Re: [Freesurfer] orientation problem resulting in talairach failure

Hi Dominic the big problem is that you'll never know if you have a left/right swap. sorry :< Bruce On Tue, 3 Nov 2009, Dominic Brendon Dwyer wrote: > Hi Bruce, > > Thanks for your quick reply. Unfortunately the images are more than 10 > years old and have only been stored on our systems in anal

Re: [Freesurfer] orientation problem resulting in talairach failure

Hi Bruce, Thanks for your quick reply. Unfortunately the images are more than 10 years old and have only been stored on our systems in analyze format. I'm trying to source the original DAT tapes, but thought I'd try to fix the problem without them. In the main I was puzzled that tkmedit reads the

Re: [Freesurfer] Between-Groups Analysis Question

You can take the min of the two maps (mri_concat with --min option). For correcting for multiple comparisons, you can apply the simulations results to the resulting map (just make sure to use positive (pos) when running the simulation). doug Derek Huffman wrote: > Hello FreeSurfer Team, > > I

[Freesurfer] Between-Groups Analysis Question

Hello FreeSurfer Team, I am in the process of running a between-groups analysis in FreeSurfer (Two groups: younger adults, older adults). We are analyzing areas of cortical thickness that are important for memory recall. I am able to perform between groups analysis in the QDEC that shows where the

Re: [Freesurfer] Semi-Inflated Surfaces

Hi Kevin, you can generate one by going to the surf directory for a subject and running mris_inflate -n lh.white lh.partially_inflated where n ranges from 1 to 10 (10 is the default that gives the fully inflated surface) cheers Bruce On Mon, 2 Nov 2009, Liang, Kelvin wrote: > Hi FS Folks

[Freesurfer] Semi-Inflated Surfaces

Hi FS Folks, I've often seen articles present their data on semi-inflated cortical surfaces, and I'd like to display my regions of interest in such a format. However, I've only found inflated, pial, and white surface options in qdec or tksurfer. Am I overlooking an option somewhere? Thank yo

Re: [Freesurfer] Surface area of subcortical structures

Hi Nick, Why do you use 128 as the value for mri_tessellate in your suggestion below? Should this value be used for all ROIs, regardless of hemisphere? Thank you, Liz Selgrade -Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: Wednesday, September 16, 2009

[Freesurfer] Job announcement

Posted on behalf of a colleague: FACULTY POSITION, MEG-fMRI NEUROIMAGING Saint Louis University, is a Jesuit, Catholic university dedicated to teaching, research, health care and community service and is seeking a scientist at an open rank level for a non-tenure track, grant-funded fac

Re: [Freesurfer] comparison of mean thickness of gyri in two groups

Well, if doing a thickness analysis, then mean cortical thickness seems the "natural" covariate to use, if you want to answer the question whether the thickness difference in a region is "beyond" any difference that would be predicted based on mean cortical thickness. This is especially relevant

Re: [Freesurfer] orientation problem resulting in talairach failure

Hi Dominic, do you have access to any format previous to the analyze one? It doesn't preserve orientation info, and all bets are off once you go through it. cheers Bruce On Mon, 2 Nov 2009, Dominic Brendon Dwyer wrote: > Dear Freesurfer developers, > > > > I have a few analyse images which are

[Freesurfer] orientation problem resulting in talairach failure

Dear Freesurfer developers, I have a few analyse images which are oriented incorrectly that are part of a larger dataset. When viewed in tkmedit, what is supposed to be coronal is actually displayed as axial and the sagittal is flipped. In these cases the Talairach transform fails spectacularl