[Freesurfer] Compare left vs right hemisphere

Dear Doug, There´s a message in the list from Dec. 2008 about interhemispheric comparison, and you said there wasn't any good way to do this. Is there some new method included in FS 5.0 for right vs left hemisphere comparison ? Thanks. Sincerely, Alex. * * _

Re: [Freesurfer] Pial surface error

Hi, Do you want me to email you in a few days about this? Allie On Tue, Apr 19, 2011 at 10:25 AM, Khoa Nguyen wrote: > Got it. I'll look at it and get back to you. > > > On Tue, 19 Apr 2011, Allie Rosen wrote: > > Hi, >> >> http://dl.dropbox.com/u/14127241/C42.tar.gz >> >> Here is the link t

Re: [Freesurfer] hyperintense artifact causing problems for segmentation

Hi Sarah, Nick will be out of the office until next week. I would suggest just trying to run the default gcut and if you find you need to tweak it a bit, doing mri_gcut --help will describe the parameter (-T) that you can adjust for a cleaner skullstrip. You could also run -skullstrip a second t

[Freesurfer] flipping left-right

Dear Fs experts, I've been processing a whole group of subjects, manually correcting the surfaces, and I just noticed that a small part of that sample was badly oriented (right-left). Should I flip the initial images and reprocess/recorrect them...? Would the result of mris_reverse be as good? T

Re: [Freesurfer] flipping left-right

Hi Irene, sorry, but you should probably reprocess them Bruce On Wed, 20 Apr 2011, Irene Altarelli wrote: > Dear Fs experts, > > I've been processing a whole group of subjects, manually correcting the > surfaces, and I just noticed that a small part of that sample was badly > oriented (right-le

[Freesurfer] Extracting LGI stats using a label file

Freesurfer team, I have run a group of subjects through the recon-all pipeline with the lgi option. I then looked at differences between two groups in qdec and ran a cluster correction. I would now like to extract the lgi statistics for 3 of these clusters. I have label files for these

Re: [Freesurfer] Power Analysis

Hi Doug, To follow up on this question, we were able to calculate effect sizes for every vertex on the surface using the gamma(var).mgh files, as well as an average effect size across each hemisphere surface using the equation below. In determining alpha, would the most appropriate method be t

Re: [Freesurfer] Power Analysis

Hi Derbin, I have not thought about doing a power calc with FDR before, but what you propose seems reasonable. Maybe someone else on the list has more experience with this. doug Derin Cobia wrote: > Hi Doug, > > To follow up on this question, we were able to calculate effect sizes > for every

[Freesurfer] fs stable 4 vs 5; preproc-sess

Hello, We have a question about preprocessing in fs4 compared to fs5. We used the preproc-sess command without specifying -surface or volume and did all our processing and analysis in fs5. I believe in fs4 you didn't have to specify this. Do you think this is a problem for doing both surface and

Re: [Freesurfer] fs stable 4 vs 5; preproc-sess

The version 4 method smooths 3D in the volume, so you run the risk of smoothing across sulci before you sample on the surface. Otherwise, it's going to be pretty similar. When you look at your results, check to see whether some activation spots look like they could be bridging a sulcus. If not

[Freesurfer] command line tksurfer

Hi Doug, I'm having issues with choosing the Color Wheel option inConfigure Overlay and not being able to see the Accept button (please see below). Can I change to Color Wheel via command line? thanks. Michelle __ I've been able to view the significance ma

Re: [Freesurfer] command line tksurfer

tksurfer-sess can no longer be used to view retinotopy on the colorwheel. I have created a script called rtview (see below) which you can use to do this. Run it with --help to get more info on how to run it. doug ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview Michelle Uma

[Freesurfer] analysis questions

Hi there, 1. A followup question regarding contrasts in glmfit - when there are multiple contrasts, does that affect the degrees of freedom, or is each contrast tested separately? 2. When analyzing exported stats tables in SPSS, i can test hypothesis regarding specific regions without correcting fo

Re: [Freesurfer] analysis questions

On 4/20/11 7:34 PM, Ilana Hairston wrote: Hi there, 1. A followup question regarding contrasts in glmfit - when there are multiple contrasts, does that affect the degrees of freedom, or is each contrast tested separately? There is not a correction for multiple contrasts, if that's what you m

[Freesurfer] tkmedit and tkregister2 permission or ? problems

Hello, I am having trouble running tkmedit and tkregister2. With tkregister2, I issue the command tkregister2 --mgz --s heinrick/mri/transforms/talairach.xfm --fstal (and sometimes I leave out the path, and sometimes I put /urs/local/freesurfer/subjects/heinrick) always, though I am root an

[Freesurfer] analysis questions

Hi there, 1. A followup question regarding contrasts in glmfit - when there are multiple contrasts, does that affect the degrees of freedom, or is each contrast tested separately? 2. When analyzing exported stats tables in SPSS, i can test hypothesis regarding specific regions without correcting fo

Re: [Freesurfer] tkmedit and tkregister2 permission or ? problems

Hi Jim, I think for --s you just want heinrick cheers, Bruce On Wed, 20 Apr 2011, jim kroger wrote: > Hello, I am having trouble running tkmedit and tkregister2. > > With tkregister2, I issue the command > > tkregister2 --mgz --s heinrick/mri/transforms/talairach.xfm --fstal > (and sometimes I