Re: [Freesurfer] Labelling SurfStat p-value surface map

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Hi Loïc,

you can load the atlases using `read_annotation` in Matlab, then of course use them for whatever purpose you like (including in surfstat). This code should get you started:

subjects_dir = '/data/mystudy'; subject_id = 'subject1'; hemi = 'lh';

aparc_file_this_hemi = fullfile(subjects_dir, subject_id, 'label', sprintf("%s.aparc.annot", hemi)); [vertices, label, colortable] = read_annotation(aparc_file_this_hemi); fprintf("Read aparc parcellation file '%s' containing %d regions.\n", aparc_file_this_hemi, length(colortable.struct_names)); for sidx = 1:length(colortable.struct_names) region = colortable.struct_names{sidx}; struct_code = colortable.table(sidx, 5); vertices_of_struct_roi = find(label == struct_code); fprintf("Found region '%s' with %d verts.\n", region, length(vertices_of_struct_roi)); end

To color the regions in surfstat, you would then need to set a colormap that has the correct number of colors (36 for Desikan, I think), using the colortable variable.

Best,

Tim

On May 23, 2019 at 11:35 AM Loïc Daumail loic.daumail@gmail.com wrote:

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Hi Bruce,

I am coming back to this request as I was wondering: would it be possible to load freesurfer surface atlases in surfstat in order to label my surfaces? Is their format compatible? I saw surfstat only accepts a limited array of formats...

Thanks, Best,

Loïc

Le lun. 20 mai 2019 à 16:15, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit :

...

sure. All the fsaverages are in the same space (they are subsets of fsaverage) On Mon, 20 May 2019, Loïc Daumail wrote:

...

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Hi Bruce,

Thanks for your response. Is it also fine for fsaverage5 surface or I

need to switch my data to

...

fsaverage?

Thanks,

Sincerely,

Loïc

Le lun. 20 mai 2019 à 15:52, Bruce Fischl fischl@nmr.mgh.harvard.edu

a écrit :

...

  Hi Loic

  if you are on the fsaverage surface you can save the -log10(p)

values

...

  using save_mgh.m, then load them in freeview and threshold them or
  whatever

  cheers
  Bruce
  On Mon, 20 May 2019, Loïc Daumail wrote:

  >
  >         External Email - Use Caution
  >
  > Also, one more thing:
  >
  > My data is on fsaverage5 resolution.
  >
  > Thanks in advance,
  >
  > Sincerely,
  >
  > Loïc
  >
  > Le lun. 20 mai 2019 à 09:49, Loïc Daumail <

loic.daumail@gmail.com> a écrit :

...

  >       Dear Freesurfer community,
  >
  > I obtained score matrices of surfaces after performing diffusion

embedding map on fMRI

...

  data.
  >
  > I am now using the SurfStat toolbox(Matlab) in order to obtain

p-value maps to compare

...

  between
  > two groups.
  >
  > After obtaining the p-value map, I would like to label the

surface in order to

...

  identify the
  > regions of significant difference between both groups.
  >
  > Would it be possible to use Freview in order to do it?
  > If so, which format should I use for my SurfStatP output p-value

map?

...

  > How would you do it, (tools to convert into a specific format,

surfaces and atlas to

...

  load on
  > Freeview, which format for those ones)?
  > I would be very grateful if you could detail a bit, as I am new

to these tools!

...

  >
  > Thanks in advance,
  >
  > Loïc Daumail
  >
  >
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