Re: [Freesurfer] Labelling SurfStat p-value surface map
glad to hear it worked out Bruce On Thu, 27 Jun 2019, Loïc Daumail wrote: 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 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 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: 1.00, 1.00, 1.00 > 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: 0.00 > ras xform present > xform info: x_r = -1., y_r = 0., z_r = 0., c_r = > 0. > : x_a = 0., y_a = 0., z_a = 1., c_a = > 0. > : x_s = 0., y_s = -1., z_s = 0., c_s = > 0. > > talairach xfm : > Orientation : LIA > Primary Slice Direction: coronal > > voxel to ras transform: > -1. 0. 0. 5121. > 0. 0. 1. -0.5000 > 0. -1. 0. 0.5000 > 0. 0. 0. 1. > > voxel-to-ras determinant -1 > > ras to voxel transform: > -1. -0. -0. 5121. > -0. -0. -1. 0.5000 > -0. 1. -0. 0.5000 > -0. -0. -0. 1. > " > 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 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 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
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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 > 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: 1.00, 1.00, 1.00 > > 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: 0.00 > > ras xform present > > xform info: x_r = -1., y_r = 0., z_r = 0., c_r = > > 0. > > : x_a = 0., y_a = 0., z_a = 1., c_a = > > 0. > > : x_s = 0., y_s = -1., z_s = 0., c_s = > > 0. > > > > talairach xfm : > > Orientation : LIA > > Primary Slice Direction: coronal > > > > voxel to ras transform: > >-1. 0. 0. 5121. > > 0. 0. 1.-0.5000 > > 0. -1. 0. 0.5000 > > 0. 0. 0. 1. > > > > voxel-to-ras determinant -1 > > > > ras to voxel transform: > >-1. -0. -0. 5121. > >-0. -0. -1. 0.5000 > >-0. 1. -0. 0.5000 > >-0. -0. -0. 1. > > " > > 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 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 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: 1.00, 1.00,
Re: [Freesurfer] Labelling SurfStat p-value surface map
External Email - Use Caution Just a short note regarding these errors: > > Le lun. 24 juin 2019 à 16:50, Loïc Daumail a > > écrit : > > > >> 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 > [...] If I had to guess I would say you are trying to run this on some HPC system that is using environment-modules (http://modules.sourceforge.net/) to make different software versions available to its users. I have no idea whether these are just warnings and whether they affect the FreeSurfer output or not (it seems they don't), but maybe you should still ask the administrators of the cluster about them. It could be that all you have to do to get rid of them is something like module load tcsh to get rid of them, but that's just guessing. Better ask the admins. 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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: 1.00, 1.00, 1.00 > 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: 0.00 > ras xform present > xform info: x_r = -1., y_r = 0., z_r = 0., c_r = > 0. > : x_a = 0., y_a = 0., z_a = 1., c_a = > 0. > : x_s = 0., y_s = -1., z_s = 0., c_s = > 0. > > talairach xfm : > Orientation : LIA > Primary Slice Direction: coronal > > voxel to ras transform: >-1. 0. 0. 5121. > 0. 0. 1.-0.5000 > 0. -1. 0. 0.5000 > 0. 0. 0. 1. > > voxel-to-ras determinant -1 > > ras to voxel transform: >-1. -0. -0. 5121. >-0. -0. -1. 0.5000 >-0. 1. -0. 0.5000 >-0. -0. -0. 1. > " > 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 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 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: 1.00, 1.00, 1.00 > >> 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: 0.00 > >> ras xform present > >> xform info: x_r = -1., y_r = 0., z_r = 0., c_r = > >> 0. > >> : x_a = 0., y_a = 0., z_a = 1., c_a = > >> 0. > >> : x_s = 0., y_s = -1., z_s = 0., c_s = > >> 0. > >> > >> talairach xfm : > >> Orientation : LIA > >> Primary Slice
Re: [Freesurfer] Labelling SurfStat p-value surface map
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: 1.00, 1.00, 1.00 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: 0.00 ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0. : x_a = 0., y_a = 0., z_a = 1., c_a = 0. : x_s = 0., y_s = -1., z_s = 0., c_s = 0. talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 5121. 0. 0. 1.-0.5000 0. -1. 0. 0.5000 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. -0. -0. 5121. -0. -0. -1. 0.5000 -0. 1. -0. 0.5000 -0. -0. -0. 1. " 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 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 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: 1.00, 1.00, 1.00 >> 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: 0.00 >> ras xform present >> xform info: x_r = -1., y_r = 0., z_r = 0., c_r = >> 0. >> : x_a = 0., y_a = 0., z_a = 1., c_a = >> 0. >> : x_s = 0., y_s = -1., z_s = 0., c_s = >> 0. >> >> talairach xfm : >> Orientation : LIA >> Primary Slice Direction: coronal >> >> voxel to ras transform: >>-1. 0. 0. 5121. >> 0. 0. 1.-0.5000 >> 0. -1. 0. 0.5000 >> 0. 0. 0. 1. >> >> voxel-to-ras determinant -1 >> >> ras to voxel transform: >>-1. -0. -0. 5121. >>-0. -0. -1. 0.5000 >>-0. 1. -0. 0.5000 >>-0. -0. -0. 1. >> " >> 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: 1.00, 1.00, 1.00 >> type: FLOAT (3) >>fov: 10242.000 >>dof: 1 >>
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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: 1.00, 1.00, 1.00
> 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: 0.00
> ras xform present
> xform info: x_r = -1., y_r = 0., z_r = 0., c_r =
> 0.
> : x_a = 0., y_a = 0., z_a = 1., c_a =
> 0.
> : x_s = 0., y_s = -1., z_s = 0., c_s =
> 0.
>
> talairach xfm :
> Orientation : LIA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
>-1. 0. 0. 5121.
> 0. 0. 1.-0.5000
> 0. -1. 0. 0.5000
> 0. 0. 0. 1.
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
>-1. -0. -0. 5121.
>-0. -0. -1. 0.5000
>-0. 1. -0. 0.5000
>-0. -0. -0. 1.
> "
> 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: 1.00, 1.00, 1.00
> 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: 0.00
> ras xform present
> xform info: x_r = -1., y_r = 0., z_r = 0., c_r =
> 5120.5000
> : x_a = 0., y_a = 0., z_a = 1., c_a =
> 0.
> : x_s = 0., y_s = -1., z_s = 0., c_s =
> -5120.5000
>
> talairach xfm :
> Orientation : LIA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
>-1. 0. 0. 5121.
> 0. 0. 1.-0.5000
> 0. -1. 0. 0.5000
> 0. 0. 0. 1.
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
>-1. -0. -0. 5121.
>-0. -0. -1. 0.5000
>-0. 1. -0. 0.5000
>-0. -0. -0. 1.
> "
>
> 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
Re: [Freesurfer] Labelling SurfStat p-value surface map
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: 1.00, 1.00, 1.00
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: 0.00
ras xform present
xform info: x_r = -1., y_r = 0., z_r = 0., c_r =
0.
: x_a = 0., y_a = 0., z_a = 1., c_a =
0.
: x_s = 0., y_s = -1., z_s = 0., c_s =
0.
talairach xfm :
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1. 0. 0. 5121.
0. 0. 1.-0.5000
0. -1. 0. 0.5000
0. 0. 0. 1.
voxel-to-ras determinant -1
ras to voxel transform:
-1. -0. -0. 5121.
-0. -0. -1. 0.5000
-0. 1. -0. 0.5000
-0. -0. -0. 1.
"
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: 1.00, 1.00, 1.00
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: 0.00
ras xform present
xform info: x_r = -1., y_r = 0., z_r = 0., c_r =
5120.5000
: x_a = 0., y_a = 0., z_a = 1., c_a =
0.
: x_s = 0., y_s = -1., z_s = 0., c_s =
-5120.5000
talairach xfm :
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1. 0. 0. 5121.
0. 0. 1.-0.5000
0. -1. 0. 0.5000
0. 0. 0. 1.
voxel-to-ras determinant -1
ras to voxel transform:
-1. -0. -0. 5121.
-0. -0. -1. 0.5000
-0. 1. -0. 0.5000
-0. -0. -0. 1.
"
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
Re: [Freesurfer] Labelling SurfStat p-value surface map
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: 0.00
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. 0. 0. 1.
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
mailto: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
> mailto: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
Re: [Freesurfer] Labelling SurfStat p-value surface map
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: 0.00
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. 0. 0. 1.
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 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 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
> >
>
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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 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 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 a
Re: [Freesurfer] Labelling SurfStat p-value surface map
why do you have 18715 elements? How did you create it? You can run mri_info on the .mgz volume to see if it has the correct dimensions. BTW: you might repost your original question early next week if you haven't resolve things. Doug is back and probably has an easy way to do what you want cheers Bruce On Fri, 21 Jun 2019, Loïc Daumail wrote: External Email - Use Caution 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 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 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 a écrit : > Hi Tim, > > 'mean_rest' is a diffusion embedding map, which contains scores for every vertex on > fsaverage5
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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/linux-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 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 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 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
Re: [Freesurfer] Labelling SurfStat p-value surface map
External Email - Use Caution 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/linux-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 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 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 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 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. > > > >
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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 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 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 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 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
> > 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
>
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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 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 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
>>> 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 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
Re: [Freesurfer] Labelling SurfStat p-value surface map
External Email - Use Caution
Hi Tim,
Your link works perfectly, it's awesome!
Thanks a lot,
Best,
Loïc
Le lun. 27 mai 2019 à 11:43, Loïc Daumail 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 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
>> 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 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 > >
>> > > 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
>> > > > > >
>> >
Re: [Freesurfer] Labelling SurfStat p-value surface map
External Email - Use Caution
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 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 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 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
> > > 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
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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 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
> > 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
> > 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
> > > > > >
> > > > > >
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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 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 > > 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 > > 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
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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 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 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
Re: [Freesurfer] Labelling SurfStat p-value surface map
External Email - Use Caution
Hi Loïc,
you can load the atlases using `read_annotation` in Matlab, then of course use
them for whatever purpose you like (including in surfstat). This code should
get you started:
subjects_dir = '/data/mystudy';
subject_id = 'subject1';
hemi = 'lh';
aparc_file_this_hemi = fullfile(subjects_dir, subject_id, 'label',
sprintf("%s.aparc.annot", hemi));
[vertices, label, colortable] = read_annotation(aparc_file_this_hemi);
fprintf("Read aparc parcellation file '%s' containing %d regions.\n",
aparc_file_this_hemi, length(colortable.struct_names));
for sidx = 1:length(colortable.struct_names)
region = colortable.struct_names{sidx};
struct_code = colortable.table(sidx, 5);
vertices_of_struct_roi = find(label == struct_code);
fprintf("Found region '%s' with %d verts.\n", region,
length(vertices_of_struct_roi));
end
To color the regions in surfstat, you would then need to set a colormap that
has the correct number of colors (36 for Desikan, I think), using the
colortable variable.
Best,
Tim
> On May 23, 2019 at 11:35 AM Loïc Daumail 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 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
> > 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
--
Tim Schäfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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 > 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
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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 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
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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 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
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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
Re: [Freesurfer] Labelling SurfStat p-value surface map
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 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] Labelling SurfStat p-value surface map
External Email - Use Caution 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] labelling
Dear freesurfer experts, I intend to create ROIs from the aparc+seg.mgz file and would like to ask whether the following assignments are correct (sorry for the long list): 10: left_thalamus 11: left_caudate 12: left_putamen 13: left_pallidum 17: left_hippocampus 18: left_amygdala 26: left_accumbens 49: right_thalamus 50: right_caudate 51: right_putamen 52: right_pallidum 53: right_hippocampus 54: right_amygdala 58: right_accumbens 1001: left_bankssts 1002: left_caudalanteriorcingulate 1003: left_caudalmiddlefrontal 1005: left_cuneus 1006: left_entorhinal 1007: left_fusiform 1008: left_inferiorparietal 1009: left_inferiortemporal 1010: left_isthumscingulate 1011: left_lateraloccipital 1012: left_lateralorbitofrontal 1013: left_lingual 1014: left_medialorbitofrontal 1015: left_middletemporal 1016: left_parahippocampal 1017: left_paracentral 1018: left_parsopercularis 1019: left_parsorbitalis 1020: left_parstriangularis 1021: left_pericalcarine 1022: left_postcentral 1023: left_posteriorcingulate 1024: left_precentral 1025: left_precuneus 1026: left_rostralanteriorcingulate 1027: left_rostralmiddlefrontal 1028: left_superiorfrontal 1029: left_superiorparietal 1030: left_superiortemporal 1031: left_supramarginal 1032: left_frontalpole 1033: left_temporalpole 1034: left_transversetemporal 1035: left_insula 2001: right_banksst 2002: right_caudalanteriorcingulate 2003: right_caudalmiddlefrontal 2005: right_cuneus 2006: right_entorhinal 2007: right_fusiform 2008: right_inferiorparietal 2009: right_inferiortemporal 2010: right_isthumscingulate 2011: right_lateraloccipital 2012: right_lateralorbitofrontal 2013: right_lingual 2014: right_medialorbitofrontal 2015: right_middletemporal 2016: right_parahippocampal 2017: right_paracentral 2018: right_parsopercularis 2019: right_parsorbitalis 2020: right_parstriangularis 2021: right_pericalcarine 2022: right_postcentral 2023: right_posteriorcingulate 2024: right_precentral 2025: right_precuneus 2026: right_rostralanteriorcingulate 2027: right_rostralmiddlefrontal 2028: right_superiorfrontal 2029: right_superiorparietal 2030: right_superiortemporal 2031: right_supramarginal 2032: right_frontalpole 2033: right_temporalpole 2034: right_transversetemporal 2035: right_insula Many thanks for the check. Best wishes André ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] labelling
Hi Andre they look right, but check the FreeSurferColorLUT.txt file - that is the definitive location cheers Bruce On Fri, 24 Apr 2015, André Schmidt wrote: Dear freesurfer experts, I intend to create ROIs from the aparc+seg.mgz file and would like to ask whether the following assignments are correct (sorry for the long list): 10: left_thalamus 11: left_caudate 12: left_putamen 13: left_pallidum 17: left_hippocampus 18: left_amygdala 26: left_accumbens 49: right_thalamus 50: right_caudate 51: right_putamen 52: right_pallidum 53: right_hippocampus 54: right_amygdala 58: right_accumbens 1001: left_bankssts 1002: left_caudalanteriorcingulate 1003: left_caudalmiddlefrontal 1005: left_cuneus 1006: left_entorhinal 1007: left_fusiform 1008: left_inferiorparietal 1009: left_inferiortemporal 1010: left_isthumscingulate 1011: left_lateraloccipital 1012: left_lateralorbitofrontal 1013: left_lingual 1014: left_medialorbitofrontal 1015: left_middletemporal 1016: left_parahippocampal 1017: left_paracentral 1018: left_parsopercularis 1019: left_parsorbitalis 1020: left_parstriangularis 1021: left_pericalcarine 1022: left_postcentral 1023: left_posteriorcingulate 1024: left_precentral 1025: left_precuneus 1026: left_rostralanteriorcingulate 1027: left_rostralmiddlefrontal 1028: left_superiorfrontal 1029: left_superiorparietal 1030: left_superiortemporal 1031: left_supramarginal 1032: left_frontalpole 1033: left_temporalpole 1034: left_transversetemporal 1035: left_insula 2001: right_banksst 2002: right_caudalanteriorcingulate 2003: right_caudalmiddlefrontal 2005: right_cuneus 2006: right_entorhinal 2007: right_fusiform 2008: right_inferiorparietal 2009: right_inferiortemporal 2010: right_isthumscingulate 2011: right_lateraloccipital 2012: right_lateralorbitofrontal 2013: right_lingual 2014: right_medialorbitofrontal 2015: right_middletemporal 2016: right_parahippocampal 2017: right_paracentral 2018: right_parsopercularis 2019: right_parsorbitalis 2020: right_parstriangularis 2021: right_pericalcarine 2022: right_postcentral 2023: right_posteriorcingulate 2024: right_precentral 2025: right_precuneus 2026: right_rostralanteriorcingulate 2027: right_rostralmiddlefrontal 2028: right_superiorfrontal 2029: right_superiorparietal 2030: right_superiortemporal 2031: right_supramarginal 2032: right_frontalpole 2033: right_temporalpole 2034: right_transversetemporal 2035: right_insula Many thanks for the check. Best wishes André ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] labelling of cluster regions
Hi Koushik, it just uses the label of the maximum. doug On 04/19/2012 05:30 PM, Govindarajan, Koushik Athreya wrote: Hi, I have a question regarding how the clusters are labeled after the results of a Monte-Carlo Simulation. Similar regions from 2 different patient populations seem to be labeled differently. On one of my results, the cluster has been labeled as in the precentral region and a similar region on another population seems to be labeled as superior frontal region. Is the labeling based on which region the majority of significant vertices fall under? In that case, would a cluster that kind of falls over 2 regions of the brain be labeled as the one with more vertices? Thanks for all the help Koushik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] labelling of cluster regions
Hi, I have a question regarding how the clusters are labeled after the results of a Monte-Carlo Simulation. Similar regions from 2 different patient populations seem to be labeled differently. On one of my results, the cluster has been labeled as in the precentral region and a similar region on another population seems to be labeled as superior frontal region. Is the labeling based on which region the majority of significant vertices fall under? In that case, would a cluster that kind of falls over 2 regions of the brain be labeled as the one with more vertices? Thanks for all the help Koushik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Labelling Results on Tksurfer
Hi Christine, what subject are you overlaying the results on? If it's fsaverage (our average subject) then it should have ?h.aparc.annot files in the label subdirectory that you can load file-label-import annotation. cheers, Bruce On Fri, 25 Jan 2008 [EMAIL PROTECTED] wrote: Hi I am using Freesurfer version 3.0.5 via Linux and I am trying to label my results on tksurfer. I have already loaded the group descriptor file and the overlay. I can visualize my results but when I click on these specific reasons, it does not tell me where these areas lie. How do I go about labellingmy results so that everytime I click on any one of these regions it will automatically tell me the name of the area? Any feedback is greatly appreciated. Christine Thornton ___ 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] Labelling Results on Tksurfer
Hi I am using Freesurfer version 3.0.5 via Linux and I am trying to label my results on tksurfer. I have already loaded the group descriptor file and the overlay. I can visualize my results but when I click on these specific reasons, it does not tell me where these areas lie. How do I go about labellingmy results so that everytime I click on any one of these regions it will automatically tell me the name of the area? Any feedback is greatly appreciated. Christine Thornton ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
