Re: [Freesurfer] white-gray contrast algorithm

2012-03-31 Thread Bruce Fischl
Hi John we can provide that for you if you download and install FreeSurfer, then run recon-all on your data. We also provide tools for computing gray/white contrast once recon-all has been run. cheers Bruce On Sat, 31 Mar 2012, John Fredy wrote: > Hello all, I am looking for a white-gray ma

[Freesurfer] masks from fsaverage label into Group FSL Feat

2012-03-31 Thread Michelle Umali
Hi Freesurfers, I've done a group feat analysis in FSL and I'd like to do an ROI analysis of V1/V2. I've also done recon-all on all my subjects. How would one generate the V1 and V2 binary masks from the fsaverage brain and then register it to the common MNI-152 brain used for the group feat analys

[Freesurfer] white-gray contrast algorithm

2012-03-31 Thread John Fredy
Hello all, I am looking for a white-gray matter contrast algorithm I see the publication: Individual Differences in Verbal Abilities Associated with Regional Blurring of the Left Gray and White Matter Boundary http://www.ncbi.nlm.nih.gov/pubmed/22031871 But,how I can obtain the coordinates of th

[Freesurfer] Tracula Siemens DTI

2012-03-31 Thread Gabor Perlaki
Dear Freesurfers, I have DTI images acquired on a Siemens 3T TIM Trio (software version VB17A). 1, Is TRACULA able to extract the correct b-values and b-vectors from the DICOM headers of Siemens IMA files or do I need to specify them? 2, I'm not sure whether the gradient directions are stored in

Re: [Freesurfer] How do I use "Subject Exclusions" in qdec

2012-03-31 Thread Nick Schmansky
Tracy, Does your 'time' factor appear in the 'Data Table View' box? If so, then when that is selected, then the 'Selected Factor' will change to that in the 'Subject Exclusions' box, which should allow you to enter a particular values for exclusion. Nick On Fri, 2012-03-30 at 09:42 -0600, Brai

Re: [Freesurfer] qdec...again

2012-03-31 Thread Nick Schmansky
Fatima, Do the aseg.stats files exist? The second error concerning vtk will go away once the first error (the missing aseg.stats file) is fixed (run recon-all -s 240 -segstats). Nick On Fri, 2012-03-30 at 12:39 +0200, Ahmed, F, Me wrote: > Hello, > > I got this error while trying to generate

Re: [Freesurfer] Qdec issue

2012-03-31 Thread Nick Schmansky
Sonya, Can you email the file? Nick On Tue, 2012-03-27 at 23:26 -0500, sonya kaur wrote: > Hi everyone, > I realize I'm quickly becoming an annoyance, but I'm having trouble > loading my data file into qdec. I keep getting the error: > QdecDataTable::Load failed to tokenize string: on line 88 o