[Freesurfer] What does trac-all do on the file 'bvecs'?

Hi, all~ I use trac-all with .nii data, not dicom. So I have to specify the bvecs and bvals in the config file. Trac-all requires a bvecs file in 3 columes, but FSL need that in 3 raws. I wonder what does trac-all do on the bvecs file that I specify. And I have check the code 'trac-preproc' and

[Freesurfer] Surface Down-Sampling

Dear Experts, What is the best strategy to downsample a surface into diffusion (e.g. FA) resolution of the same subject? Thanks, Sourena Soheili ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] FA question

Dear Antonella, In theory, FA can be sqrt(3/2) = 1.2247449. This occurs if eigenvalues 2 and 3 are zero. You will find these high FA values (1) mainly outside the brain. Ed On 3 Feb 2012, at 11:31, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Dear all, I use dt_recon to process my DTI

Re: [Freesurfer] Surface Down-Sampling

Hi Sourena what are you trying to do? You can sample the diffusion onto the surface easily enough, or map the surface into the diffusion coordinates with mri_surf2surf and bbregister, but why do you want to downsample it? Bruce On Fri, 3 Feb 2012, Sourena Soheilinezhad wrote: Dear Experts,

Re: [Freesurfer] FA question

HI Ed, I believe that you are referring to the RA measure of anisotropy. FA is theoretically limited to the range 0-1. FA's greater than 1 can arise when you have negative estimates of the eigenvalues, which can arise when using linear least squares estimation of the tensor. cheers, -MH On

[Freesurfer] /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory

Hi all Now I am learning the trac-all using with DICOM data, but came across a problem. +++ mv -f /xxx/dmri/dwi_orig_flip.mghdti.bvecs //dmri/bvecs mv: cannot stat `/xxx/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory +++ I check the dir /xxx/dmri/ and there are only two files

Re: [Freesurfer] TRACULA bvecs question

Hi Tanja, I think the problem may be due to the trailing slash you've included while specifying $dtroot, $SUBJECTS_DIR etc. setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/ should be setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1 trac-all usually adds the

Re: [Freesurfer] TRACULA bvecs question

Hi Priti, I changed the dmrirc file to the one you sent, but unfortunately got the same error. I attach the log (although it is basically the same). Do you have any ideas what else can cause it? Thanks again, Tanja. On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu

Re: [Freesurfer] What does trac-all do on the file 'bvecs'?

When the DWIs are transformed to LAS and processed with eddy_correct, the same transformations are applied to the respective bvecs. On Fri, 3 Feb 2012, Xiangzhen Kong wrote: Hi, all~   I use trac-all with .nii data, not dicom. So I have to specify the bvecs and bvals in the config file.

Re: [Freesurfer] TRACULA bvecs question

Hi Tanja, Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs was created at all? It looks like that may not have been created and that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals and bvecs information is not encoded in the dicom header, then you can

Re: [Freesurfer] /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory

Unless your dicoms came from the same acquisition as the default MGH/Siemens one, you'll have to set bvecfile and bvalfile and provide those files yourself. On Fri, 3 Feb 2012, Xiangzhen Kong wrote: Hi all Now I am learning the trac-all using with DICOM data, but came across a problem. +++

Re: [Freesurfer] Surface Down-Sampling

Hi Dr. Fischl Actually it's about generating the cortico-cortical connectivity matrix, and working with the original surface and upsampling the DW image results in creation of an enormous connectivity matrix. I have the impression that reducing T1 resolution down to DW and then running surface

[Freesurfer] Visualising the FA group analysis results

Dear Experts, I completed my FA group analysis and I expect my FA to be larger in controls versus patients (based on the uncorrected results). I corrected by multiple comparisons using: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1000 3 permcsd \ --sim-sign pos \

Re: [Freesurfer] Surface Down-Sampling

Hi Sourena what we usually do is it map it into fsaverage space, then downsample the icosahedron to ico5 (10K vertices) or so. Then it's manageable. cheers Bruce On Fri, 3 Feb 2012, Sourena Soheilinezhad wrote: Hi Dr. Fischl Actually it's about generating the cortico-cortical connectivity

Re: [Freesurfer] What does trac-all do on the file 'bvecs'?

Could you give me something about the transpsition here? I checked the code flip4fsl and found there are two kinds of sign. line 59. set sign = `echo $inorient | sed s/[LAS]/+\ /g; s/[RPI]/-\ /g` line 99. set sign = `echo $inorient | sed s/[RAS]/+\ /g; s/[LPI]/-\ /g` e.g. When the

Re: [Freesurfer] What does trac-all do on the file 'bvecs'?

You don't have to multiply the bvecs with anything yourself, it will do it for you. Of course you should check that it does it correctly, check the help of the flip4fsl script for how to do that. Could you give me something about the transpsition here? I checked the code flip4fsl and found