[Freesurfer] 5.3.0, mri_segstats

Dear experts, I updated FreeSurfer as a 5.3.0 version but have a problem about the missing ribbon.mgz when running recon-all procedure. I found the ftp address but couldn't find the mri_segstats. (ftp:/surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats) Could you let me know the

Re: [Freesurfer] WM/GM boundary changes and control points

I uploaded the EK_test_new.tar file to the ftp incoming folder. I think it might work. Thank you for you time and consideration. 2012/10/15 EK Kim > I've been struggling to upload the file to the ftp server, but failed in > several times. > Sorry for bothering you, but I will

Re: [Freesurfer] WM/GM boundary changes and control points

t format is it? Or maybe it's corrupted... > > > On Sat, 13 Oct 2012, EK Kim wrote: > > Bruce, and other experts, thank you for your time :) >> >> I'm now uploading the data folder (before cp and after cp) to the >> freesurfer incoming directory. >> &

Re: [Freesurfer] WM/GM boundary changes and control points

t; parameters and resolution? Also, I can't diagnose your problem from just > the volume I'll need the entire (tarred and gzipped) subject directory. > Finally, please cc the list on these emails so that others can help you! > > Bruce > > On Thu, 11 Oct 2012, EK Kim wrote: &

Re: [Freesurfer] WM/GM boundary changes and control points

re) 4. recon-all -autorecon2-cp and this figure was made by a commnad line, [tkmedit wm.mgz -aux brain.mgz -surfs]. Best, EK. 2012/10/10 Bruce Fischl > what was the name of the file that you transferred? > > On Wed, 10 Oct 2012, EK Kim wrote: > > I already uploaded this problem 2 da

Re: [Freesurfer] anisotropic input data

Yes I found it :) Thank you for your help! Sincerely, EK. 2012/5/4 Bruce Fischl > run: > > mri_info $SUBJECTS_DIR/$subject/mri/**orig.mgz > > and you should see that it is 1mm isotropic > > > cheers > Bruce > On Fri, 4 May 2012, EK Kim wrote: > > Thank you

Re: [Freesurfer] anisotropic input data

convert was preprocessed or not. How can I confirm the processes? Sorry for bothering you. Thank you in advance. 2012년 5월 4일 금요일에 Bruce Fischl님이 작성: > if you give it to recon-all it will convert it internally, so you don't need to convert it yourself > On Fri, 4 May 2012, EK Kim wrote: >

Re: [Freesurfer] anisotropic input data

> > cheers > Bruce > On Fri, 4 May 2012, EK Kim wrote: > >> Dear freesurfers, >> >> I wondered is it okay to analyze isotropic data which was converted to the >> anisotropic one. >> >> The original data has (0.390625, 0.390625, 1.5) mm size and

[Freesurfer] anisotropic input data

Dear freesurfers, I wondered is it okay to analyze isotropic data which was converted to the anisotropic one. The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512, 104) voxels. It obtained from 3T scanner. I know the Freesurfer recommend isotropic data (1,1,1)mm. Does it have an

[Freesurfer] recon-all error (nu_correct problem)

Hello, Freesurfers, I got an error message when I trying to use recon-all function in freesurfer on the XUbuntu system installed on the VirtualBox on a Windows 7 machine. I searched the e-mailing list but I can't find any answers. My problem is related to the nu_correct and nu_estimate_np_and_em.

Re: [Freesurfer] negative thickness value problem

Hello Nick. I'm really sorry for bothering you but I'm still waiting for your answer. :) Thank you 2010/4/6 eunkyung kim : > Hello Nick. > Bruce said you can give me the latest Freesurfer version. > Actually, as I already mentioned, I have a problem with negative > cortical thickness and it bothe