External Email - Use Caution
I also tried saving the last file in 10242 x 1 x 1.. but nothing is coming
neither.
Thanks,
Sincerely,
Loïc
Le lun. 24 juin 2019 à 16:50, Loïc Daumail <loic.daum...@gmail.com> a
écrit :
> 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
>>> > > > >
>>> > > > > _______________________________________________
>>> > > > > 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
>>> > >
>>> > >
>>> > >_______________________________________________
>>> > 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
>> 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
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
