Hi Doug, I've already smoothed by 5 during preproc-sess, so does this mean I should do additional smoothing during fieldsign-sess step?

Also, is this the correct command to use the sphere and not the patch: fieldsign-sess -a rtopy.self.lh -fwhm 5 -sphere -s sj09

Thanks. Michelle

Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:

Try smoothing (eg, -fwhm 5) when running fieldsign-sess. You can also try using the sphere instead of the occip patch. doug

Michelle Umali wrote:

...

Hi Doug,

Thanks again for your advice, the heat maps look much better. However, they still do not visualize the continuous range of angles or eccentricities but rather divide it into two intervals such as red vs. blue. Is there any way to adjust the color range to make it more appropriate for this kind of data?

The heat map for the field sign data still looks speckled. I attached an image showing the heat maps for polar angle, eccentricity, and field sign, with the corresponding overlay settings.

I used 5mm smoothing.

Thank you very much, Michelle

Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:

...

The activation looks pretty reasonable. As you point out, the angles are a mess. How did you set the color scale for the angles? You should leave it as a heat scale (if you're using tksurfer-sess). How much did you smooth?

doug

Michelle Umali wrote:

...

Hi Doug, Attached is a pic of the significance and angle maps for polar and eccen.

What do you think?

Thanks. Michelle

Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:

...

what does the activation look like? Does it look right? Can you send a pic? doug

Michelle Umali wrote:

...

Hi Doug, The z-values are consistently near or greater than 4. It just seems that the visualization of the angles is somehow incorrect...

Is there be anything else that I need to check?

Thanks. 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

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-- 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

Hi Doug, So I did the additional smoothing and the map looks better.. It's still hard to interpret though. I was expecting alternating red and blue bands to signify V1/V2/V3 boundaries, but it's very irregular with red curves running every which way into blue splotches. Do you have any suggestions how to interpret this?

So then I just looked at the automatic parcellation of V1 and V2, which seems very different from the actual fieldsign results.. The boundaries overlap quite a bit, which seems odd. How should I treat the overlap?

Thanks for your help. Michelle

Alsouoting Douglas N Greve greve@nmr.mgh.harvard.edu:

Michelle Umali wrote:

...

Hi Doug, I've already smoothed by 5 during preproc-sess, so does this mean I should do additional smoothing during fieldsign-sess step?

Try the additional one now to see if it fixes the map.

...

Also, is this the correct command to use the sphere and not the patch: fieldsign-sess -a rtopy.self.lh -fwhm 5 -sphere -s sj09

yes doug

...

Thanks. Michelle

Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:

...

Try smoothing (eg, -fwhm 5) when running fieldsign-sess. You can also try using the sphere instead of the occip patch. doug

Michelle Umali wrote:

...

Hi Doug,

Thanks again for your advice, the heat maps look much better. However, they still do not visualize the continuous range of angles or eccentricities but rather divide it into two intervals such as red vs. blue. Is there any way to adjust the color range to make it more appropriate for this kind of data?

The heat map for the field sign data still looks speckled. I attached an image showing the heat maps for polar angle, eccentricity, and field sign, with the corresponding overlay settings.

I used 5mm smoothing.

Thank you very much, Michelle

Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:

...

The activation looks pretty reasonable. As you point out, the angles are a mess. How did you set the color scale for the angles? You should leave it as a heat scale (if you're using tksurfer-sess). How much did you smooth?

doug

Michelle Umali wrote:

...

Hi Doug, Attached is a pic of the significance and angle maps for polar and eccen.

What do you think?

Thanks. Michelle

Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:

> what does the activation look like? Does it look right? Can > you send a pic? > doug > > Michelle Umali wrote: > >> Hi Doug, >> The z-values are consistently near or greater than 4. It just >> seems that the >> visualization of the angles is somehow incorrect... >> >> Is there be anything else that I need to check? >> >> Thanks. >> 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. >

---

---

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-- 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

----- End forwarded message -----

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---

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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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-- 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

Dear Bruce & Doug, Thanks I'll do the label comparison. I am attaching a fieldsign pic to show the irregularity of the blue/red bands. Can you suggest a method of determining V1/2/3 based on the odd pattern?

Thank you very much. Michelle

...

they have to overlap unless the classification was 100% accurate with no variability. You can just pick the label with the highest probability at each vertex

Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:

can you send a pic?

Michelle Umali wrote:

...

Hi Doug, So I did the additional smoothing and the map looks better.. It's still hard to interpret though. I was expecting alternating red and blue bands to signify V1/V2/V3 boundaries, but it's very irregular with red curves running every which way into blue splotches. Do you have any suggestions how to interpret this?

So then I just looked at the automatic parcellation of V1 and V2, which seems very different from the actual fieldsign results.. The boundaries overlap quite a bit, which seems odd. How should I treat the overlap?

Thanks for your help. Michelle

Alsouoting Douglas N Greve greve@nmr.mgh.harvard.edu:

...

Michelle Umali wrote:

...

Hi Doug, I've already smoothed by 5 during preproc-sess, so does this mean I should do additional smoothing during fieldsign-sess step?

Try the additional one now to see if it fixes the map.

...

Also, is this the correct command to use the sphere and not the patch: fieldsign-sess -a rtopy.self.lh -fwhm 5 -sphere -s sj09

yes doug

...

Thanks. Michelle

Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:

...

Try smoothing (eg, -fwhm 5) when running fieldsign-sess. You can also try using the sphere instead of the occip patch. doug

Michelle Umali wrote:

...

Hi Doug,

Thanks again for your advice, the heat maps look much better. However, they still do not visualize the continuous range of angles or eccentricities but rather divide it into two intervals such as red vs. blue. Is there any way to adjust the color range to make it more appropriate for this kind of data?

The heat map for the field sign data still looks speckled. I attached an image showing the heat maps for polar angle, eccentricity, and field sign, with the corresponding overlay settings.

I used 5mm smoothing.

Thank you very much, Michelle

Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:

> The activation looks pretty reasonable. As you point out, the angles > are a mess. How did you set the color scale for the angles? You should > leave it as a heat scale (if you're using tksurfer-sess). How much did > you smooth? > > doug > > Michelle Umali wrote: > > >> Hi Doug, >> Attached is a pic of the significance and angle maps for >> polar and eccen. >> >> What do you think? >> >> Thanks. >> Michelle >> >> Quoting Douglas N Greve greve@nmr.mgh.harvard.edu: >> >> >> >>> what does the activation look like? Does it look right? Can >>> you send a pic? >>> doug >>> >>> Michelle Umali wrote: >>> >>> >>>> Hi Doug, >>>> The z-values are consistently near or greater than 4. It >>>> just seems that the >>>> visualization of the angles is somehow incorrect... >>>> >>>> Is there be anything else that I need to check? >>>> >>>> Thanks. >>>> 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 >> >> > -- > 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 > > ----- End forwarded message -----

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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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-- 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

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-- 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

Hi Michelle

they have to overlap unless the classification was 100% accurate with no variability. You can just pick the label with the highest probability at each vertex

cheers Bruce On Tue, 16 Aug 2011, Michelle Umali wrote:

Hi Doug, So I did the additional smoothing and the map looks better.. It's still hard to interpret though. I was expecting alternating red and blue bands to signify V1/V2/V3 boundaries, but it's very irregular with red curves running every which way into blue splotches. Do you have any suggestions how to interpret this?

So then I just looked at the automatic parcellation of V1 and V2, which seems very different from the actual fieldsign results.. The boundaries overlap quite a bit, which seems odd. How should I treat the overlap?

Thanks for your help. Michelle

Alsouoting Douglas N Greve greve@nmr.mgh.harvard.edu:

...

Michelle Umali wrote:

...

Hi Doug, I've already smoothed by 5 during preproc-sess, so does this mean I should do additional smoothing during fieldsign-sess step?

Try the additional one now to see if it fixes the map.

...

Also, is this the correct command to use the sphere and not the patch: fieldsign-sess -a rtopy.self.lh -fwhm 5 -sphere -s sj09

yes doug

...

Thanks. Michelle

Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:

...

Try smoothing (eg, -fwhm 5) when running fieldsign-sess. You can also try using the sphere instead of the occip patch. doug

Michelle Umali wrote:

...

Hi Doug,

Thanks again for your advice, the heat maps look much better. However, they still do not visualize the continuous range of angles or eccentricities but rather divide it into two intervals such as red vs. blue. Is there any way to adjust the color range to make it more appropriate for this kind of data?

The heat map for the field sign data still looks speckled. I attached an image showing the heat maps for polar angle, eccentricity, and field sign, with the corresponding overlay settings.

I used 5mm smoothing.

Thank you very much, Michelle

Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:

...

The activation looks pretty reasonable. As you point out, the angles are a mess. How did you set the color scale for the angles? You should leave it as a heat scale (if you're using tksurfer-sess). How much did you smooth?

doug

Michelle Umali wrote:

> Hi Doug, > Attached is a pic of the significance and angle maps for polar > and eccen. > > What do you think? > > Thanks. > Michelle > > Quoting Douglas N Greve greve@nmr.mgh.harvard.edu: > > >> what does the activation look like? Does it look right? Can >> you send a pic? >> doug >> >> Michelle Umali wrote: >> >>> Hi Doug, >>> The z-values are consistently near or greater than 4. It just >>> seems that the >>> visualization of the angles is somehow incorrect... >>> >>> Is there be anything else that I need to check? >>> >>> Thanks. >>> 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

>

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

----- End forwarded message -----

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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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