[Freesurfer] Recon-all-long

Dear FS experts I tried to run recon-all-long, but there is no such command. I use FS 4.0.5 on a MacIntel. Where can I find this command and is there any documentation about a longitudinal FS analysis? Thanks in advance Best regards Juergen -

[Freesurfer] What is included in the ICV value

Hello, I am measuring the shrinkage of the limbic system over time for several subjects and need to know what is included in the ICV value in aseg.stats to do this. We are putting our raw scans into freesurfer without any manual edits until after QA at the end. My understanding is that the b

[Freesurfer] Cerebellum Segmentations

Hello, I am processing a large number of scans with the goal of segmenting the cerebellum into subregions, particularly the Vermis. Without editing each scan individually using tkmedit, what is the best way to achieve this subregion segmentation for a large number of subjects? Thank you in a

RE: [Freesurfer] WM intensity < CSF intensity?

Thanks, Bruce. The file upload to your server just finished. -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, September 03, 2008 12:34 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WM intensity < CSF intensity? hmmm,

RE: [Freesurfer] WM intensity < CSF intensity?

hmmm, do you want to send it to us and we'll take a look? On Wed, 3 Sep 2008, Juranek, Jenifer wrote: Yes, in the T1.mgz, the WM is around 110 in the slices I sampled across the ant-post extent of the brain. -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednes

RE: [Freesurfer] WM intensity < CSF intensity?

Yes, in the T1.mgz, the WM is around 110 in the slices I sampled across the ant-post extent of the brain. -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, September 03, 2008 11:41 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Fre

Re: [Freesurfer] WM intensity < CSF intensity?

is the white matter in the T1.mgz close to 110? On Wed, 3 Sep 2008, Juranek, Jenifer wrote: Hi, I'm running fsv405 on RHEL5. I received the following message and reviewed the input images, but could not spot the problem. Any suggestions about where I should be looking in the T1.mgz? Many

[Freesurfer] WM intensity < CSF intensity?

Hi, I'm running fsv405 on RHEL5. I received the following message and reviewed the input images, but could not spot the problem. Any suggestions about where I should be looking in the T1.mgz? Many Thanks, Jenifer White matter intensity 0 is lower than CSF intensity 14. Please examine input imag

Re: [Freesurfer] Surface area measurement

You'll find surface area measurements for each cortical parcellation area in your ?h.aparc.stats file within the stats directory for each subject. Allison On Wed, 3 Sep 2008, Barkay, Gavriel wrote: Can I do surface area measurement using freesurfer? -- Gavriel Barkay M.D. M.Sc. Psychopharmaco

[Freesurfer] Surface area measurement

Can I do surface area measurement using freesurfer? -- Gavriel Barkay M.D. M.Sc. Psychopharmacology Fellow Office: 317-433-1771 Pager: 317-312-2448 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/lis

Re: [Freesurfer] Newbie problem...

Bonjour Dr Philippe My guess is *" * *Getting Series No * *INFO: Found 250 files in /home/philfeu/freesurfer/subjects/ghca* *INFO: Scanning for Series Number 2* *Scanning Directory * *INFO: found 128 files in series* *INFO: loading series header info.* *"* I think it should be better in th

[Freesurfer] Newbie problem...

Hello, I am evaluating FreeSurfer, installed and runned the tutorial without major troubles. Now, we have set up the MPRAGE sequence as stated here: http://www.nmr.mgh.harvard.edu/~andre/Sequences/SagMPR8Min.html and we have also a problem, surely a newbie and trivial one (sorry about that...)