Re: [Freesurfer] a "redraw failed: no gl window open" problem

Hello, Nick, The freesurfer I am using now is freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0-full.tar.gz Yes, the glxgears work well. Guang > Subject: Re: [Freesurfer] a "redraw failed: no gl window open" problem > From: ni...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesu

Re: [Freesurfer] frontal gray matter and frontal white matter volumes

That will not be able to separate the only frontal WM from the rest of the WM, isn't it? I have used FSL (a mix of bet,flirt and fnirt) with an atlas of the lobes (that covers WM and GM) for that kind of job roberto On Tue, Aug 18, 2009 at 9:24 PM, Douglas N Greve wrote: > You can get the WM from

[Freesurfer] Question about "Getting started with your own data"

Hi freesurfer gurus, We are trying to do reconstruction in tksurfer section according to the text. We have a question in "Getting started with your own data" section. In the text, the following commands are written, recon-all -s \ -i /9-2-1.dcm -i /9-3-1.dcm In the above commands,

Re: [Freesurfer] Convert to original orientation

Hi, also I would suggest to give mri_robust_register a try for the registration. It is very accurate especially in cases with differences in the images (jaw movement...). It can detect outlier voxel and remove them from the registration. Oh, and why do you use the T1.mgz? The norm.mgz is only bra

Re: [Freesurfer] a "redraw failed: no gl window open" problem

Guang, which version of freesurfer are you running? does glxgears work? can you send me your /etc/X11/xorg.conf file? Nick On Tue, 2009-08-18 at 17:53 -0500, Guang Zeng wrote: > yeah, it didn't work > > > __ > From: p...@ne

Re: [Freesurfer] a "redraw failed: no gl window open" problem

yeah, it didn't work From: p...@netfilter.com.br Date: Tue, 18 Aug 2009 19:46:02 -0300 Subject: Re: [Freesurfer] a "redraw failed: no gl window open" problem To: freesurfer...@hotmail.com I suppose you have tried the trick bellow setenv doublebuffer_flag 1--

[Freesurfer] a "redraw failed: no gl window open" problem

Hi, there, I am still facing the problem of "redraw failed: no gl window open", I got another linux machine with Nvidia graphic card, I ran the tksurfer command "tksurfer bert lh inflated", it still gave me the "redraw failed: no gl window open" error. surfer: current subjects dir: /home/

Re: [Freesurfer] frontal gray matter and frontal white matter volumes

You can get the WM from our white matter segmentation (wmparc.mgz and stats table wmparc.stats). You'd need to pick the cortical labels that you want to define as the "frontal lobes". You should create a binary mask with mri_binarize, passing the indices of the segments you want to use with the

[Freesurfer] frontal gray matter and frontal white matter volumes

Hi freesurfer gurus, We are doing some freesurfer processing for a collaborating lab and the PI has asked us for a measure of gray matter volume and a measure of white matter volume, both of which need to be specific to just the frontal lobes. Does anyone know of a simple, and accurate, way of

Re: [Freesurfer] Convert to original orientation

You can also use mri_label2vol. Bruce Fischl wrote: > Hi Renske, > > you can use the -rl mri/orig/001.mgz switch in mri_convert ("reslice > like"). Note that depending on the resolution etc. of the 001.mgz it may > do an additional interpolation. You shouldn't need to do this though for > regis

Re: [Freesurfer] WM intensity normalization problem

Garth, I spoke too soon. Looking at the files in your mri/orig directory, 001.mgz is a structural, but 002.mgz appears to be an epi (partial brain), so the orig.mgz is a mix of the two (with the wacky intensity profile). You should delete 002.mgz and either just run with 001.mgz (which looks goo

Re: [Freesurfer] ROI reliability

Hi Nick, It appears mri_compute_seg_overlap only works with .mgz files and not .label files, which is how I saved the ROIs. I tried renaming the labels as .mgz files, but that did not work. Any suggestions? Thanks. > the utility for comparing segs is 'mri_compute_seg_overlap', included > w

Re: [Freesurfer] WM intensity normalization problem

sure. Good luck. Bruce On Tue, 18 Aug 2009, Garth Coombs wrote: > Hi Nick and Bruce, > > I followed those instructions and am rerunning the recon, so hopefully that > will solve the problem. I'll let you know if any other issues arise with this > patient. Thanks for your help! > > -Garth > > On

Re: [Freesurfer] WM intensity normalization problem

Hi Nick and Bruce, I followed those instructions and am rerunning the recon, so hopefully that will solve the problem. I'll let you know if any other issues arise with this patient. Thanks for your help! -Garth On Aug 18, 2009, at 11:03 AM, Nick Schmansky wrote: > Garth, > > I had a look at

Re: [Freesurfer] WM intensity normalization problem

Garth, I had a look at the subject in tkregister, and it is badly misaligned, in a way that explains the intensity normalization problem. Follow these instructions to correct it: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Also, I'll take a look at why our tal alignment code wa

Re: [Freesurfer] WM intensity normalization problem

Hi Garth, sorry, I don't understand. You can try running mri_normalize without the tal stuff by giving it -no1d (you can find the full command line in the scripts/recon-all.log file). If the tal is too far off it will cause the first step (the 1d part) of the normalization to fail. cheers, Bru

Re: [Freesurfer] Convert to original orientation

you can change the orientation without reslicing, but if the voxel dimensions of the 001.mgz are different from the orig.mgz then it will have to reslice. I don't see why you need to at all though - both contain ras2vox xforms that tell you how to initialize a transform. cheers Bruce On Tue,

Re: [Freesurfer] Convert to original orientation

Hi Bruce, Thank you for your answer. What I forgot to mention is that I will not be using FreeSurfer for the registration. We have our own registration method that I prefer in this case. I thought of using the -rl switch in mri_convert but as you mentioned this will also resample the data. Do I

Re: [Freesurfer] WM intensity normalization problem

When I check the talairach.xfm using tkregister2 --mgz --s amcg_anat -- fstal --surf orig, it does not extend into the "darker" portion of the cortex and cuts short as if the cortex has been shaved off, but is only slightly off. In other areas, it looks very misaligned. It looks like possib

Re: [Freesurfer] Convert to original orientation

Hi Renske, you can use the -rl mri/orig/001.mgz switch in mri_convert ("reslice like"). Note that depending on the resolution etc. of the 001.mgz it may do an additional interpolation. You shouldn't need to do this though for registration as it should read this information from the header. Mart

Re: [Freesurfer] (no subject)

Hi Aize, I think hippocampus will probably be the hardest since it shares so much of a border with dark things that will be low contrast in your images. I didn't really look at other structures - did they appear accurate? One thing you can try is to manually correct a single image, then there

[Freesurfer] Convert to original orientation

Hi, I would like to register a FreeSurfer segmentation (or actually the corresponding T1 image) to another scan of the same subject. In order to perform this registration, the mri/T1.mgz file needs to have the same orientation as the original T1 scan (mri/orig/001.mgz). Resampling is not neces

Re: [Freesurfer] installing FS - permission denied

You don't have permission to write in /usr/local Try using sudo before the mv Enviado do meu celular Nokia -Msg original- De: Ahmed, F, Me Enviada: 18/08/2009 05:37:54 Para: Freesurfer Mailing List Assunto: [Freesurfer] installing FS - permission denied Hello. I am trying to install

[Freesurfer] installing FS - permission denied

Hello. I am trying to install FS and tried the following command: [...@localhost Desktop]$ mv freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar.gz /usr/local mv: cannot move `freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar.gz' to `/usr/local/freesurfer-Linux-centos4-stable-pub-v4.3.1-ful