Re: [Freesurfer] dt_recon

All standard tensor analysis use a glm, they just don't often call it that. The design matrix are columns formed from the cross products of the gradients (of which there are 6) plus a column of 1s, and the log() of the input data is taken before the glm. After that, it's just a glm. Siddharth

Re: [Freesurfer] "preproc-sess" failing at 3dvolreg

does that file exist? Did that disk run out of space? Krishna Srihasam wrote: Hi, I am trying to analyze my fMRI data ( collected at MGH) using FSFAST and I was following the tutrial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastWorkFlows). I was able to unpack the data. But when I run "pre

Re: [Freesurfer] adding uncached variable to qdec

Jenifer, Hi, you can do this: recon-all -qcache -measure your_measure where you replace 'your_measure' with the name of the measure, for instance: recon-all -qcache -measure lgi_pial normally the -qcache function defaults to a set of known measures (thickness, curv, area, etc.), but if the -

Re: [Freesurfer] dt_recon

Hi Douglas, Thanks for the reply. can i get a link to a publication or report that describes the GLM analysis applied to tensors? thanks, sid. On Mon, Feb 9, 2009 at 10:22 AM, Douglas N Greve wrote: > > It will probably be the case that it j

[Freesurfer] adding uncached variable to qdec

Hi, Running FSv4.2.0 on RHEL4. I'd like to add a variable such as lgi to qdec analyses. I created a .Qdecrc and .fsgd file, ran the lgi files through mris_preproc & mri_surf2surf (following instructions for Uncached Data posted under Group Analysis of the FsTutorial). While the output of mri_gl

Re: [Freesurfer] dt_recon

It will probably be the case that it just gives the entire volume (the "masking" routine just looks for 0-valued voxels). I don't think it actually uses the mask for anything, though. glmfit is run because that's what the tensor analysis is. Siddharth Srivastava wrote: Hi everyone,

Re: [Freesurfer] SPM Issues

there's nothing in the directory (ie, /space/seymour/1/users/folate_subjects/FB110059A ) Dave Brohawn wrote: Hello, I am having issues with SPM Register-Sess and I am not sure why. The command I am entering and the response I receive are spmregister-sess -s FB11059A -

[Freesurfer] SPM Issues

Hello, I am having issues with SPM Register-Sess and I am not sure why. The command I am entering and the response I receive are spmregister-sess -s FB11059A -- spmregister-sess logfile is /autofs/space/seymour_001/users/folate_subject

Re: [Freesurfer] Work with MRI and PET simultaneously

yes, Doug has used bbregister to register and overlay PET images. cheers, Bruce On Mon, 9 Feb 2009, Rafa x wrote: Hello FS team, I would like to know if it's possible to load a PET image in tkmedit and tksurfer, and overall I need to know if I can coregistrer a PET image with a MRI (of the sa

[Freesurfer] Work with MRI and PET simultaneously

Hello FS team, I would like to know if it's possible to load a PET image in tkmedit and tksurfer, and overall I need to know if I can coregistrer a PET image with a MRI (of the same patient). I have the tags of the cortical segmentation generated by recon2 based on the MRI and I want to work with t