[Freesurfer] cortical surface pattern matching

Hi, has anyone created functionality to compare the spatial correlation/similarity of two patterns in the form of cortical surface overlays. What I am looking at is a have scalar at every point on the cortical surface. obviously this is just a list of vertices with a scalar value associated

[Freesurfer] perl & bbregister conflicts

Hi folks, somebody stuck me with Ubuntu 16 for a month and I found the perl problem and so switched to the dev version which solved that problem. discovered that with the dev version bbregister throws an error having to do with fsl flirt throws an error `terminate after throwing an instanc

[Freesurfer] resampling data onto cortical surface

External Email - Use Caution I have R1 values that I want to resample onto the cortical surface. The R1 values were computed from a multi echo T1 sequence that was also used to create the T1 weighted image that was used in recon-all to produce the cortical surface reconstruction

Re: [Freesurfer] resampling data onto cortical surface

probably measuring R2*, not R1. On 10/22/2018 12:55 PM, GREGORY R KIRK wrote: > > External Email - Use Caution > > > I have R1 values that I want to resample onto the cortical surface. > The R1 values were computed from a multi echo > > T1 sequence that was also used t

Re: [Freesurfer] resampling data onto cortical surface

(run mri_vol2vol with --help to get more info). btw, if you have multi echo data, you are probably measuring R2*, not R1. On 10/22/2018 12:55 PM, GREGORY R KIRK wrote: > > External Email - Use Caution > > > I have R1 values that I want to resample onto the cortical surface.

[Freesurfer] mri_glmfit-sim error

hi folks, when i run mri_glmfit-sim --glmdir rh.measure_t7cort.glmdir --cache 2.0 neg i get an error message ERROR: cannot find /apps/x86_64_sci5/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/neg/th20/mc-z.csd there is fsaverage... should i just make a soft link ? also when i

[Freesurfer] resampling vol to surface

Hi guys, i am using the freesurfer-fsl integration to use labels from the freesurfer cortical surface as seeds for probtrackx probabilistic diffusion tractography. when the output of probtrackx is generated it is already in the freesurfer conformed space. I want to resample the output of probtr

[Freesurfer] resample data to surface that is already in conformed space

I have probabilistic tractography output that is already in freesurfer conformed space, i need to resample it onto the cortical surface, how can I ? i.e. mri_vol2surf does not have an option for the data already being in registration ( requires transform. i know i can load in freesurfer and sav

[Freesurfer] little bug in mri_cvs_register

running mri_cvs_register --mov 004 --template 003 get error executing surf2vol at /apps/x86_64_sci5/freesurfer-latest/bin/elastic_registration_CVS.pl line 162. line 162 is system($cmdLine)==0 or die "error executing surf2vol"; i saw martin kavec posted the same error but did not see a respon

[Freesurfer] tracula tutorial data

can i get an update on the eta for the tracula associated tutorial data sets greg ___ 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

[Freesurfer] tracula - fix bad bbregister's

Hi, I processed about 80 subjects with -prep stage and then checked the bbregister registrations with tkregister2 --mov /study5/aa-scratch/TEENEMO/freesurfer_local/toot/057/dmri/dwi.nii.gz --reg /study5/aa-scratch/TEENEMO/freesurfer_local/toot/057/dmri/xfms/anatorig2diff.bbr.dat --surf foun

[Freesurfer] tracula pub

i thought at one time i saw a paper on the tracula methods, maybe it was the better tractography allignment paper. is there a paper specifically about the global tractography method and related, or an mit tech. report or anything thanks greg ___ Free

[Freesurfer] cortical label values

Hi, I am using the cortical labels mapped into the aparc+aseg volume for seeding qball imaging. i looked around and did not find a complete listing of the numerical values of all the cortical parcellation labels. I can of course load the aparc on the surface in tksurfer and map them to the ap

[Freesurfer] extract time series on surface

Hi, i want to extract epi time series on the surface, seems if i want every last drop of accuracy from bbregister i will need to run bbregister --mov epi_i_.nii --bold \ --s fbirn-anat-101.v4 \ --init-fsl --reg register_i_.dat on every epi volume in the time series and then mri_vol2surf