Dear freessurfer experts,
I created my polar und eccen maps using the retinotopy pipeline. I also visualize them using the the rtview command on the inflated surface. But how can I interpret the colors (red to blue in the RYGB Wheel) in my eccen map? Which color refers to which timepoint (volume) of my functional run?
Best,
Erhan
Hi Erhan, the results are collapsed across all time points, so no color represents a particular time point. The colors in the color wheel are hard to interpret, which is why I recommend against using the color wheel. If you click on a point, I believe the value (phase) will be displayed in the control panel. doug
Erhan Genc wrote:
Dear freessurfer experts,
I created my polar und eccen maps using the retinotopy pipeline. I also visualize them using the the rtview command on the inflated surface. But how can I interpret the colors (red to blue in the RYGB Wheel) in my eccen map? Which color refers to which timepoint (volume) of my functional run?
Best,
Erhan
Hi Doug,
I see. My eccen run has 8 cycles of an expanding ring and each cycle take about 64 sec. So in general the color "red" would show the average of the 8 cycles for the first let say 10 sec. I know from my protocol which eccen (1°-12° per hemisphere) was shown when, but how can I exactly find a area of a specific eccentricity on my surfce without using the color wheel?
I just would like to draw a label consisting 1°-5° in the visual field.
Can you recommend me another strategy?
Best,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Erhan, the results are collapsed across all time points, so no color represents a particular time point. The colors in the color wheel are hard to interpret, which is why I recommend against using the color wheel. If you click on a point, I believe the value (phase) will be displayed in the control panel. doug
Erhan Genc wrote:
Dear freessurfer experts,
I created my polar und eccen maps using the retinotopy pipeline. I also visualize them using the the rtview command on the inflated surface. But how can I interpret the colors (red to blue in the RYGB Wheel) in my eccen map? Which color refers to which timepoint (volume) of my functional run?
Best,
Erhan
-- 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.
If you run something like this: tksurfer-sess -a rtopy.self.lh -s sessid -map angle it will show you the angle in radians (I think). Thresholding this map is going to be tricky in tksurfer (can't remove things above a value). An alternative is to run mri_binarize on the angle file itself. mri_biniarize allows you to set upper and lower thresholds. You can then run tksurfer on the result. doug
Erhan Genc wrote:
Hi Doug,
I see. My eccen run has 8 cycles of an expanding ring and each cycle take about 64 sec. So in general the color "red" would show the average of the 8 cycles for the first let say 10 sec. I know from my protocol which eccen (1°-12° per hemisphere) was shown when, but how can I exactly find a area of a specific eccentricity on my surfce without using the color wheel?
I just would like to draw a label consisting 1°-5° in the visual field.
Can you recommend me another strategy?
Best,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Erhan, the results are collapsed across all time points, so no color represents a particular time point. The colors in the color wheel are hard to interpret, which is why I recommend against using the color wheel. If you click on a point, I believe the value (phase) will be displayed in the control panel. doug
Erhan Genc wrote:
Dear freessurfer experts,
I created my polar und eccen maps using the retinotopy pipeline. I also visualize them using the the rtview command on the inflated surface. But how can I interpret the colors (red to blue in the RYGB Wheel) in my eccen map? Which color refers to which timepoint (volume) of my functional run?
Best,
Erhan
-- 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.
Hi Doug,
thanks a lot it worked for the eccen maps. I have now my eccen of interest... Is there a command to make a intersection area between two labels? I just found the command mri_mergelabels which merge two labels into a bigger one.
cheers,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
If you run something like this: tksurfer-sess -a rtopy.self.lh -s sessid -map angle it will show you the angle in radians (I think). Thresholding this map is going to be tricky in tksurfer (can't remove things above a value). An alternative is to run mri_binarize on the angle file itself. mri_biniarize allows you to set upper and lower thresholds. You can then run tksurfer on the result. doug
Erhan Genc wrote:
Hi Doug,
I see. My eccen run has 8 cycles of an expanding ring and each cycle take about 64 sec. So in general the color "red" would show the average of the 8 cycles for the first let say 10 sec. I know from my protocol which eccen (1°-12° per hemisphere) was shown when, but how can I exactly find a area of a specific eccentricity on my surfce without using the color wheel?
I just would like to draw a label consisting 1°-5° in the visual field.
Can you recommend me another strategy?
Best,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Erhan, the results are collapsed across all time points, so no color represents a particular time point. The colors in the color wheel are hard to interpret, which is why I recommend against using the color wheel. If you click on a point, I believe the value (phase) will be displayed in the control panel. doug
Erhan Genc wrote:
Dear freessurfer experts,
I created my polar und eccen maps using the retinotopy pipeline. I also visualize them using the the rtview command on the inflated surface. But how can I interpret the colors (red to blue in the RYGB Wheel) in my eccen map? Which color refers to which timepoint (volume) of my functional run?
Best,
Erhan
-- 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.
-- 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
Nothing that is easy to do. You can try it in matlab. Another thing you can do is to convert the label into a binary mask in a "volume" format (eg, mgh or nifti) with mri_label2labe (using the --outmask option). Do this for both of your labels, then use fscalc to compute an "and" of the masks. You can view this mask in tksurfer by loading it as an overlay with a threshold of 0.5 (-fthresh 0.5). This could also be converted back to an annotation with mris_seg2annot.
doug
Erhan Genc wrote:
Hi Doug,
thanks a lot it worked for the eccen maps. I have now my eccen of interest... Is there a command to make a intersection area between two labels? I just found the command mri_mergelabels which merge two labels into a bigger one.
cheers,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
If you run something like this: tksurfer-sess -a rtopy.self.lh -s sessid -map angle it will show you the angle in radians (I think). Thresholding this map is going to be tricky in tksurfer (can't remove things above a value). An alternative is to run mri_binarize on the angle file itself. mri_biniarize allows you to set upper and lower thresholds. You can then run tksurfer on the result. doug
Erhan Genc wrote:
Hi Doug,
I see. My eccen run has 8 cycles of an expanding ring and each cycle take about 64 sec. So in general the color "red" would show the average of the 8 cycles for the first let say 10 sec. I know from my protocol which eccen (1°-12° per hemisphere) was shown when, but how can I exactly find a area of a specific eccentricity on my surfce without using the color wheel?
I just would like to draw a label consisting 1°-5° in the visual field.
Can you recommend me another strategy?
Best,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Erhan, the results are collapsed across all time points, so no color represents a particular time point. The colors in the color wheel are hard to interpret, which is why I recommend against using the color wheel. If you click on a point, I believe the value (phase) will be displayed in the control panel. doug
Erhan Genc wrote:
Dear freessurfer experts,
I created my polar und eccen maps using the retinotopy pipeline. I also visualize them using the the rtview command on the inflated surface. But how can I interpret the colors (red to blue in the RYGB Wheel) in my eccen map? Which color refers to which timepoint (volume) of my functional run?
Best,
Erhan
-- 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.
-- 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,
thanks for your advice. By modifiying the mri_mergelabels command we find a solution to create labels with an "and" connection. To be sure about the output, what exactly does the columns represent in the label file. I assume that the first column is the index of the vertex, the next three are coordinates of that vertex (?) and what about the forth column?
cheers,
Erhan
2011/11/9 Douglas N Greve greve@nmr.mgh.harvard.edu:
Nothing that is easy to do. You can try it in matlab. Another thing you can do is to convert the label into a binary mask in a "volume" format (eg, mgh or nifti) with mri_label2labe (using the --outmask option). Do this for both of your labels, then use fscalc to compute an "and" of the masks. You can view this mask in tksurfer by loading it as an overlay with a threshold of 0.5 (-fthresh 0.5). This could also be converted back to an annotation with mris_seg2annot.
doug
Erhan Genc wrote:
Hi Doug,
thanks a lot it worked for the eccen maps. I have now my eccen of interest... Is there a command to make a intersection area between two labels? I just found the command mri_mergelabels which merge two labels into a bigger one.
cheers,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
If you run something like this: tksurfer-sess -a rtopy.self.lh -s sessid -map angle it will show you the angle in radians (I think). Thresholding this map is going to be tricky in tksurfer (can't remove things above a value). An alternative is to run mri_binarize on the angle file itself. mri_biniarize allows you to set upper and lower thresholds. You can then run tksurfer on the result. doug
Erhan Genc wrote:
Hi Doug,
I see. My eccen run has 8 cycles of an expanding ring and each cycle take about 64 sec. So in general the color "red" would show the average of the 8 cycles for the first let say 10 sec. I know from my protocol which eccen (1°-12° per hemisphere) was shown when, but how can I exactly find a area of a specific eccentricity on my surfce without using the color wheel?
I just would like to draw a label consisting 1°-5° in the visual field.
Can you recommend me another strategy?
Best,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Erhan, the results are collapsed across all time points, so no color represents a particular time point. The colors in the color wheel are hard to interpret, which is why I recommend against using the color wheel. If you click on a point, I believe the value (phase) will be displayed in the control panel. doug
Erhan Genc wrote:
Dear freessurfer experts,
I created my polar und eccen maps using the retinotopy pipeline. I also visualize them using the the rtview command on the inflated surface. But how can I interpret the colors (red to blue in the RYGB Wheel) in my eccen map? Which color refers to which timepoint (volume) of my functional run?
Best,
Erhan
-- 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.
-- 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
-- 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 first column is the index. 2-4 are xyz (ignored for surfaces). The last is a statistic which can be 0. doug
Erhan Genc wrote:
Hi Doug,
thanks for your advice. By modifiying the mri_mergelabels command we find a solution to create labels with an "and" connection. To be sure about the output, what exactly does the columns represent in the label file. I assume that the first column is the index of the vertex, the next three are coordinates of that vertex (?) and what about the forth column?
cheers,
Erhan
2011/11/9 Douglas N Greve greve@nmr.mgh.harvard.edu:
Nothing that is easy to do. You can try it in matlab. Another thing you can do is to convert the label into a binary mask in a "volume" format (eg, mgh or nifti) with mri_label2labe (using the --outmask option). Do this for both of your labels, then use fscalc to compute an "and" of the masks. You can view this mask in tksurfer by loading it as an overlay with a threshold of 0.5 (-fthresh 0.5). This could also be converted back to an annotation with mris_seg2annot.
doug
Erhan Genc wrote:
Hi Doug,
thanks a lot it worked for the eccen maps. I have now my eccen of interest... Is there a command to make a intersection area between two labels? I just found the command mri_mergelabels which merge two labels into a bigger one.
cheers,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
If you run something like this: tksurfer-sess -a rtopy.self.lh -s sessid -map angle it will show you the angle in radians (I think). Thresholding this map is going to be tricky in tksurfer (can't remove things above a value). An alternative is to run mri_binarize on the angle file itself. mri_biniarize allows you to set upper and lower thresholds. You can then run tksurfer on the result. doug
Erhan Genc wrote:
Hi Doug,
I see. My eccen run has 8 cycles of an expanding ring and each cycle take about 64 sec. So in general the color "red" would show the average of the 8 cycles for the first let say 10 sec. I know from my protocol which eccen (1°-12° per hemisphere) was shown when, but how can I exactly find a area of a specific eccentricity on my surfce without using the color wheel?
I just would like to draw a label consisting 1°-5° in the visual field.
Can you recommend me another strategy?
Best,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Erhan, the results are collapsed across all time points, so no color represents a particular time point. The colors in the color wheel are hard to interpret, which is why I recommend against using the color wheel. If you click on a point, I believe the value (phase) will be displayed in the control panel. doug
Erhan Genc wrote:
> Dear freessurfer experts, > > I created my polar und eccen maps using the retinotopy pipeline. I > also visualize them using the the rtview command on the inflated > surface. But how can I interpret the colors (red to blue in the RYGB > Wheel) in my eccen map? Which color refers to which timepoint (volume) > of my functional run? > > Best, > > Erhan > > > >
>
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.
-- 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
-- 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,
What kind of a statistic is the last one?
cheers,
Erhan
2011/11/30 Douglas N Greve greve@nmr.mgh.harvard.edu:
The first column is the index. 2-4 are xyz (ignored for surfaces). The last is a statistic which can be 0.
doug
Erhan Genc wrote:
Hi Doug,
thanks for your advice. By modifiying the mri_mergelabels command we find a solution to create labels with an "and" connection. To be sure about the output, what exactly does the columns represent in the label file. I assume that the first column is the index of the vertex, the next three are coordinates of that vertex (?) and what about the forth column?
cheers,
Erhan
2011/11/9 Douglas N Greve greve@nmr.mgh.harvard.edu:
Nothing that is easy to do. You can try it in matlab. Another thing you can do is to convert the label into a binary mask in a "volume" format (eg, mgh or nifti) with mri_label2labe (using the --outmask option). Do this for both of your labels, then use fscalc to compute an "and" of the masks. You can view this mask in tksurfer by loading it as an overlay with a threshold of 0.5 (-fthresh 0.5). This could also be converted back to an annotation with mris_seg2annot.
doug
Erhan Genc wrote:
Hi Doug,
thanks a lot it worked for the eccen maps. I have now my eccen of interest... Is there a command to make a intersection area between two labels? I just found the command mri_mergelabels which merge two labels into a bigger one.
cheers,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
If you run something like this: tksurfer-sess -a rtopy.self.lh -s sessid -map angle it will show you the angle in radians (I think). Thresholding this map is going to be tricky in tksurfer (can't remove things above a value). An alternative is to run mri_binarize on the angle file itself. mri_biniarize allows you to set upper and lower thresholds. You can then run tksurfer on the result. doug
Erhan Genc wrote:
Hi Doug,
I see. My eccen run has 8 cycles of an expanding ring and each cycle take about 64 sec. So in general the color "red" would show the average of the 8 cycles for the first let say 10 sec. I know from my protocol which eccen (1°-12° per hemisphere) was shown when, but how can I exactly find a area of a specific eccentricity on my surfce without using the color wheel?
I just would like to draw a label consisting 1°-5° in the visual field.
Can you recommend me another strategy?
Best,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
> > Hi Erhan, the results are collapsed across all time points, so no > color > represents a particular time point. The colors in the color wheel are > hard > to interpret, which is why I recommend against using the color wheel. > If > you > click on a point, I believe the value (phase) will be displayed in > the > control panel. > doug > > Erhan Genc wrote: > > > >> >> Dear freessurfer experts, >> >> I created my polar und eccen maps using the retinotopy pipeline. I >> also visualize them using the the rtview command on the inflated >> surface. But how can I interpret the colors (red to blue in the RYGB >> Wheel) in my eccen map? Which color refers to which timepoint >> (volume) >> of my functional run? >> >> Best, >> >> Erhan >> >> >> >> >> > > -- > 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. > > > > >
-- 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
-- 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
-- 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 Erhan
it's a placeholder for any type of statistic you would want to store in a label (t, F, p-value, etc...).
cheers Bruce
On Wed, 30 Nov 2011, Erhan Genc wrote:
Hi doug,
What kind of a statistic is the last one?
cheers,
Erhan
2011/11/30 Douglas N Greve greve@nmr.mgh.harvard.edu:
The first column is the index. 2-4 are xyz (ignored for surfaces). The last is a statistic which can be 0.
doug
Erhan Genc wrote:
Hi Doug,
thanks for your advice. By modifiying the mri_mergelabels command we find a solution to create labels with an "and" connection. To be sure about the output, what exactly does the columns represent in the label file. I assume that the first column is the index of the vertex, the next three are coordinates of that vertex (?) and what about the forth column?
cheers,
Erhan
2011/11/9 Douglas N Greve greve@nmr.mgh.harvard.edu:
Nothing that is easy to do. You can try it in matlab. Another thing you can do is to convert the label into a binary mask in a "volume" format (eg, mgh or nifti) with mri_label2labe (using the --outmask option). Do this for both of your labels, then use fscalc to compute an "and" of the masks. You can view this mask in tksurfer by loading it as an overlay with a threshold of 0.5 (-fthresh 0.5). This could also be converted back to an annotation with mris_seg2annot.
doug
Erhan Genc wrote:
Hi Doug,
thanks a lot it worked for the eccen maps. I have now my eccen of interest... Is there a command to make a intersection area between two labels? I just found the command mri_mergelabels which merge two labels into a bigger one.
cheers,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
If you run something like this: tksurfer-sess -a rtopy.self.lh -s sessid -map angle it will show you the angle in radians (I think). Thresholding this map is going to be tricky in tksurfer (can't remove things above a value). An alternative is to run mri_binarize on the angle file itself. mri_biniarize allows you to set upper and lower thresholds. You can then run tksurfer on the result. doug
Erhan Genc wrote:
> > Hi Doug, > > I see. My eccen run has 8 cycles of an expanding ring and each cycle > take about 64 sec. So in general the color "red" would show the > average of the 8 cycles for the first let say 10 sec. I know from my > protocol which eccen (1°-12° per hemisphere) was shown when, but how > can I exactly find a area of a specific eccentricity on my surfce > without using the color wheel? > > I just would like to draw a label consisting 1°-5° in the visual > field. > > Can you recommend me another strategy? > > Best, > > Erhan > > 2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu: > > > >> >> Hi Erhan, the results are collapsed across all time points, so no >> color >> represents a particular time point. The colors in the color wheel are >> hard >> to interpret, which is why I recommend against using the color wheel. >> If >> you >> click on a point, I believe the value (phase) will be displayed in >> the >> control panel. >> doug >> >> Erhan Genc wrote: >> >> >> >>> >>> Dear freessurfer experts, >>> >>> I created my polar und eccen maps using the retinotopy pipeline. I >>> also visualize them using the the rtview command on the inflated >>> surface. But how can I interpret the colors (red to blue in the RYGB >>> Wheel) in my eccen map? Which color refers to which timepoint >>> (volume) >>> of my functional run? >>> >>> Best, >>> >>> Erhan >>> >>> >>> >>> >>> >> >> -- >> 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. >> >> >> >> >> > > >
-- 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
-- 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
-- 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
There is no specification for it. It is just a number. The value can be used by some label manipulation routines to exclude values below a certain threshold. Mostly it is just ignored. doug
Erhan Genc wrote:
Hi doug,
What kind of a statistic is the last one?
cheers,
Erhan
2011/11/30 Douglas N Greve greve@nmr.mgh.harvard.edu:
The first column is the index. 2-4 are xyz (ignored for surfaces). The last is a statistic which can be 0.
doug
Erhan Genc wrote:
Hi Doug,
thanks for your advice. By modifiying the mri_mergelabels command we find a solution to create labels with an "and" connection. To be sure about the output, what exactly does the columns represent in the label file. I assume that the first column is the index of the vertex, the next three are coordinates of that vertex (?) and what about the forth column?
cheers,
Erhan
2011/11/9 Douglas N Greve greve@nmr.mgh.harvard.edu:
Nothing that is easy to do. You can try it in matlab. Another thing you can do is to convert the label into a binary mask in a "volume" format (eg, mgh or nifti) with mri_label2labe (using the --outmask option). Do this for both of your labels, then use fscalc to compute an "and" of the masks. You can view this mask in tksurfer by loading it as an overlay with a threshold of 0.5 (-fthresh 0.5). This could also be converted back to an annotation with mris_seg2annot.
doug
Erhan Genc wrote:
Hi Doug,
thanks a lot it worked for the eccen maps. I have now my eccen of interest... Is there a command to make a intersection area between two labels? I just found the command mri_mergelabels which merge two labels into a bigger one.
cheers,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
If you run something like this: tksurfer-sess -a rtopy.self.lh -s sessid -map angle it will show you the angle in radians (I think). Thresholding this map is going to be tricky in tksurfer (can't remove things above a value). An alternative is to run mri_binarize on the angle file itself. mri_biniarize allows you to set upper and lower thresholds. You can then run tksurfer on the result. doug
Erhan Genc wrote:
> Hi Doug, > > I see. My eccen run has 8 cycles of an expanding ring and each cycle > take about 64 sec. So in general the color "red" would show the > average of the 8 cycles for the first let say 10 sec. I know from my > protocol which eccen (1°-12° per hemisphere) was shown when, but how > can I exactly find a area of a specific eccentricity on my surfce > without using the color wheel? > > I just would like to draw a label consisting 1°-5° in the visual > field. > > Can you recommend me another strategy? > > Best, > > Erhan > > 2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu: > > > > >> Hi Erhan, the results are collapsed across all time points, so no >> color >> represents a particular time point. The colors in the color wheel are >> hard >> to interpret, which is why I recommend against using the color wheel. >> If >> you >> click on a point, I believe the value (phase) will be displayed in >> the >> control panel. >> doug >> >> Erhan Genc wrote: >> >> >> >> >>> Dear freessurfer experts, >>> >>> I created my polar und eccen maps using the retinotopy pipeline. I >>> also visualize them using the the rtview command on the inflated >>> surface. But how can I interpret the colors (red to blue in the RYGB >>> Wheel) in my eccen map? Which color refers to which timepoint >>> (volume) >>> of my functional run? >>> >>> Best, >>> >>> Erhan >>> >>> >>> >>> >>> >>> >> -- >> 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. >> >> >> >> >> >> >
>
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
-- 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
-- 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
Alright, thanks a lot.
cheers,
Erhan
2011/11/30 Douglas N Greve greve@nmr.mgh.harvard.edu:
There is no specification for it. It is just a number. The value can be used by some label manipulation routines to exclude values below a certain threshold. Mostly it is just ignored.
doug
Erhan Genc wrote:
Hi doug,
What kind of a statistic is the last one?
cheers,
Erhan
2011/11/30 Douglas N Greve greve@nmr.mgh.harvard.edu:
The first column is the index. 2-4 are xyz (ignored for surfaces). The last is a statistic which can be 0.
doug
Erhan Genc wrote:
Hi Doug,
thanks for your advice. By modifiying the mri_mergelabels command we find a solution to create labels with an "and" connection. To be sure about the output, what exactly does the columns represent in the label file. I assume that the first column is the index of the vertex, the next three are coordinates of that vertex (?) and what about the forth column?
cheers,
Erhan
2011/11/9 Douglas N Greve greve@nmr.mgh.harvard.edu:
Nothing that is easy to do. You can try it in matlab. Another thing you can do is to convert the label into a binary mask in a "volume" format (eg, mgh or nifti) with mri_label2labe (using the --outmask option). Do this for both of your labels, then use fscalc to compute an "and" of the masks. You can view this mask in tksurfer by loading it as an overlay with a threshold of 0.5 (-fthresh 0.5). This could also be converted back to an annotation with mris_seg2annot.
doug
Erhan Genc wrote:
Hi Doug,
thanks a lot it worked for the eccen maps. I have now my eccen of interest... Is there a command to make a intersection area between two labels? I just found the command mri_mergelabels which merge two labels into a bigger one.
cheers,
Erhan
2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu:
> > If you run something like this: > tksurfer-sess -a rtopy.self.lh -s sessid -map angle > it will show you the angle in radians (I think). Thresholding this > map > is > going to be tricky in tksurfer (can't remove things above a value). > An > alternative is to run mri_binarize on the angle file itself. > mri_biniarize > allows you to set upper and lower thresholds. You can then run > tksurfer > on > the result. > doug > > Erhan Genc wrote: > > > >> >> Hi Doug, >> >> I see. My eccen run has 8 cycles of an expanding ring and each cycle >> take about 64 sec. So in general the color "red" would show the >> average of the 8 cycles for the first let say 10 sec. I know from my >> protocol which eccen (1°-12° per hemisphere) was shown when, but how >> can I exactly find a area of a specific eccentricity on my surfce >> without using the color wheel? >> >> I just would like to draw a label consisting 1°-5° in the visual >> field. >> >> Can you recommend me another strategy? >> >> Best, >> >> Erhan >> >> 2011/11/1 Douglas N Greve greve@nmr.mgh.harvard.edu: >> >> >> >> >>> >>> Hi Erhan, the results are collapsed across all time points, so no >>> color >>> represents a particular time point. The colors in the color wheel >>> are >>> hard >>> to interpret, which is why I recommend against using the color >>> wheel. >>> If >>> you >>> click on a point, I believe the value (phase) will be displayed in >>> the >>> control panel. >>> doug >>> >>> Erhan Genc wrote: >>> >>> >>> >>> >>>> >>>> Dear freessurfer experts, >>>> >>>> I created my polar und eccen maps using the retinotopy pipeline. I >>>> also visualize them using the the rtview command on the inflated >>>> surface. But how can I interpret the colors (red to blue in the >>>> RYGB >>>> Wheel) in my eccen map? Which color refers to which timepoint >>>> (volume) >>>> of my functional run? >>>> >>>> Best, >>>> >>>> Erhan >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> -- >>> 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. >>> >>> >>> >>> >>> >>> >> >> >> > > -- > 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 > > > > >
-- 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
-- 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
-- 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Erhan Genc