Re: [Freesurfer] Custom color map in Freeview

[Bruce Fischl]

there is some code around to display each parcel with a different value, 
but I'm not sure exactly what it is. YOu could certainly do it in matlab

if you wanted to (use read_annotation.m to read in the .annot file)

Cheers
Bruce

On Wed, 11 Jul 2018, Ben Smith wrote:



External Email - Use Caution

Hi Bruce,
Some background: 

I have already extracted ROI timeseries using the following method:
 *  use mri_vol2vol to transform the functional images to structural space (yes 
these were very
large images; I did it one at a time)
 *  use mri_segstats to segment the image into cortical parcellations and 
subcortical segmentations
That gave me raw timecourses for each segment and parcellation. I used my own 
code to mean-center
and high-pass filter (specificaly, linear, quadratic, and cubic regressors); 
then applied an HRF
function. I was then able to extract a single activity value for each ROI and 
each event in my
design.
So for each subject I now have an N*M matrix where N is the number of events 
and M is the number of
ROIs, representing mean activity in each ROI during each event.
I'm then estimating the covariance of activity in these ROIs with reward 
prediction error according
to an RL model.
---

So back to freesurfer - I have a single covariance value for each ROI and I 
want to show that
covariance in an illustration, where each ROI is color-coded according to its 
covariance value.

It's good to know the annotations (e.g., label/rh.aparc.a2009s.annot, right?) 
are what I need for
this, but they're not plain text, so I don't know how to use them to create a 
colormap like Ruopeng
suggested.





___
Ben Smith, MSc.
Ph.D. Candidate
University of Southern California
https://bjsmith.github.io/
p | +1 323-385 9349
skype | ben.smith.nz



On Tue, Jul 10, 2018 at 5:54 PM Bruce Fischl  wrote:
  Hi Ben

  can you explain a bit more explicitly what you are trying to do? The
  annotations are exactly what you suggest (a parcellation ID for every
  vertex)

  cheers
  Bruce
  On Tue, 10 Jul 2018, Ben Smith wrote:

  >
  > External Email - Use Caution
  >
  > Got it, thanks!
  > Could you tell me how I can map a particular ROI (for instance the 
Destrieux cortical
  surface ROIs)
  > to a set of vertices that make up the ROI? Is there a lookup table I 
can use?
  > ___
  > Ben Smith, MSc.
  > Ph.D. Candidate
  > University of Southern California
  > https://bjsmith.github.io/
  > p | +1 323-385 9349
  > skype | ben.smith.nz
  >
  >
  >
  > On Tue, Jul 10, 2018 at 2:08 PM Ruopeng Wang 
 wrote:
  >
  >       Hi Ben,
  >
  >       My last email was referring to how to load custom color map for 
volume viewing.
  If you
  >       want to load custom color for surface, you need to create and 
load an RGB map
  file. The
  >       file can be a text file contains N lines of RGB color like this:
  >
  >       R1, G1, B1
  >       R2, G2, B2
  >
  >       ...
  >
  >       or a volume file with dimension of  N x 3 x1. N must match the 
number of
  vertices of the
  >       surface.
  >
  >       Best,
  >       Ruopeng
  >
  >
  >       On 07/10/2018 04:57 PM, Ben Smith wrote:
  >
  >       External Email - Use Caution
  >
  >       I've been trying to do this as well, but I can't see the right 
place to specify
  in
  >       freesurfer to specify an alternative lookup table.
  > For instance, if I am coloring a pial surface, then the first 
possibility is to set a
  > Color (where I can "load RGB map"). But I get an error "Cannot load 
RGB" file if I try
  > to use that to load an LUT format file. The other option is where it says 
"heatmap" i
  > can change the option to select a custom label, but if I try to enter 
an LUT file into
  > there, freeview crashes (which is fine, I guess that was the wrong 
place).
  >
  > So can anyone tell me what I'm missing for the place to load the LUT 
file or an
  > alternative colormap?
  >
  > Thanks for your help!
  >
  > Regards
  >
  > Ben
  >
  > On Tue, Mar 27, 2018 at 1:10 PM Ruopeng Wang 
 wrote:
  >
  >       It looks like a customized look up table will work for your case. 
You can
  >       simply select "Lookup table" as the colormap and load your own 
lookup table.
  >       To create your own look up table, you can refer to the content of
  >       FreeSurferColorLUT.txt file in your freesurfer installation 
directory.
  >
  >       Best,
  >       Ruopeng
  >
  >       On 03/27/2018 03:59 PM, Anna Mynick wrote:
  >       Hi all, 
  > I’m wondering whether there’s a way to create a custom color map in 
Freeview
  > that would operate as a 

Re: [Freesurfer] Custom color map in Freeview

[Ben Smith]

External Email - Use Caution

Hi Bruce,

Some background:

I have already extracted ROI timeseries using the following method:

   - use mri_vol2vol to transform the functional images to structural space
   (yes these were very large images; I did it one at a time)
   - use mri_segstats to segment the image into cortical parcellations and
   subcortical segmentations

That gave me raw timecourses for each segment and parcellation. I used my
own code to mean-center and high-pass filter (specificaly, linear,
quadratic, and cubic regressors); then applied an HRF function. I was then
able to extract a single activity value for each ROI and each event in my
design.
So for each subject I now have an N*M matrix where N is the number of
events and M is the number of ROIs, representing mean activity in each ROI
during each event.
I'm then estimating the covariance of activity in these ROIs with reward
prediction error according to an RL model.
---

So back to freesurfer - I have a single covariance value for each ROI and I
want to show that covariance in an illustration, where each ROI is
color-coded according to its covariance value.

It's good to know the annotations (e.g., label/rh.aparc.a2009s.annot,
right?) are what I need for this, but they're not plain text, so I don't
know how to use them to create a colormap like Ruopeng suggested.





___
Ben Smith, MSc.
Ph.D. Candidate
University of Southern California
https://bjsmith.github.io/
p | +1 323-385 9349
skype | ben.smith.nz



On Tue, Jul 10, 2018 at 5:54 PM Bruce Fischl 
wrote:

> Hi Ben
>
> can you explain a bit more explicitly what you are trying to do? The
> annotations are exactly what you suggest (a parcellation ID for every
> vertex)
>
> cheers
> Bruce
> On Tue, 10 Jul 2018, Ben Smith wrote:
>
> >
> > External Email - Use Caution
> >
> > Got it, thanks!
> > Could you tell me how I can map a particular ROI (for instance the
> Destrieux cortical surface ROIs)
> > to a set of vertices that make up the ROI? Is there a lookup table I can
> use?
> > ___
> > Ben Smith, MSc.
> > Ph.D. Candidate
> > University of Southern California
> > https://bjsmith.github.io/
> > p | +1 323-385 9349
> > skype | ben.smith.nz
> >
> >
> >
> > On Tue, Jul 10, 2018 at 2:08 PM Ruopeng Wang 
> wrote:
> >
> >   Hi Ben,
> >
> >   My last email was referring to how to load custom color map for
> volume viewing. If you
> >   want to load custom color for surface, you need to create and load
> an RGB map file. The
> >   file can be a text file contains N lines of RGB color like this:
> >
> >   R1, G1, B1
> >   R2, G2, B2
> >
> >   ...
> >
> >   or a volume file with dimension of  N x 3 x1. N must match the
> number of vertices of the
> >   surface.
> >
> >   Best,
> >   Ruopeng
> >
> >
> >   On 07/10/2018 04:57 PM, Ben Smith wrote:
> >
> >   External Email - Use Caution
> >
> >   I've been trying to do this as well, but I can't see the right
> place to specify in
> >   freesurfer to specify an alternative lookup table.
> > For instance, if I am coloring a pial surface, then the first
> possibility is to set a
> > Color (where I can "load RGB map"). But I get an error "Cannot load RGB"
> file if I try
> > to use that to load an LUT format file. The other option is where it
> says "heatmap" i
> > can change the option to select a custom label, but if I try to enter an
> LUT file into
> > there, freeview crashes (which is fine, I guess that was the wrong
> place).
> >
> > So can anyone tell me what I'm missing for the place to load the LUT
> file or an
> > alternative colormap?
> >
> > Thanks for your help!
> >
> > Regards
> >
> > Ben
> >
> > On Tue, Mar 27, 2018 at 1:10 PM Ruopeng Wang 
> wrote:
> >
> >   It looks like a customized look up table will work for your case.
> You can
> >   simply select "Lookup table" as the colormap and load your own
> lookup table.
> >   To create your own look up table, you can refer to the content of
> >   FreeSurferColorLUT.txt file in your freesurfer installation
> directory.
> >
> >   Best,
> >   Ruopeng
> >
> >   On 03/27/2018 03:59 PM, Anna Mynick wrote:
> >   Hi all,
> > I’m wondering whether there’s a way to create a custom color map in
> Freeview
> > that would operate as a alternative to the preset Greyscale, Heatmap,
> NIH,
> > PET, Jet and GE Color options.
> >
> > Ideally, I could assign each number value a given color, e.g. every “0”
> > value in an .nii file is black, every “1” value is red, every “2” value
> is
> > blue, every “3" is green and so on. I already have the RGB values worked
> out
> > for each number value; I just need to know how to format this information
> > and where to put it so that I can my custom colormap as an option in
> > Freeview.
> >
> > For my purposes, there would be no need to adjust the assigned colors
> based
> > on the overall range of 

Re: [Freesurfer] Custom color map in Freeview

[Bruce Fischl]

Hi Ben

can you explain a bit more explicitly what you are trying to do? The 
annotations are exactly what you suggest (a parcellation ID for every 
vertex)


cheers
Bruce
On Tue, 10 Jul 2018, Ben Smith wrote:



External Email - Use Caution

Got it, thanks!
Could you tell me how I can map a particular ROI (for instance the Destrieux 
cortical surface ROIs)
to a set of vertices that make up the ROI? Is there a lookup table I can use?
___
Ben Smith, MSc.
Ph.D. Candidate
University of Southern California
https://bjsmith.github.io/
p | +1 323-385 9349
skype | ben.smith.nz



On Tue, Jul 10, 2018 at 2:08 PM Ruopeng Wang  wrote:

  Hi Ben,

  My last email was referring to how to load custom color map for volume 
viewing. If you
  want to load custom color for surface, you need to create and load an RGB 
map file. The
  file can be a text file contains N lines of RGB color like this:

  R1, G1, B1
  R2, G2, B2

  ...

  or a volume file with dimension of  N x 3 x1. N must match the number of 
vertices of the
  surface.

  Best,
  Ruopeng


  On 07/10/2018 04:57 PM, Ben Smith wrote:

  External Email - Use Caution

  I've been trying to do this as well, but I can't see the right place to 
specify in
  freesurfer to specify an alternative lookup table.
For instance, if I am coloring a pial surface, then the first possibility is to 
set a
Color (where I can "load RGB map"). But I get an error "Cannot load RGB" file 
if I try
to use that to load an LUT format file. The other option is where it says 
"heatmap" i
can change the option to select a custom label, but if I try to enter an LUT 
file into
there, freeview crashes (which is fine, I guess that was the wrong place).

So can anyone tell me what I'm missing for the place to load the LUT file or an
alternative colormap?

Thanks for your help!

Regards

Ben

On Tue, Mar 27, 2018 at 1:10 PM Ruopeng Wang  wrote:

  It looks like a customized look up table will work for your case. You can
  simply select "Lookup table" as the colormap and load your own lookup 
table.
  To create your own look up table, you can refer to the content of
  FreeSurferColorLUT.txt file in your freesurfer installation directory.

  Best,
  Ruopeng

  On 03/27/2018 03:59 PM, Anna Mynick wrote:
  Hi all, 
I’m wondering whether there’s a way to create a custom color map in Freeview
that would operate as a alternative to the preset Greyscale, Heatmap, NIH,
PET, Jet and GE Color options. 

Ideally, I could assign each number value a given color, e.g. every “0”
value in an .nii file is black, every “1” value is red, every “2” value is
blue, every “3" is green and so on. I already have the RGB values worked out
for each number value; I just need to know how to format this information
and where to put it so that I can my custom colormap as an option in
Freeview. 

For my purposes, there would be no need to adjust the assigned colors based
on the overall range of values. For instance, there would be no need to
assign a different color value to a “1” value depending on whether the
highest value in the overall .nii file is 1 or 100. 

I did try reading the related conversation here but I can’t seem to find the
file it references, annotval2surfoverlay.m, in the Freesurfer directory. 

Thanks very much for your help! 
Anna 



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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Custom color map in Freeview

[Ben Smith]

External Email - Use Caution

Got it, thanks!

Could you tell me how I can map a particular ROI (for instance the
Destrieux cortical surface ROIs) to a set of vertices that make up the ROI?
Is there a lookup table I can use?
___
Ben Smith, MSc.
Ph.D. Candidate
University of Southern California
https://bjsmith.github.io/
p | +1 323-385 9349
skype | ben.smith.nz



On Tue, Jul 10, 2018 at 2:08 PM Ruopeng Wang 
wrote:

> Hi Ben,
>
> My last email was referring to how to load custom color map for volume
> viewing. If you want to load custom color for surface, you need to create
> and load an RGB map file. The file can be a text file contains N lines of
> RGB color like this:
>
> R1, G1, B1
> R2, G2, B2
>
> ...
>
> or a volume file with dimension of  N x 3 x1. N must match the number of
> vertices of the surface.
>
> Best,
> Ruopeng
>
> On 07/10/2018 04:57 PM, Ben Smith wrote:
>
> External Email - Use Caution
> I've been trying to do this as well, but I can't see the right place to
> specify in freesurfer to specify an alternative lookup table.
>
> For instance, if I am coloring a pial surface, then the first possibility
> is to set a Color (where I can "load RGB map"). But I get an error "Cannot
> load RGB" file if I try to use that to load an LUT format file. The other
> option is where it says "heatmap" i can change the option to select a
> custom label, but if I try to enter an LUT file into there, freeview
> crashes (which is fine, I guess that was the wrong place).
>
> So can anyone tell me what I'm missing for the place to load the LUT file
> or an alternative colormap?
>
> Thanks for your help!
>
> Regards
>
> Ben
>
> On Tue, Mar 27, 2018 at 1:10 PM Ruopeng Wang 
> wrote:
>
>> It looks like a customized look up table will work for your case. You can
>> simply select "Lookup table" as the colormap and load your own lookup
>> table. To create your own look up table, you can refer to the content of
>> FreeSurferColorLUT.txt file in your freesurfer installation directory.
>>
>> Best,
>> Ruopeng
>> On 03/27/2018 03:59 PM, Anna Mynick wrote:
>>
>> Hi all,
>>
>> I’m wondering whether there’s a way to create a custom color map in
>> Freeview that would operate as a alternative to the preset Greyscale,
>> Heatmap, NIH, PET, Jet and GE Color options.
>>
>> Ideally, I could assign each number value a given color, e.g. every “0”
>> value in an .nii file is black, every “1” value is red, every “2” value is
>> blue, every “3" is green and so on. I already have the RGB values worked
>> out for each number value; I just need to know how to format this
>> information and where to put it so that I can my custom colormap as an
>> option in Freeview.
>>
>> For my purposes, there would be no need to adjust the assigned colors
>> based on the overall range of values. For instance, there would be no need
>> to assign a different color value to a “1” value depending on whether the
>> highest value in the overall .nii file is 1 or 100.
>>
>> I did try reading the related conversation here
>> 
>>  but
>> I can’t seem to find the file it references, annotval2surfoverlay.m, in
>> the Freesurfer directory.
>>
>> Thanks very much for your help!
>> Anna
>>
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 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 . 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 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Custom color map in Freeview

[Ruopeng Wang]

Hi Ben,

My last email was referring to how to load custom color map for volume 
viewing. If you want to load custom color for surface, you need to 
create and load an RGB map file. The file can be a text file contains N 
lines of RGB color like this:


R1, G1, B1
R2, G2, B2

...

or a volume file with dimension of  N x 3 x1. N must match the number of 
vertices of the surface.


Best,
Ruopeng


On 07/10/2018 04:57 PM, Ben Smith wrote:


External Email - Use Caution

I've been trying to do this as well, but I can't see the right place 
to specify in freesurfer to specify an alternative lookup table.


For instance, if I am coloring a pial surface, then the first 
possibility is to set a Color (where I can "load RGB map"). But I get 
an error "Cannot load RGB" file if I try to use that to load an LUT 
format file. The other option is where it says "heatmap" i can change 
the option to select a custom label, but if I try to enter an LUT file 
into there, freeview crashes (which is fine, I guess that was the 
wrong place).


So can anyone tell me what I'm missing for the place to load the LUT 
file or an alternative colormap?


Thanks for your help!

Regards

Ben

On Tue, Mar 27, 2018 at 1:10 PM Ruopeng Wang 
mailto:rpw...@nmr.mgh.harvard.edu>> wrote:


It looks like a customized look up table will work for your case.
You can simply select "Lookup table" as the colormap and load your
own lookup table. To create your own look up table, you can refer
to the content of FreeSurferColorLUT.txt file in your freesurfer
installation directory.

Best,
Ruopeng

On 03/27/2018 03:59 PM, Anna Mynick wrote:

Hi all,

I’m wondering whether there’s a way to create a custom color map
in Freeview that would operate as a alternative to the preset
Greyscale, Heatmap, NIH, PET, Jet and GE Color options.

Ideally, I could assign each number value a given color, e.g.
every “0” value in an .nii file is black, every “1” value is red,
every “2” value is blue, every “3" is green and so on. I already
have the RGB values worked out for each number value; I just need
to know how to format this information and where to put it so
that I can my custom colormap as an option in Freeview.

For my purposes, there would be no need to adjust the assigned
colors based on the overall range of values. For instance, there
would be no need to assign a different color value to a “1” value
depending on whether the highest value in the overall .nii file
is 1 or 100.

I did try reading the related conversation here

 
but
I can’t seem to find the file it references,
annotval2surfoverlay.m, in the Freesurfer directory.

Thanks very much for your help!
Anna



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The information in this e-mail is intended only for the person to
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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
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you in error
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sender and properly
dispose of the e-mail.



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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.

Re: [Freesurfer] Custom color map in Freeview

[Ben Smith]

External Email - Use Caution

I've been trying to do this as well, but I can't see the right place to
specify in freesurfer to specify an alternative lookup table.

For instance, if I am coloring a pial surface, then the first possibility
is to set a Color (where I can "load RGB map"). But I get an error "Cannot
load RGB" file if I try to use that to load an LUT format file. The other
option is where it says "heatmap" i can change the option to select a
custom label, but if I try to enter an LUT file into there, freeview
crashes (which is fine, I guess that was the wrong place).

So can anyone tell me what I'm missing for the place to load the LUT file
or an alternative colormap?

Thanks for your help!

Regards

Ben

On Tue, Mar 27, 2018 at 1:10 PM Ruopeng Wang 
wrote:

> It looks like a customized look up table will work for your case. You can
> simply select "Lookup table" as the colormap and load your own lookup
> table. To create your own look up table, you can refer to the content of
> FreeSurferColorLUT.txt file in your freesurfer installation directory.
>
> Best,
> Ruopeng
> On 03/27/2018 03:59 PM, Anna Mynick wrote:
>
> Hi all,
>
> I’m wondering whether there’s a way to create a custom color map in
> Freeview that would operate as a alternative to the preset Greyscale,
> Heatmap, NIH, PET, Jet and GE Color options.
>
> Ideally, I could assign each number value a given color, e.g. every “0”
> value in an .nii file is black, every “1” value is red, every “2” value is
> blue, every “3" is green and so on. I already have the RGB values worked
> out for each number value; I just need to know how to format this
> information and where to put it so that I can my custom colormap as an
> option in Freeview.
>
> For my purposes, there would be no need to adjust the assigned colors
> based on the overall range of values. For instance, there would be no need
> to assign a different color value to a “1” value depending on whether the
> highest value in the overall .nii file is 1 or 100.
>
> I did try reading the related conversation here
> 
>  but
> I can’t seem to find the file it references, annotval2surfoverlay.m, in
> the Freesurfer directory.
>
> Thanks very much for your help!
> Anna
>
>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Custom color map in Freeview

[Ruopeng Wang]

It looks like a customized look up table will work for your case. You 
can simply select "Lookup table" as the colormap and load your own 
lookup table. To create your own look up table, you can refer to the 
content of FreeSurferColorLUT.txt file in your freesurfer installation 
directory.


Best,
Ruopeng

On 03/27/2018 03:59 PM, Anna Mynick wrote:

Hi all,

I’m wondering whether there’s a way to create a custom color map in 
Freeview that would operate as a alternative to the preset Greyscale, 
Heatmap, NIH, PET, Jet and GE Color options.


Ideally, I could assign each number value a given color, e.g. every 
“0” value in an .nii file is black, every “1” value is red, every “2” 
value is blue, every “3" is green and so on. I already have the RGB 
values worked out for each number value; I just need to know how to 
format this information and where to put it so that I can my custom 
colormap as an option in Freeview.


For my purposes, there would be no need to adjust the assigned colors 
based on the overall range of values. For instance, there would be no 
need to assign a different color value to a “1” value depending on 
whether the highest value in the overall .nii file is 1 or 100.


I did try reading the related conversation here 
 but 
I can’t seem to find the file it references, annotval2surfoverlay.m, 
in the Freesurfer directory.


Thanks very much for your help!
Anna



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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] Custom color map in Freeview

[Anna Mynick]

Hi all,

I’m wondering whether there’s a way to create a custom color map in Freeview 
that would operate as a alternative to the preset Greyscale, Heatmap, NIH, PET, 
Jet and GE Color options.

Ideally, I could assign each number value a given color, e.g. every “0” value 
in an .nii file is black, every “1” value is red, every “2” value is blue, 
every “3" is green and so on. I already have the RGB values worked out for each 
number value; I just need to know how to format this information and where to 
put it so that I can my custom colormap as an option in Freeview.

For my purposes, there would be no need to adjust the assigned colors based on 
the overall range of values. For instance, there would be no need to assign a 
different color value to a “1” value depending on whether the highest value in 
the overall .nii file is 1 or 100.

I did try reading the related conversation 
here
 but I can’t seem to find the file it references, annotval2surfoverlay.m, in 
the Freesurfer directory.

Thanks very much for your help!
Anna

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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.