Re: [Freesurfer] selxavg3 can't find image that exists

Scott, can you run selxavg3-sess -analysis ya.ATLLoc.spm.sm8.lh -s ya24 -d /cluster/kuperberg/SemPrMM/MRI/functionals/ -debug |& tee debug.log and send me debug.log? doug Scott Burns wrote: > Freesurfers -- > > Here's the output of my terminal... > > kerryave:functionals $ cd /cluster/kuperbe

[Freesurfer] ICV error and talairach registration bad outputs...

Hi: In the image that I am sending attach, there exist a not exact talairach registration in the superior part of the brain... That difference produce an important error in the ICV, or not ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailin

Re: [Freesurfer] erroneous ICV volume ?...

Freesurfer's estimate of ICV ("eTIV") is designed to be insensitive to brain atrophy -- after all, it is an estimate of "intracranial volume", not brain volume. See the Buckner et al. (2004) paper for a validation of this. cheers, -MH On Fri, 2011-04-08 at 17:04 -0500, Gonzalo Rojas Costa wrote

[Freesurfer] erroneous ICV volume ?...

Hi: I have an MRI of a 34 years old patient that have a brain atrophy, but with freesurefer I got an ICV of 1120 cc that is near the normal size for her age... I review the talairach transform, but I think it is ok... What could be the problem ?... Could I upload the MRI volume ?... Sinc

[Freesurfer] selxavg3 can't find image that exists

Freesurfers -- Here's the output of my terminal... kerryave:functionals $ cd /cluster/kuperberg/SemPrMM/MRI/functionals/ kerryave:functionals $ rm /cluster/kuperberg/SemPrMM/MRI/functionals/ya24/scripts/atlloc_fs-stats.log kerryave:functionals $ selxavg3-sess -analysis ya.ATLLoc.spm.sm8.lh -s ya

[Freesurfer] Job Opening: Research Technician in Brain Imaging

The Solodkin/Small Brain Circuits Laboratory at the University of California, Irvine, will soon have an opening for a research technician in image processing. This job would be ideal for someone interested in applying basic skills in signal processing or applied mathematics to a variety of function

Re: [Freesurfer] funcroi-config -frame question

Hi Eiran, there are a few modifications you need to make in your command lines to get to where you want to be. 1. funcroi-config -roi v1.rh.frame0 -label rh.V1 -analysis context_FIR.rh -frame 0 In this case, it does not make sense to specify a frame because the frame only applies to the sig

Re: [Freesurfer] functional ROI analysis problem

Hi Katie, this is a problem in version 4 in which the scaling is a little weird. It has no effect on the statistics (ie, p-values), but when you extract the percent signal change, they appear to be very low. This has been fixed in 5.X. For 4.X, you will need to compute a scaling factor. This c

Re: [Freesurfer] How to overlay anatomical surfaces with externally calculated quantities?

Hi Christian try the following: 1. Remove the 1st two lines from the file so there is no header info. 2. Load this file using the file->curvature->load curvature command. 3. At the tcl prompt type "curv_to_val". 4. Reload the curvature you want to display (e.g. curv or sulc) we'll figure out wha

Re: [Freesurfer] How to overlay anatomical surfaces with externally calculated quantities?

Dear FreeSurfer team, unfortunately I continue having this problem. Maybe it's a very small thing but I couldn't find a solution on the web. The ascii file I want to overlay has the following form: #!ascii 145819 and then 145819 lines of format In addition I tried a different format a