Dear freesurfer team,
I was trying to obtain the values at a vertex in tksurfer and this is what is written in tksurfer manual.
....*At first, an empty plot will be displayed in a separate window. To generate a plot for a particular vertex, select a point by clicking on the parametric map at that vertex and the plot window will be updated accordingly.*
But is it possible to enter the desired vertex and get the plot rather than trying to point the mouse to exact vertex and update the plot because it looks like I am not good at pointing mouse to exact vertex I want.
Thank you and excuse me for the naive query.
Best, Nabin
Hi Nabin
note that tksurfer is deprecated - we are not developing it anymore.
That said, I thing you can type:
select_vertex_by_vno <N>
at the tcl prompt, where <N> is the number of the vertex you want to select
cheers Bruce
On Fri, 20 Jan 2017, Nabin Koirala wrote:
Dear freesurfer team, I was trying to obtain the values at a vertex in tksurfer and this is what is written in tksurfer manual.
....At first, an empty plot will be displayed in a separate window. To generate a plot for a particular vertex, select a point by clicking on the parametric map at that vertex and the plot window will be updated accordingly.
But is it possible to enter the desired vertex and get the plot rather than trying to point the mouse to exact vertex and update the plot because it looks like I am not good at pointing mouse to exact vertex I want.
Thank you and excuse me for the naive query.
Best, Nabin
Dear Bruce,
Thank you for the reply but as you mentioned that tksurfer is deprecated, is it possible to do the same from QDEC ? i.e Can I get all the values from the plot (or save the plot) which we get in QDEC for significant cluster ?
Thank you.
Regards, Nabin
On Fri, Jan 20, 2017 at 4:06 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Nabin
note that tksurfer is deprecated - we are not developing it anymore.
That said, I thing you can type:
select_vertex_by_vno <N>
at the tcl prompt, where <N> is the number of the vertex you want to select
cheers Bruce
On Fri, 20 Jan 2017, Nabin Koirala wrote:
Dear freesurfer team,
I was trying to obtain the values at a vertex in tksurfer and this is what is written in tksurfer manual.
....At first, an empty plot will be displayed in a separate window. To generate a plot for a particular vertex, select a point by clicking on the parametric map at that vertex and the plot window will be updated accordingly.
But is it possible to enter the desired vertex and get the plot rather than trying to point the mouse to exact vertex and update the plot because it looks like I am not good at pointing mouse to exact vertex I want.
Thank you and excuse me for the naive query.
Best, Nabin
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btw, in tksurfer you can type the vertex no you want into the vertex field. If you want to extract it programatically, then you can run something like
mri_segstats --vox vertexno 0 0 --id 1 --i yoursurfacemap.mgh --avgwf out.dat
On 01/23/2017 05:29 AM, Nabin Koirala wrote:
Dear Bruce,
Thank you for the reply but as you mentioned that tksurfer is deprecated, is it possible to do the same from QDEC ? i.e Can I get all the values from the plot (or save the plot) which we get in QDEC for significant cluster ?
Thank you.
Regards, Nabin
On Fri, Jan 20, 2017 at 4:06 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Nabin note that tksurfer is deprecated - we are not developing it anymore. That said, I thing you can type: select_vertex_by_vno <N> at the tcl prompt, where <N> is the number of the vertex you want to select cheers Bruce On Fri, 20 Jan 2017, Nabin Koirala wrote: Dear freesurfer team, I was trying to obtain the values at a vertex in tksurfer and this is what is written in tksurfer manual. ....At first, an empty plot will be displayed in a separate window. To generate a plot for a particular vertex, select a point by clicking on the parametric map at that vertex and the plot window will be updated accordingly. But is it possible to enter the desired vertex and get the plot rather than trying to point the mouse to exact vertex and update the plot because it looks like I am not good at pointing mouse to exact vertex I want. Thank you and excuse me for the naive query. Best, Nabin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 <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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Dear Doug,
Thank you for the repy but may be couple of things. One, when I used the above command it said segmentation volume is missing , so I added the segmentation volume as in the command below and it worked and I also got the out.dat but not as I wanted. With this command :
mri_segstats --seg /home/freesurfer/subjects/qdec/Untitled/y.mgh --vox 10157 0 0 --id 1 --i ./qdec/Untitled/...../Cor/sig.mgh --avgwf ./qdec/out.dat
Output was -5.718 , which was the log of p-value for that voxel. What I wanted is the (say) thickness values for all the subjects in that voxel (example as shown below), which is shown in this plot normally. I could get it from the GUI from tksurfer by typing the vertex as you mentioned but not with the command line yet.
Sub_10 Main 122.0 -0.0433319658041 0 Sub_101 Main 219.0 0.022786360234 0 Sub_104 Main 363.0 0.0189986526966 0 Sub_105 Main 687.0 -0.216253831983 0 Sub_106 Main 764.0 -0.763142108917 0 Sub_107 Main 175.0 0.0671334266663 0 Sub_108 Main 203.0 -0.0709587186575 0 Sub_109 Main 122.0 0.109558776021 0
Should I change something in the command line above ?
Many thanks again for your support.
Regards, Nabin
On Mon, Jan 23, 2017 at 6:21 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
btw, in tksurfer you can type the vertex no you want into the vertex field. If you want to extract it programatically, then you can run something like
mri_segstats --vox vertexno 0 0 --id 1 --i yoursurfacemap.mgh --avgwf out.dat
On 01/23/2017 05:29 AM, Nabin Koirala wrote:
Dear Bruce,
Thank you for the reply but as you mentioned that tksurfer is deprecated, is it possible to do the same from QDEC ? i.e Can I get all the values from the plot (or save the plot) which we get in QDEC for significant cluster ?
Thank you.
Regards, Nabin
On Fri, Jan 20, 2017 at 4:06 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Nabin note that tksurfer is deprecated - we are not developing it anymore. That said, I thing you can type: select_vertex_by_vno <N> at the tcl prompt, where <N> is the number of the vertex you want to select cheers Bruce On Fri, 20 Jan 2017, Nabin Koirala wrote: Dear freesurfer team, I was trying to obtain the values at a vertex in tksurfer and this is what is written in tksurfer manual. ....At first, an empty plot will be displayed in a separate window. To generate a plot for a particular vertex, select a point by clicking on the parametric map at that vertex and the plot window will be updated accordingly. But is it possible to enter the desired vertex and get the plot rather than trying to point the mouse to exact vertex and update the plot because it looks like I am not good at pointing mouse to exact vertex I want. Thank you and excuse me for the naive query. Best, Nabin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 <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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