.par -nskip 4 fwhm 0 5) selxavg3-sess -a rtopy.self.rh -s sj09 6) fieldsign-sess -a rtopy.self.rh -occip -s sj09
When I looked at the fieldsign map using: 7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign
all I got were blue and red speckles. The polar and eccentricity maps seemed ok.
Any help would be great.
Michelle _______________________________________________ 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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
are you sure it's registered well to the anatomical/surface? On Thu, 7 Jul 2011, Michelle Umali wrote:
Hi Doug, The eccen and polar maps look ok, although activation tends to be limited to the occipital poles and lateral surface not really along the calcarine.
Is it possible to find out how the colors in the eccen and polar images correspond to positions in the stimulus using rtview? There's no legend.
Thanks. Michelle
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Michelle, do the eccen and polar maps look ok? Also, I would probably smooth them a little bit. The field sign calculation is basically a spatial derivative so it can be sensitive to noise. doug
Michelle Umali wrote:
Dear all, I've been having issues with my fieldsign images all I get are speckles. I did the following and did not get any errors:
- ran recon-all -all
- cut and saved occipital patches (rh.occip.patch.3d) from inflated surface
- ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d
rh.occip.patch.flat 4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 paradigm rtopy.par -nskip 4 fwhm 0 5) selxavg3-sess -a rtopy.self.rh -s sj09 6) fieldsign-sess -a rtopy.self.rh -occip -s sj09
When I looked at the fieldsign map using: 7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign
all I got were blue and red speckles. The polar and eccentricity maps seemed ok.
Any help would be great.
Michelle _______________________________________________ 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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Michelle Umali