Re: [Freesurfer] scrambled boundaries

Hi Brendan if you send us the sample we can take a look, but in general the thickness is the average of the distance from the white to the pial with the distance from the pial to the white. Sometimes things can seem like a knot or tangle, but really it's just that the surface is almost parallel

[Freesurfer] scrambled boundaries

Hi, I have a set of fairly old MRIs which have been run on freesurfer. Occasionally scans have scrambled pial or white matter boundaries - a knot-like appearance especially in sulci. I am wondering how freesurfer estimates cortical thickness in these regions. For example, does it take the pial boun

Re: [Freesurfer] GM volume and cortical thickness

Dear Bruce, Thank you very much for your patient instruction! In fact, I used *"file--load overlay*", then with below error information. Maybe I can try mris_calc. Thanks again! Best regards! Joe 2010/2/2 Bruce Fischl > it looks like you are trying to load the volume

Re: [Freesurfer] Freesurfer , wfu pick atlas

yes, the pick atlas is just an atlas in standard space, so you lose all the subject-specific info doug Sharmili 57 wrote: > Hey, > > I want to do Cortical thickness analysis for regions defined by the > wfu atlas in a MEG study. How can I define these areas in Freesurfer? > It is imprecise to

Re: [Freesurfer] Painting two contrasts simultaneously

sorry, I don't think we do, although doing it in matlab would be easy enough On Wed, 27 Jan 2010, John Gelburg wrote: > Dear all, > > I am using tksurfer to paint in single subject contrast (step 6 here: > http://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting). However, I would > like to see two

Re: [Freesurfer] GM volume and cortical thickness

it looks like you are trying to load the volume measures as a surface, not as an overlay. Use file->load overlay. Note that you can also use mris_calc to generate the volume measures. cheers Bruce On Tue, 2 Feb 2010, keepmoon wrote: > Dear Bruce, > >This is the all information in tci:

Re: [Freesurfer] Freesurfer , wfu pick atlas

sorry, what is the WFU atlas? On Tue, 2 Feb 2010, Sharmili 57 wrote: > > Hey, > > I want to do Cortical thickness analysis for regions defined by the wfu atlas > in a MEG study. How can I define these areas in Freesurfer? It is imprecise > to use the atlases implemented in Freesurfer, isn't it?

Re: [Freesurfer] segmentation without conform

you need to run recon-all on your T1.nii, then register your spectroscopy images to the recons (we use bbregister for this). Then you can use our segmentations to analyze the spectroscopy data. cheers, Bruce On Tue, 2 Feb 2010, magnet scanner wrote: > Hi, Bruce, > > Thanks for your quick respo

Re: [Freesurfer] segmentation without conform

Hi, Bruce, Thanks for your quick response. here is what I am going to do with my spectroscopy data; 1. mri_convert to convert all my T1 and T2 images to nifti format mri_convert -it dicom {T1 filename} -ot nii {T1.nii} --out_orientation RPS mri_convert -it dicom{T2 filename} -ot nii {T2.ni

[Freesurfer] Freesurfer , wfu pick atlas

Hey, I want to do Cortical thickness analysis for regions defined by the wfu atlas in a MEG study. How can I define these areas in Freesurfer? It is imprecise to use the atlases implemented in Freesurfer, isn't it? Thanks for your help Sharmili _

Re: [Freesurfer] segmentation without conform

Hi Mag, no, the conform is a necessary step, but it wouldn't be applied to your spectroscopy data in any case. You would register that to the anatomicals (that were conformed). Is that what you mean? Bruce On Tue, 2 Feb 2010, magnet scanner wrote: > Hi, > > Please excuse me if this is an old q

[Freesurfer] segmentation without conform

Hi, Please excuse me if this is an old question. I was wondering if there is a way of not doing conform when segmentation on the whole brain since I am dealing with spectroscopy data and need affine matrix. So I have to make sure the matrix is the same. Thanks, Mag __

Re: [Freesurfer] GM volume and cortical thickness

Dear Bruce, This is the all information in tci: % $ tksurfer xalbertM lh inflated surfer: current subjects dir: /home/Joe/study surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/Joe/study surfer: Readin

[Freesurfer] unpacksdcm/mri_convert question

Dear List, I got a question/problem regarding unpacksdcmdir and mri_convert (of version 4.5.0 centos4_x86_64). When I unpack the siemens DICOMs (syngo B17, from a recent tim trio) as bshorts, mri_info reports the proper FOV of 96; when I unpack them as nii, I get a wrong FOV of 64 (also the xs

Re: [Freesurfer] GM volume and cortical thickness

can you send us the complete output in the tcl window (the one with the % prompt) On Tue, 2 Feb 2010, keepmoon wrote: > Dear Bruce and All, > > In my *View--Configure*there are three button which are activated > (*Light, caption and phase Encoded Dat Display*), without "*functional > ov

Re: [Freesurfer] why FreeSurfer Surface Atlas does not contain subcortical region

we keep the subcortical information in a different atlas. The surface-based one contains info about cortical geometry, which doesn't apply for non-cortical structures On Tue, 2 Feb 2010, Guang Zeng wrote: > > Hi, there, > > Kind of wondering, why FreeSurfer Surface Atlas does not contain subcor

[Freesurfer] why FreeSurfer Surface Atlas does not contain subcortical region

Hi, there, Kind of wondering, why FreeSurfer Surface Atlas does not contain subcortical region? Thanks! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go

Re: [Freesurfer] GM volume and cortical thickness

Dear Bruce and All, In my *View--Configure*there are three button which are activated (*Light, caption and phase Encoded Dat Display*), without "*functional overlay*" option. And in these activated buttons: light(light 0,...,light 3, with the value, 0.4, 0.0, 0.6, 0.2. and bright

[Freesurfer] Postdoctoral position in multimodal imaging (autism) available

Postdoctoral position in multimodal imaging (autism) available I would like to make known the availability of a two year postdoctoral position in my laboratory. Strong MRI/DTI/Spectroscopy signal processing analysis skills plus experience with and commitment to multimodal imaging are require

Re: [Freesurfer] Reorientation of raw images?

Hi Chunhui you should not need to reorient your data. What version are you using? cheers, Bruce On Tue, 2 Feb 2010, chenchunhuichina wrote: Hello Bruce, and Freesurfers, Sorry for asking an old question, but I really need more confirmation. I am running recon-all to processing my structura

Re: [Freesurfer] GM volume and cortical thickness

have you tried changing the threshold in configure->functional overlay? What kind of values do you see? On Tue, 2 Feb 2010, keepmoon wrote: > Dear all experters, > >First I am appreciated for the help of Bruce. > I tried to following his instruction, but I still have some problem and I >

Re: [Freesurfer] GM volume and cortical thickness

Dear all experters, First I am appreciated for the help of Bruce. I tried to following his instruction, but I still have some problem and I can't show any result on the flated surface. I don't know whether my method to calculate the volume is wrong or I display it wrongly. Expecting som

Re: [Freesurfer] Reorientation of raw images?

in some regions like left amygdata, the difference exceed 5% 2010-02-02 Chunhui Chen _ Institute of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 发件人： Bruce Fischl 发送时间： 2010-01-22 12:38:11 收件人： chenchunhuichina 抄送： 主题： Re: Re: [Fr

[Freesurfer] Reorientation of raw images?

Hello Bruce, and Freesurfers, Sorry for asking an old question, but I really need more confirmation. I am running recon-all to processing my structural data, but i am not sure do I have to reorient the data or not. The data were acquired in sagital view, and dicom data were converted into nift