[Freesurfer] The atlas specification

Hi, everybody. I am wondering the specification of the atlas which is used for surface registration. Please answer what kinds of subjects are used and how many subjects are used to generate the atlas included in Freesurfer. Or please tell me the link about the atlas specification. Sincere

Re: [Freesurfer] Vertex-by-vertex analyses within ROIS?

1. Yes. 2. Ignore everything outside of the ROI and do a bonferroni correction by the # of vertices in the ROI. cheers Bruce On Thu, 24 Mar 2011, Dalwani, Manish wrote: > Hello Freesurfers, > > We are interested in comparing cortical thickness in 2 groups. Due to small > sample size (and thus

[Freesurfer] N3 correction issues

Hi all, We are processing longitudinal structural MRI data on Freesurfer 5. 0. As our images have some intensity problems, we were running an N3 correction outside of FreeSurfer using a mask in order to maximize this step (as per recommended by Boyes et al., 2008). We first ran autorecon1 and t

[Freesurfer] Vertex-by-vertex analyses within ROIS?

Hello Freesurfers, We are interested in comparing cortical thickness in 2 groups. Due to small sample size (and thus less power), we are swaying away from whole-brain vertex analyses. Instead we would like to compare specific ROIs between two groups. We understand that we can get an estimate

Re: [Freesurfer] Fwd: fMRI and anatomical T1 overlaid

You need to include a registration file with your tksurfer command, something like: tksurfer subjectid rh inflated -reg featdir/reg/freesurfer/register.dat -overlay featdir/rendered_thresh_zstat1.nii.gz Did you check the registration with tkregister2? If not, do so first. You can also load it on

[Freesurfer] Fwd: fMRI and anatomical T1 overlaid

Thanks Doug. After doing reg-feat2anat , I checked the registration and overlaid zstat file: tksurfer subjectid rh inflated -overlay featdir/rendered_thresh_zstat1.nii.gz I have attached an image of tksurfer interface . I'm not quite sure about what blue and red clusters mean. They are suposed t

Re: [Freesurfer] single subject versus a group map in qdec

I'm curious about the use of this method as well (thanks for the paper PPJ). Bruce/Doug, how exactly does QDEC treat this design? Can a single-subject comparison properly be done? Thanks. -Derin On Mar 23, 2011, at 4:11 PM, Pedro Paulo de Magalhães Oliveira Junior wrote: > We have dono s

Re: [Freesurfer] parametric modulator with FS-FAST

Hi Yuko, this has been asked about several times, so I just prepared as wiki page for it: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation Take a look and let me know if you have any questions. doug Yuko Yotsumoto wrote: > Hi, > > I am wondering whether it is possible to

[Freesurfer] isxconcat-sess question

Hi, Is there a way to use” isxconcat-sess” to average monkey fMRI data? i.e. I have two groups of monkeys (say, test and control groups) and I want to do group analysis on their data.. Regards, krishna ___ Freesurfer mailing list Freesurfer@nmr.mg

[Freesurfer] ROI-based fixed effect analysis

Hi everyone, Is there any way to do ROI-based fixed effect group analysis in Freesurfer? I want to get the average ces and cesvar (fixed effect) in a specific ROI. Can I just average the gamma and gammavar that in the osgm folder after I ran the voxel-based ffx group analysis in that ROI to get th

Re: [Freesurfer] data preparation for SVM classification

Thank you very much for such a quick response! I am going to classify two group of patients: responders versus non-responders... As the matter of fact, I also have fMRI and DTI data of these subjects - but I would prefer to start from structural images... Therefore I'd like to clarify structural (

Re: [Freesurfer] data preparation for SVM classification

Sorry for the advertisement :) I wrote a paper using this technique: Use of SVM methods with surface-based cortical and volumetric subcortical measurements to detect Alzheimer's disease. Oliveira PP Jr, Nitrini R, Busatto G, Buchpiguel C, Sato JR, Ama

Re: [Freesurfer] data preparation for SVM classification

what are you trying to classify and what is your hypothesis? cheers, Bruce On Thu, 24 Mar 2011, Alexander Ivanov wrote: > *Dear Freesurfers,* > > Could you please suggest me the best way to prepare structural data for SVM > classification? I googled, searched the archives - there're no examples

[Freesurfer] data preparation for SVM classification

*Dear Freesurfers,* Could you please suggest me the best way to prepare structural data for SVM classification? I googled, searched the archives - there're no examples of such preparation using freesurfer algorithms (to my knowledge)... Thank you beforehand. --- *Regards,* *A. Hasfatin* __

[Freesurfer] parametric modulator with FS-FAST

Hi, I am wondering whether it is possible to use "parametric modulator (SPM term)" in FS-FAST. For example, say I have 4 experimental conditions. These conditions are not independent. Conditions 1-4 are determined post-hoc by subjects responses - for example, attractiveness judgements. Conditi