I have a question about the retinotopy analysis in freesurfer 5. I was following these instructions : http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis with some minor edits because we don't have eccen data. And now I'm ready to view the data, but I'm confused by what I am seeing.
I have a lot of previous retinotopy experience with older versions of freesurfer, and have this data all analyzed using Freesurfer4.5 and it works fine. However, with Freesurfer 5 when I use this command (with the correct sessid and hemisphere added in):
tksurfer-sess -a rtopy.self.?h -s sessid
it gives me a heat map, instead of the standard colors that match to the upper, lower, and horizontal meridians (i.e. red, green, and blue). I also tried using the "raw angle" code:
tksurfer-sess -a rtopy.self.?h -s sessid -map angle
but it doesn't give me the three colors either, but a sort of heat like map with 2 colors, but the colors don't map to the different visual areas, even in occipital cortex. Field sign doesn't work because I don't have the eccen data (and because I'm care about parietal retinotopy, not occipital). Is there a way to get the standard view of retinotopy out of freesurfer 5?
For reference in freesurfer4.5, I would load retinotopy data by using this command:
tksurfer subjname ?h inflated
and then load the map-imag-lh.w in one overlay layer, and map-real-lh.w in the second overlay layer, then configuring the overlay to display the color wheel color scale and complex display options, and then configuring the phase encoding display to 2 angle cycles and an appropriate angle offset.
Can you help me figure out how to get my data to display correctly?
Thanks,
Katie
Hi Katie, the color wheel became difficult to support (and I think it is inferior for viewing for various reasons). There is an alternative called rtview. It is not in the distribution, but you can get it from
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview
Look at the --help to see how to run it.
doug
Katie Bettencourt wrote:
I have a question about the retinotopy analysis in freesurfer 5. I was following these instructions : http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis with some minor edits because we don't have eccen data. And now I'm ready to view the data, but I'm confused by what I am seeing.
I have a lot of previous retinotopy experience with older versions of freesurfer, and have this data all analyzed using Freesurfer4.5 and it works fine. However, with Freesurfer 5 when I use this command (with the correct sessid and hemisphere added in):
tksurfer-sess -a rtopy.self.?h -s sessid
it gives me a heat map, instead of the standard colors that match to the upper, lower, and horizontal meridians (i.e. red, green, and blue). I also tried using the "raw angle" code:
tksurfer-sess -a rtopy.self.?h -s sessid -map angle
but it doesn't give me the three colors either, but a sort of heat like map with 2 colors, but the colors don't map to the different visual areas, even in occipital cortex. Field sign doesn't work because I don't have the eccen data (and because I'm care about parietal retinotopy, not occipital). Is there a way to get the standard view of retinotopy out of freesurfer 5?
For reference in freesurfer4.5, I would load retinotopy data by using this command:
tksurfer subjname ?h inflated
and then load the map-imag-lh.w in one overlay layer, and map-real-lh.w in the second overlay layer, then configuring the overlay to display the color wheel color scale and complex display options, and then configuring the phase encoding display to 2 angle cycles and an appropriate angle offset.
Can you help me figure out how to get my data to display correctly?
Thanks,
Katie
Without the color wheel, how are you supposed to see the different meridians so that you can draw the boundaries for visual areas? I know that field sign can do that in occipital if you have polar and eccen, but it doesn't work well with parietal retinotopy or if you don't have eccen data (which so far is not worthwhile to collect for parietal retinotopy). What do you recommend using? We looked at the sig maps and the angle maps per the instructions on the wiki page, but neither of them gave us the boundaries, even within occipital, and we've done this data with 4.5 and know that it comes out correctly there, so it's not an error in our data.
Katie
On Thu, Feb 16, 2012 at 3:26 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Katie, the color wheel became difficult to support (and I think it is inferior for viewing for various reasons). There is an alternative called rtview. It is not in the distribution, but you can get it from
ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/rtviewftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview
Look at the --help to see how to run it.
doug
Katie Bettencourt wrote:
I have a question about the retinotopy analysis in freesurfer 5. I was following these instructions : http://surfer.nmr.mgh.harvard.** edu/fswiki/**FsFastIndividualRetinotopyAnal**ysishttp://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis with some minor edits because we don't have eccen data. And now I'm ready to view the data, but I'm confused by what I am seeing.
I have a lot of previous retinotopy experience with older versions of freesurfer, and have this data all analyzed using Freesurfer4.5 and it works fine. However, with Freesurfer 5 when I use this command (with the correct sessid and hemisphere added in):
tksurfer-sess -a rtopy.self.?h -s sessid
it gives me a heat map, instead of the standard colors that match to the upper, lower, and horizontal meridians (i.e. red, green, and blue). I also tried using the "raw angle" code:
tksurfer-sess -a rtopy.self.?h -s sessid -map angle
but it doesn't give me the three colors either, but a sort of heat like map with 2 colors, but the colors don't map to the different visual areas, even in occipital cortex. Field sign doesn't work because I don't have the eccen data (and because I'm care about parietal retinotopy, not occipital). Is there a way to get the standard view of retinotopy out of freesurfer 5?
For reference in freesurfer4.5, I would load retinotopy data by using this command:
tksurfer subjname ?h inflated
and then load the map-imag-lh.w in one overlay layer, and map-real-lh.w in the second overlay layer, then configuring the overlay to display the color wheel color scale and complex display options, and then configuring the phase encoding display to 2 angle cycles and an appropriate angle offset.
Can you help me figure out how to get my data to display correctly?
Thanks,
Katie
-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/**compliancelinehttp://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.
rtview will give you the colorwheel, see if that works for you doug
Katie Bettencourt wrote:
Without the color wheel, how are you supposed to see the different meridians so that you can draw the boundaries for visual areas? I know that field sign can do that in occipital if you have polar and eccen, but it doesn't work well with parietal retinotopy or if you don't have eccen data (which so far is not worthwhile to collect for parietal retinotopy). What do you recommend using? We looked at the sig maps and the angle maps per the instructions on the wiki page, but neither of them gave us the boundaries, even within occipital, and we've done this data with 4.5 and know that it comes out correctly there, so it's not an error in our data.
Katie
On Thu, Feb 16, 2012 at 3:26 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Katie, the color wheel became difficult to support (and I think it is inferior for viewing for various reasons). There is an alternative called rtview. It is not in the distribution, but you can get it from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview Look at the --help to see how to run it. doug Katie Bettencourt wrote: I have a question about the retinotopy analysis in freesurfer 5. I was following these instructions : http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis with some minor edits because we don't have eccen data. And now I'm ready to view the data, but I'm confused by what I am seeing. I have a lot of previous retinotopy experience with older versions of freesurfer, and have this data all analyzed using Freesurfer4.5 and it works fine. However, with Freesurfer 5 when I use this command (with the correct sessid and hemisphere added in): tksurfer-sess -a rtopy.self.?h -s sessid it gives me a heat map, instead of the standard colors that match to the upper, lower, and horizontal meridians (i.e. red, green, and blue). I also tried using the "raw angle" code: tksurfer-sess -a rtopy.self.?h -s sessid -map angle but it doesn't give me the three colors either, but a sort of heat like map with 2 colors, but the colors don't map to the different visual areas, even in occipital cortex. Field sign doesn't work because I don't have the eccen data (and because I'm care about parietal retinotopy, not occipital). Is there a way to get the standard view of retinotopy out of freesurfer 5? For reference in freesurfer4.5, I would load retinotopy data by using this command: tksurfer subjname ?h inflated and then load the map-imag-lh.w in one overlay layer, and map-real-lh.w in the second overlay layer, then configuring the overlay to display the color wheel color scale and complex display options, and then configuring the phase encoding display to 2 angle cycles and an appropriate angle offset. Can you help me figure out how to get my data to display correctly? Thanks, Katie -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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.
Sorry Doug this is a very basic question, Should I put the rtview file in the freesurfer/fstast/bin directory or somewhere else?
Thanks, Maryam
On Thu, Feb 16, 2012 at 3:57 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
rtview will give you the colorwheel, see if that works for you doug
Katie Bettencourt wrote:
Without the color wheel, how are you supposed to see the different meridians so that you can draw the boundaries for visual areas? I know that field sign can do that in occipital if you have polar and eccen, but it doesn't work well with parietal retinotopy or if you don't have eccen data (which so far is not worthwhile to collect for parietal retinotopy). What do you recommend using? We looked at the sig maps and the angle maps per the instructions on the wiki page, but neither of them gave us the boundaries, even within occipital, and we've done this data with 4.5 and know that it comes out correctly there, so it's not an error in our data.
Katie
On Thu, Feb 16, 2012 at 3:26 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Hi Katie, the color wheel became difficult to support (and I think it is inferior for viewing for various reasons). There is an alternative called rtview. It is not in the distribution, but you can get it from
ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/rtviewftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview
Look at the --help to see how to run it.
doug
Katie Bettencourt wrote:
I have a question about the retinotopy analysis in freesurfer 5. I was following these instructions : http://surfer.nmr.mgh.harvard.**edu/fswiki/**FsFastIndividualRetinotopyAnal**ysishttp://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis with some minor edits because we don't have eccen data. And now I'm ready to view the data, but I'm confused by what I am seeing.
I have a lot of previous retinotopy experience with older versions of freesurfer, and have this data all analyzed using Freesurfer4.5 and it works fine. However, with Freesurfer 5 when I use this command (with the correct sessid and hemisphere added in): tksurfer-sess -a rtopy.self.?h -s sessid it gives me a heat map, instead of the standard colors that match to the upper, lower, and horizontal meridians (i.e. red, green, and blue). I also tried using the "raw angle" code: tksurfer-sess -a rtopy.self.?h -s sessid -map angle but it doesn't give me the three colors either, but a sort of heat like map with 2 colors, but the colors don't map to the different visual areas, even in occipital cortex. Field sign doesn't work because I don't have the eccen data (and because I'm care about parietal retinotopy, not occipital). Is there a way to get the standard view of retinotopy out of freesurfer 5? For reference in freesurfer4.5, I would load retinotopy data by using this command: tksurfer subjname ?h inflated and then load the map-imag-lh.w in one overlay layer, and map-real-lh.w in the second overlay layer, then configuring the overlay to display the color wheel color scale and complex display options, and then configuring the phase encoding display to 2 angle cycles and an appropriate angle offset. Can you help me figure out how to get my data to display correctly? Thanks, Katie-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://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/**compliancelinehttp://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer/fstast/bin is fine
Maryam Vaziri Pashkam wrote:
Sorry Doug this is a very basic question, Should I put the rtview file in the freesurfer/fstast/bin directory or somewhere else?
Thanks, Maryam
On Thu, Feb 16, 2012 at 3:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
rtview will give you the colorwheel, see if that works for you doug Katie Bettencourt wrote: Without the color wheel, how are you supposed to see the different meridians so that you can draw the boundaries for visual areas? I know that field sign can do that in occipital if you have polar and eccen, but it doesn't work well with parietal retinotopy or if you don't have eccen data (which so far is not worthwhile to collect for parietal retinotopy). What do you recommend using? We looked at the sig maps and the angle maps per the instructions on the wiki page, but neither of them gave us the boundaries, even within occipital, and we've done this data with 4.5 and know that it comes out correctly there, so it's not an error in our data. Katie On Thu, Feb 16, 2012 at 3:26 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Hi Katie, the color wheel became difficult to support (and I think it is inferior for viewing for various reasons). There is an alternative called rtview. It is not in the distribution, but you can get it from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview Look at the --help to see how to run it. doug Katie Bettencourt wrote: I have a question about the retinotopy analysis in freesurfer 5. I was following these instructions : http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis with some minor edits because we don't have eccen data. And now I'm ready to view the data, but I'm confused by what I am seeing. I have a lot of previous retinotopy experience with older versions of freesurfer, and have this data all analyzed using Freesurfer4.5 and it works fine. However, with Freesurfer 5 when I use this command (with the correct sessid and hemisphere added in): tksurfer-sess -a rtopy.self.?h -s sessid it gives me a heat map, instead of the standard colors that match to the upper, lower, and horizontal meridians (i.e. red, green, and blue). I also tried using the "raw angle" code: tksurfer-sess -a rtopy.self.?h -s sessid -map angle but it doesn't give me the three colors either, but a sort of heat like map with 2 colors, but the colors don't map to the different visual areas, even in occipital cortex. Field sign doesn't work because I don't have the eccen data (and because I'm care about parietal retinotopy, not occipital). Is there a way to get the standard view of retinotopy out of freesurfer 5? For reference in freesurfer4.5, I would load retinotopy data by using this command: tksurfer subjname ?h inflated and then load the map-imag-lh.w in one overlay layer, and map-real-lh.w in the second overlay layer, then configuring the overlay to display the color wheel color scale and complex display options, and then configuring the phase encoding display to 2 angle cycles and an appropriate angle offset. Can you help me figure out how to get my data to display correctly? Thanks, Katie -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Katie Bettencourt -
Maryam Vaziri Pashkam