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 >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>
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