Re: [Freesurfer] Covariate for results of cortical parcellation

Hi, you could try including average cortical thickness over the entire > hemisphere as a covariate. This was Mike Harms' suggestion, and I think a > good one. why is it a good one? for cortical thickness: i'm not so sure. my 2 cents (and i may be wrong!): - controlling for intracranial volume is

Re: [Freesurfer] Covariate for results of cortical parcellation

it all depends on your hypothesis. If you think there are regionally varying differences in the thickness and want to be conservative, then overall mean is a good way to test this, and is probably a more stable measure than ICV. It's all speculation I think as no one has really quantified the e

Re: [Freesurfer] Covariate for results of cortical parcellation

Hi Joost, If you want to control for possible global differences in thickness, then an appropriate covariate of some sort is need. To me, a logical covariate for a thickness analysis is the mean cortical thickness, as this is more directly related to the measure of interest than something like th

[Freesurfer] implementation of topology correction

Hi freesurfer experts, I have some volumes, which are grey matter surface, to be corrected. So I want to compare the performance of various topology correction methods. Can I only implement the topology correction method in freesurfer? thanks in advance, Jerald __

[Freesurfer] 3T Philips scanner

Hello, My name is Alfredo and I'm interested in performing freesurfer with a 3T PHILIPS scanner. I would like to know what are the recommended parameters in this machine to obtain good quality T1 data (equivalent to Siemens MPRAGE or GE SPGR). Thanks a lot, Alfredo Damasceno

Re: [Freesurfer] Problems segmenting monkey brain

Krishna, How have you processed this data? Have you used any of the suggested flags and/or parameters for monkeys? See: https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData -- On Wed, 7 Apr 2010, Srihasam, Krishna wrote: > Hi, > > I have a (0.35 mm)^3 resolution monkey brain which I am tryin

Re: [Freesurfer] 3T Philips scanner

For our GE 3T scanner (MR-750), we use the following parameters: TE/TR=3.7 / 9.2 ms, flip angle 12°, bandwith= 25; Prep Time= 650; Fov= 25.6; Arc (self calibrated parallel imaging). - Original Message - From: Alfredo Damasceno To: freesurfer@nmr.mgh.harvard.edu Sent: Thursda

Re: [Freesurfer] implementation of topology correction

sorry, I don't understand. You are welcome to our source code if you want it, which includes 2 surface-based and one volumetric topology correction algorithm. cheers Bruce On Thu, 8 Apr 2010, Jerald Zhao wrote: > Hi freesurfer experts, > > I have some volumes, which are grey matter surface, to

[Freesurfer] submitting manual Talairached data into FreeSurfer pipeline

Hello, We've noticed that FreeSurfer has been doing a poor job with our data on the first few steps prior to segmentation. All of our data has been aligned and Talairached manually for another project, and we were wondering if it is possible to submit that data into the FreeSurfer pipeline so tha

Re: [Freesurfer] submitting manual Talairached data into FreeSurfer pipeline

Hi Janessa, you need to convert your transforms to the MNI .xfm format, then put the transform in the subject's mri/transforms/talairach.xfm file. You should definitely check them with tkregister2 to make sure that there is no offset or other source of conversion-related inaccuracy. Note thoug

[Freesurfer] tksurfer: Load multiple overlays from command line

Hi all, What would be the syntax for loading multiple significance maps into different tksurfer overlay layers from the command line? I tried: tksurfer D14 lh.inflated -overlay lh.Tstat1.mgh -overlay lh.Tstat2.mgh --overlay lh.Tstat3.mgh And tksurfer D14 lh.inflated -overlay lh.Tstat1mgh lh.

Re: [Freesurfer] tksurfer: Load multiple overlays from command line

Hi Annelise, the new tksurfer will work with this syntax (the current released one just overwrites the previous overlay). If you want a new version let us know your software/hardware env and we'll get you one. cheers Bruce On Thu, 8 Apr 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote: > Hi al

Re: [Freesurfer] Covariate for results of cortical parcellation

Hello, Thanks for all the suggestion. Just a few follow-up questions: 1 How should the average thickness be calculated? (The average thickness measure was defined as a ratio between the sum of product of thickness and surface area measures in each individual ROI and sum of surface measure e

Re: [Freesurfer] 3T Philips scanner

Hi Alfredo, you might try the ADNI mprage parameters, which exist on the Philips 3T I think. Not sure what they are offhand. Ron Killiany (ccd) probably knows. If not, you can get them from one of the ADNI sites. cheers Bruce On Thu, 8 Apr 2010, Alfredo Damasceno wrote: > > Hello, > > My na

[Freesurfer] Retinotopy with bow ties

Hello Everyone, I am a new FreeSurfer user, trying to do retinotopy. My stimulus has the following configurations: - 96 TRs in total per run, including 8 blanks in the beginning and 8 in the end - Polar angle: - bowtie checkerboard wedges - 16 unique positions - 5 repetitions per run