External Email - Use Caution
Hi Tim,
Thanks a lot for the effort!
Indeed, I self-created an mgh file from a matrix of 10242x1x1 elements.
After a few adjustments, it perfectly works in order to view the data on
Freeview.
I overlayed the individuals' data on lh.pial of fsaverage5 (created during
recon-all), as our diffusion embedding data has the same resolution.
Thanks everyone for all of your help!!
Sincerely,
Loïc
Le mer. 26 juin 2019 à 11:14, Tim Schäfer <ts...@rcmd.org> a écrit :
> External Email - Use Caution
>
> I found it hard to read the quoted mails and to follow along, but if I'm
> not mistaken you are trying to overlay a self-created mgh file with
> dimension 10242x1x1 onto the pial surface of sub-002 at
> sub-002/surf/lh.pial.
>
> How many vertices does sub-002/surf/lh.pial have? If the answer is not
> 10242, this is not gonna work.
>
> In one of the earlier mails you mentioned fsaverage5. Could it it be that
> you really intend to overlay onto
> $FREESURFER_HOME/subjects/fsaverage5/surf/lh.pial?
>
> Best,
>
> Tim
>
> > On June 26, 2019 at 10:48 AM Loïc Daumail <loic.daum...@gmail.com>
> wrote:
> >
> >
> > External Email - Use Caution
> >
> > Hi Freesurfer,
> > Getting back the former request,
> > I am still trying to load an overlay of my data onto a surface.. but it
> > still doesn't work well.
> > Here is the info of my overlay:
> > " mri_info lh_emb_comp_sub-002.mgz
> > Volume information for lh_emb_comp_sub-002.mgz
> > type: MGH
> > dimensions: 10242 x 1 x 1
> > voxel sizes: 1.000000, 1.000000, 1.000000
> > type: FLOAT (3)
> > fov: 10242.000
> > dof: 1
> > 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
> > "
> > Here is what I get when loading on freeview:
> >
> > "
> > freeview -f
> >
> ~/Documents/recon_all_success/freesurfer/sub-002/surf/lh.pial:overlay=lh_emb_comp_sub-002.mgz
> > Number of vertices in overlay data does not match with surface.
> > QClipboard: Unable to receive an event from the clipboard manager in a
> > reasonable time
> > "
> > The data was normalized in MNI space.
> > When I try to load it in FSLeyes, it works, but the overlay is completely
> > absent, it seems that it's empty. On the FSLeyes GUI, it's written
> > 'overlay out of bounds'...
> > The endpoint of this process would be to define ROIs in specific regions,
> > and Freeview is very handy with atlases.
> > Any advice is welcome!
> >
> > Thanks in advance,
> >
> > Sincerely,
> >
> > Loïc
> >
> >
> > Le lun. 24 juin 2019 à 17:01, Loïc Daumail <loic.daum...@gmail.com> a
> > écrit :
> >
> > >
> > > 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
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> > >>
> > >>
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> > 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
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