External Email - Use Caution        

Hi Doug,

Thanks for your help!

However, using mri_convert, I still get the same message with tclsh.
"
mri_convert lh.thickness template.mgh
/usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or
directory
/usr/share/modules/init/bash: line 58: export: _moduleraw: not a function
/usr/share/modules/init/bash: line 60: export: module: not a function
mri_convert.bin lh.thickness template.mgh
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from lh.thickness...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to template.mgh...
"
There is progess though, as here, we see that template.mgh seems not empty:
"
mri_info template.mgh
Volume information for template.mgh
          type: MGH
    dimensions: 10242 x 1 x 1
   voxel sizes: 1.000000, 1.000000, 1.000000
          type: FLOAT (3)
           fov: 10242.000
           dof: 0
        xstart: -5121.0, xend: 5121.0
        ystart: -0.5, yend: 0.5
        zstart: -0.5, zend: 0.5
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
       nframes: 1
       PhEncDir: UNKNOWN
       FieldStrength: 0.000000
ras xform present
    xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =
0.0000
              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =
0.0000
              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =
0.0000

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.0000   0.0000   0.0000  5121.0000
                0.0000   0.0000   1.0000    -0.5000
                0.0000  -1.0000   0.0000     0.5000
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
               -1.0000  -0.0000  -0.0000  5121.0000
               -0.0000  -0.0000  -1.0000     0.5000
               -0.0000   1.0000  -0.0000     0.5000
               -0.0000  -0.0000  -0.0000     1.0000
"
Also, using MRIread and MRIwrite, we can see that it's not empty neither:

"
Volume information for lh_emb_comp_sub-002.mgz
          type: MGH
    dimensions: 1 x 10242 x 1
   voxel sizes: 1.000000, 1.000000, 1.000000
          type: FLOAT (3)
           fov: 10242.000
           dof: 1
        xstart: -0.5, xend: 0.5
        ystart: -5121.0, yend: 5121.0
        zstart: -0.5, zend: 0.5
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
       nframes: 1
       PhEncDir: UNKNOWN
       FieldStrength: 0.000000
ras xform present
    xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =
 5120.5000
              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =
0.0000
              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =
-5120.5000

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.0000   0.0000   0.0000  5121.0000
                0.0000   0.0000   1.0000    -0.5000
                0.0000  -1.0000   0.0000     0.5000
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
               -1.0000  -0.0000  -0.0000  5121.0000
               -0.0000  -0.0000  -1.0000     0.5000
               -0.0000   1.0000  -0.0000     0.5000
               -0.0000  -0.0000  -0.0000     1.0000
"

But then, trying to load the overlay on the lh.pial still isn't possible,
with endless "FreadFloat: fread failed"

Thanks in advance for your help,

Sincerely,

Loïc

Le lun. 24 juin 2019 à 14:21, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

> It is probably using a tcsh shell to do the compression.
> Try using MRIwrite instead. You will have to create an mri structure. The
> easiest way to do that is to
> mri_convert lh.thickness template.mgh
> then read the template in to matlab
> template = MRIread('template.mgh');
> template.vol = yourdata
> MRIwrite(template,'yourdata.mgz')
>
>
>
> On 6/24/2019 11:54 AM, Loïc Daumail wrote:
>
>         External Email - Use Caution
> Hi Bruce and Doug,
>
> To respond to your questions:
> I projected the BOLD data on the surface using mri_vol2surf function. Then
> obtained a .mgz file of size 10242 x 1 x 1 x 200.
>
> Then I performed diffusion embedding (unsupervised dimensionality
> reduction technique) on this .mgz file, whose output was a .npy file.
> I then loaded this file into a matrix on python, which size was 1 x 18715
> x 5.
> I then saved this file as a .mat file.
> Then loaded it on matlab, and kept only 1 x 18715 x 1 part of the matrix,
> and stored it into a zeros(1, 20484).
> Then kept only the part from (0:10242) and used save_mgh function to save
> this data into a .mgz file
> Looking at the info of my .mgz file created with save_mgh, I see that the
> file doesn't seem to include the data:
>
> "
> mri_info lh_emb_sub-002_compassion.mgz
> Volume information for lh_emb_sub-002_compassion.mgz
>           type: MGH
>     dimensions: 1 x 16 x 1
>    voxel sizes:   -nan,   -nan,   -nan
>           type: FLOAT (3)
>            fov: -nan
>            dof: 1
>         xstart: -nan, xend: -nan
>         ystart: -nan, yend: -nan
>         zstart: -nan, zend: -nan
>             TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
> degrees
>        nframes: 1
>        PhEncDir: UNKNOWN
>        FieldStrength: 0.000000
> ras xform present
>     xform info: x_r =     -nan, y_r =     -nan, z_r =     -nan, c_r =
>   -nan
>               : x_a =     -nan, y_a =     -nan, z_a =     -nan, c_a =
>   -nan
>               : x_s =     -nan, y_s =     -nan, z_s =     -nan, c_s =
>   -nan
>
> talairach xfm :
> Orientation   : III
> Primary Slice Direction: axial
>
> voxel to ras transform:
>                   -nan     -nan     -nan       -nan
>                   -nan     -nan     -nan       -nan
>                   -nan     -nan     -nan       -nan
>                 0.0000   0.0000   0.0000     1.0000
>
> voxel-to-ras determinant -nan
>
> ras to voxel transform:
> mat = NULL!
> MatrixFree: NULL mat POINTER!
> "
> It seems that save_mgh function requires tclsh package, as when I ran
> save_mgh for the first time with this command line:
> save_mgh('freeview_overlay',
> ['/home/loic/Documents/emb_output/mgh_format/emb_' char(subjectsList(1))
> '_' char(statesList(1)) '.MGZ'], M);
>
> I was getting this message in return in the matlab window:
> "
> /usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or
> directory
> /usr/share/modules/init/bash: line 58: export: _moduleraw: not a function
> /usr/share/modules/init/bash: line 60: export: module: not a function
> "
> Checking into the '/usr/bin/tclsh' directory, the only package
> called/related to tclsh was 'tclsh8.6'.
> I thus changed the name from 'tclsh8.6' to 'tclsh'.
>
> Then tried to save the matrix again with save_mgh function. Now I don't
> see the error message anymore.
> However I still get a .mgz file with nans, as seen in the previous
> mri_info message above.
>
> Would any of you have an advice on how I could make this work, in order to
> visualize this .mgz file on the left hemisphere pial surface in Freeview?
>
> Thanks in advance,
>
> Sincerely,
>
> Loïc
>
>
>
> Le ven. 21 juin 2019 à 16:24, Bruce Fischl <fis...@nmr.mgh.harvard.edu> a
> écrit :
>
>> I don't think it matters but I would use eye instead of nan for M. But
>> the
>> critical issue is where you get your data and what dimensions it has
>> cheers
>> Bruce
>>
>> On Fri, 21 Jun 2019, Loïc Daumail wrote:
>>
>> >
>> >         External Email - Use Caution
>> >
>> > Me again,
>> >
>> > Also, here is how I save the matrix on matlab:
>> >
>> > M = nan(4,4);
>> > save_mgh('freeview_overlay',
>> ['/home/loic/Documents/emb_output/mgh_format/lh_emb_'
>> > char(subjectsList(1)) '_' char(statesList(1)) '.mgz'], M);
>> >
>> > Thanks,
>> >
>> > Sincerely,
>> >
>> > Loïc
>> >
>> > Le ven. 21 juin 2019 à 12:25, Loïc Daumail <loic.daum...@gmail.com> a
>> écrit :
>> >       Hi Bruce,
>> >
>> > Thanks for your tip. Unfortunately, I am still running through an
>> error...
>> > I have a matrix of 18715 elements regarding both hemispheres.
>> > The size of fsaverage5 is 20484 I believe, so I filled the remaining
>> elements with zeros, and
>> > also tried with rand().
>> >
>> > The other issue is that I am not so sure which part of the matrix is
>> for lh and the other one
>> > for rh. Thus, I divided 18715/2 and took the 9357 first elements of the
>> 18715 matrix. Then
>> > filled it with zeros or random values to reach 10242.
>> >
>> > Then I saved it with save_mgh function and tried to load it with
>> freeview using the following
>> > command line:
>> > freeview
>> -f~/Documents/recon_all_success/freesurfer/fsaverage5/surf/lh.pial:overlay=~/Documents/emb_output/mgh
>> > _format/lh_emb_sub-002_compassion.mgz
>> >
>> > I am getting the following error:
>> > "
>> > Did not find any volume info
>> > 2 [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access
>> > out of range
>> > [0]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > [0]PETSC ERROR: or see
>> >
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>> ERROR:
>> > or try http://valgrind.org on linux or man libgmalloc on Apple to find
>> memory corruption
>> > errors
>> > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> > [0]PETSC ERROR: to get more information on the crash.
>> > [0]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> > [0]PETSC ERROR: Signal received!
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
>> 17:29:26 CDT 2008 HG
>> > revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
>> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> > [0]PETSC ERROR: See docs/index.html for manual pages.
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: Unknown Name on a linux-gnu named loic-HP-ZBook-17 by
>> loic Fri Jun 21 12:15:53
>> > 2019
>> > [0]PETSC ERROR: Libraries linked
>> from/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/lin
>> > ux-gnu-c-opt
>> > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
>> > [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
>> --with-fc=g77
>> > --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0
>> > --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: User provided function() line 0 in unknown directory
>> unknown file
>> > [unset]: aborting job:
>> > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0"
>> >
>> > Any idea of what could be wrong in my process?
>> >
>> > Thanks
>> >
>> > Sincerely,
>> >
>> > Loïc
>> >
>> >
>> >
>> > Le jeu. 20 juin 2019 à 19:39, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>> a écrit :
>> >       Hi Loïc
>> >
>> >       the .mgz file should having dimensions nvertices x 1 x 1 for
>> freeview to
>> >       know it is a surface overlay I believe
>> >
>> >       cheers
>> >       Bruce
>> >
>> >
>> >
>> >       On Thu, 20 Jun 2019, Loïc Daumail wrote:
>> >
>> >       >
>> >       >         External Email - Use Caution
>> >       >
>> >       > Hi Bruce,
>> >       >
>> >       > I am reaching out to you, as I am trying to load the surface
>> scalar values of
>> >       diffusion embedding
>> >       > for overlay on a pial surface in Freeview.
>> >       >
>> >       > I used save_mgh to save a scalar matrix containing surface
>> embedding values in
>> >       an .mgz format.
>> >       > However I can't load it in freeview, be either only half of the
>> matrix data (one
>> >       hemisphere I
>> >       > assume) or the whole matrix saved in the same file.
>> >       >
>> >       > Is there anything specific I need to do in order to be able to
>> visualize a
>> >       scalar overlay on a
>> >       > surface? Is .mgz a wrong format for scalar values? I also tried
>> with .nii.gz, or
>> >       .mgh. I am not even
>> >       > sure save_mgh can do all this...
>> >       >
>> >       > Thanks in advance,
>> >       >
>> >       > Sincerely,
>> >       >
>> >       > Loïc
>> >       >
>> >       >
>> >       >
>> >       > Le lun. 27 mai 2019 à 11:54, Loïc Daumail <
>> loic.daum...@gmail.com> a écrit :
>> >       >       Hi Tim,
>> >       >
>> >       > Your link works perfectly, it's awesome!
>> >       > Thanks a lot,
>> >       >
>> >       > Best,
>> >       >
>> >       > Loïc
>> >       >
>> >       > Le lun. 27 mai 2019 à 11:43, Loïc Daumail <
>> loic.daum...@gmail.com> a écrit :
>> >       >       Hi Tim,
>> >       >
>> >       > 'mean_rest' is a diffusion embedding map, which contains scores
>> for every vertex
>> >       on
>> >       > fsaverage5 surface resolution.
>> >       > 'surf.b' is the pial surface of both hemispheres of
>> fsaverage5... I also tried
>> >       forjust
>> >       > lh hemisphere, but it gives me the same result...
>> >       >
>> >       > Thanks for the link!
>> >       >
>> >       > Best,
>> >       >
>> >       > Loïc
>> >       >
>> >       > Le lun. 27 mai 2019 à 11:20, Tim Schäfer <ts...@rcmd.org> a
>> écrit :
>> >       >               External Email - Use Caution
>> >       >
>> >       >       Hi Loïc,
>> >       >
>> >       >       that does not look correct, the data is definitely off.
>> I'm not sure where
>> >       >       the variables `mean_rest` and `surf.b` come from in your
>> code, and I
>> >       suspect
>> >       >       that something is wrong with them.
>> >       >
>> >       >       In the meantime, I got interested in this myself and put
>> together some
>> >       code
>> >       >       that will load the Desikan data for both hemispheres and
>> display it in
>> >       >       surfstat. Feel free to use it, there also is an example
>> screenshot of the
>> >       >       results:
>> >       >
>> >       >
>> >       >
>> >
>> https://github.com/dfsp-spirit/comp_neuro_science/tree/master/surfstat_desikan
>> >       >
>> >       >       Best,
>> >       >
>> >       >       Tim
>> >       >
>> >       >       --
>> >       >       Dr. Tim Schäfer
>> >       >       Postdoc Computational Neuroimaging
>> >       >       Department of Child and Adolescent Psychiatry,
>> Psychosomatics and
>> >       >       Psychotherapy
>> >       >       University Hospital Frankfurt, Goethe University
>> Frankfurt am Main,
>> >       Germany
>> >       >
>> >       >       > On May 27, 2019 at 11:01 AM Loïc Daumail <
>> loic.daum...@gmail.com> wrote:
>> >       >       >
>> >       >       >
>> >       >       >         External Email - Use Caution
>> >       >       >
>> >       >       > Hi Tim,
>> >       >       >
>> >       >       > Thanks a lot for your help, indeed, this is exactly
>> what I needed!
>> >       >       > I wrote this :
>> >       >       > "
>> >       >       > subjects_dir =
>> '/home/loic/Documents/recon_all_success/freesurfer/';
>> >       >       > subject_id = 'sub-004';
>> >       >       > 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
>> >       >       > fig1 = figure();
>> >       >       > SurfStatView(mean_rest, surf.b);
>> >       >       > SurfStatColormap(colortable.table(:,1:3)/255);
>> >       >       > "
>> >       >       > However, the image I obtain seems a bit fuzzy...( see
>> attached)
>> >       >       > Is it because of my data?
>> >       >       >
>> >       >       > Thanks in advance,
>> >       >       >
>> >       >       > Loïc
>> >       >       >
>> >       >       >
>> >       >       > Le jeu. 23 mai 2019 à 17:20, Tim Schäfer <
>> ts...@rcmd.org> a écrit :
>> >       >       >
>> >       >       > >         External Email - Use Caution
>> >       >       > >
>> >       >       > > Afaik SurfStat is not maintained anymore and I think
>> it's been this
>> >       way
>> >       >       > > for quite a while now. Maybe someone else knows
>> better?
>> >       >       > >
>> >       >       > > The website is at
>> http://www.math.mcgill.ca/keith/surfstat/ and it
>> >       says
>> >       >       > > 'Updated 26 September 2008'. I'm not sure whether
>> that's really true,
>> >       >       but
>> >       >       > > at least for the last 14 months (the only time frame
>> I know about),
>> >       >       there
>> >       >       > > have not been any changes to that website or any new
>> releases of
>> >       >       SurfStat.
>> >       >       > >
>> >       >       > > Tim
>> >       >       > >
>> >       >       > > > On May 23, 2019 at 4:36 PM Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> >       >       > > wrote:
>> >       >       > > >
>> >       >       > > >
>> >       >       > > > Hi Loic
>> >       >       > > >
>> >       >       > > > sorry, can you ask whoever maintains surfstat? Or
>> maybe someone else
>> >       >       on
>> >       >       > > the
>> >       >       > > > list knows? I don't. You can label surfaces
>> manually with the dev
>> >       >       > > version
>> >       >       > > > of freeview if you want.
>> >       >       > > >
>> >       >       > > > cheers
>> >       >       > > > Bruce
>> >       >       > > >
>> >       >       > > >
>> >       >       > > > On Thu, 23 May 2019, Loïc
>> >       >       > > > Daumail wrote:
>> >       >       > > >
>> >       >       > > > >
>> >       >       > > > >         External Email - Use Caution
>> >       >       > > > >
>> >       >       > > > > 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
>> >       >       <fis...@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:
>> >       >       > > > >
>> >       >       > > > >       >
>> >       >       > > > >       >         External Email - Use Caution
>> >       >       > > > >       >
>> >       >       > > > >       > 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
>> <
>> >       >       > > fis...@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.daum...@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
>> >       >       > > > >       >       >
>> >       >       > > > >       >       >
>> >       >       > > > >       >
>>  >_______________________________________________
>> >       >       > > > >       >       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
>> >       >       > > > >
>> >       >       > > > >
>> >       >       > > > >_______________________________________________
>> >       >       > > > Freesurfer mailing list
>> >       >       > > > Freesurfer@nmr.mgh.harvard.edu
>> >       >       > > >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >       >       > >
>> >       >       > > --
>> >       >       > > Dr. Tim Schäfer
>> >       >       > > Postdoc Computational Neuroimaging
>> >       >       > > Department of Child and Adolescent Psychiatry,
>> Psychosomatics and
>> >       >       > > Psychotherapy
>> >       >       > > University Hospital Frankfurt, Goethe University
>> Frankfurt am Main,
>> >       >       Germany
>> >       >       > >
>> >       >       > > _______________________________________________
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>> >       >       > >
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>> >       >       > _______________________________________________
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>> >       >       >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >       >
>> >       >       _______________________________________________
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>> >       >
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>> >       >
>> >       >
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>> >
>> >
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