Re: [Freesurfer] freediffusion dtrecon mask

Hi Akram, I have access to that directory, but those logs don't seem to be there. What was the exact command you ran using dtrecon? Thanks, Dennis Akram Bakkour wrote: Hello, [EMAIL PROTECTED] doesn't seem to exist, so I'm hoping one of you can help me out. I seem to be having trouble

[Freesurfer] freediffusion dtrecon mask

Hello, [EMAIL PROTECTED] doesn't seem to exist, so I'm hoping one of you can help me out. I seem to be having trouble with the -mask 0 flag in dtrecon. It doesn't apply a brainmask! I tried -mask 1 but that didn't work either. I unpacked the data properly, then ran diff-flirt -i f -o unwarp/f

Re: [Freesurfer] Partitioning GM/WM boundary surface

yes, I think -aseg is the default now, so you don't need to specify it (it uses the aseg to figure out what's cortex and what's not) On Wed, 25 Jul 2007, Morgan Hough wrote: Thanks Bruce, From the ReconAllDevTable I see mris_make_surfaces -mgz -w 0 -T1 brainfinalsurfs.mgz $subject $hemi whi

Re: [Freesurfer] Recon-all

Hi Sharon, that's good to hear :). Yes, that's the way we run our analysis also these days. With reasonable quality data there are very few failures and it's not worth the time to check stuff if you have a lot of sets to get through (although you should always check things at the end of course

[Freesurfer] FS installation for FC 7 + ATI Mobility FireGL V5000 graphics card

Hi All, Does anyone have any experience with FS installation under Fedora Core 7 Linux + ATI Mobility FireGL V5000 (256K) graphics card? Which is the correct version to use? Do I need any additional patches to download or are any other configuration settings necessary? Thanks in advance,

Re: [Freesurfer] Partitioning GM/WM boundary surface

Morgan, Generally you would want to use: recon-all -finalsurfs -s -hemi which will ensure calling mris_make_surfaces with the right parameters. Nick On Wed, 2007-07-25 at 16:59 +0100, Morgan Hough wrote: > Thanks Bruce, > > From the ReconAllDevTable I see > > mris_make_surfaces -mgz -w

Re: [Freesurfer] Partitioning GM/WM boundary surface

Thanks Bruce, From the ReconAllDevTable I see mris_make_surfaces -mgz -w 0 -T1 brainfinalsurfs.mgz $subject $hemi which will produce new ?h.thickness, area, curv, white and pial surfaces as well. Are these the options I should rerun with? Cheers, -Morgan Bruce Fischl wrote: rerun mris_make

[Freesurfer] Recon-all

Dear Freesurfers. I am facing a crucial point.:)and I need your help. After examining most of our subjects, we decided that there is no need to run all the procedures- work flow, since our data is not prone to too many failures, and just start with recon-all-all, get all the data and then start

Re: [Freesurfer] Partitioning GM/WM boundary surface

rerun mris_make_surfaces and it will create them (and not deform the surface in regions outside the label) On Wed, 25 Jul 2007, Morgan Hough wrote: Hi Bruce, These subjects were run with an older version of FreeSurfer and don't have ?h.cortex.label. I am afraid I don't see a generating comma

Re: [Freesurfer] Partitioning GM/WM boundary surface

Hi Bruce, These subjects were run with an older version of FreeSurfer and don't have ?h.cortex.label. I am afraid I don't see a generating command in the ReconAllDevTable. In ReconAllFilesVsSteps it looks like it is coming from mris_make_surfaces. Can I generate these labels from the old reco