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 fischl@nmr.mgh.harvard.edu 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 <rpwang@nmr.mgh.harvard.edu> 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 <rpwang@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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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 list > Freesurfer@nmr.mgh.harvard.edu > https://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.