[Freesurfer] mri_vol2surf error

500 0. 0. 0. 1. " Thanks in advance for your help, Sincerely, Loïc Daumail Université Lyon 1 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_vol2surf error

External Email - Use Caution Dear Doug Greve, Sorry, issue solved! I had used a wrong path directory in the commandline... it’s now working perfectly well. Thanks for your help, Sincerely, Loïc Daumail Le mer. 17 avr. 2019 à 17:25, Greve, Douglas N.,Ph.D. <

[Freesurfer] Labelling SurfStat p-value surface map

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

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

Re: [Freesurfer] Labelling SurfStat p-value surface map

e 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 m

Re: [Freesurfer] Labelling SurfStat p-value surface map

... 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,

Re: [Freesurfer] Labelling SurfStat p-value surface map

sychosomatics 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, > > > &

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 > v

Re: [Freesurfer] Labelling SurfStat p-value surface map

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 >

Re: [Freesurfer] Labelling SurfStat p-value surface map

ely, 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: >

Re: [Freesurfer] Labelling SurfStat p-value surface map

, 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 believ

Re: [Freesurfer] Labelling SurfStat p-value surface map

w 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 > cr

Re: [Freesurfer] Labelling SurfStat p-value surface map

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: > >

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,

Re: [Freesurfer] Labelling SurfStat p-value surface map

;... 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

Re: [Freesurfer] Labelling SurfStat p-value surface map

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 > wrot

[Freesurfer] Error with running retinotopy glm

External Email - Use Caution Dear FreeSurfer experts, I am trying to perform a retinotopy analysis using fs-fast with Freesurfer version 7.3.2 on a Mac OS Monterey Version 12.6.2 Here is the error I am having (I saw this same error in the archive, but I wasn't able to find any so

Re: [Freesurfer] Error with running retinotopy glm

/R2023a/bin/matlab -nojvm -nodesktop -r "run /home/tonglab/Documents/Loic/retinotopy/${SUB}_sourceData/sxa3.m"; done " Please see attached the annalysis info file of one of the runs (though the error applies to all the runs) Any advice would be highly appreciated at this stage. Than