Re: [Freesurfer] RE: extending the pial surface and scuba

Hi, you can try adding control points in the white matter that is dimmer than you want it to be then rerun autorecon2-cp and autorecon3. Make sure that you only select control points in locations that are *not* partial volumed, and that have an intensity in the brain.mgz of <110. If you want

[Freesurfer] RE: extending the pial surface and scuba

Dear freesurfer I’m one of the neurologists in South Korea and having an interest in the functional neuroimaging studies in neurodegenerative diseases. Recently, I’m planning to study the cortical thickness of various degenerative disorders and trying to learn the freesurfer (version 4.0.5),

Re: [Freesurfer] WM segmentation

Hi Christian, these are both bugs. I've fixed both of them. The fix will be available in the next release, but if you give me your platform details, I can get you a binary to test out. doug [EMAIL PROTECTED] wrote: Hi Freesurfers, I have a couple of questions regarding WM segmentation. My d

Re: [Freesurfer] SNR maps

You don't necessarily have to exclude them as you can use weighted random effects (it will de-weight the noisy scans). All the same, it is a good idea to try to track down why a few are noisier. The prime suspect is motion, so check the motion plots. There might be scanner spikes as well (try

Re: [Freesurfer] Re-processing

Petr, The easiest way to do this is to multiply your v3.0.0 ICV values by 0.744. The fix in v3.0.2 was merely changing the scaling factor (reduced by 0.744), so rerunning all the data under v3.0.2 is not necessary to get this corrected ICV value. But if you wanted to rerun, you can just run -aut

Re: [Freesurfer] dt_recon & stage 3

What's your cmd line? Is this from a Siemens scanner? MRI CDPI wrote: Dear group, i am trying to run dt_recon on some dti data, the first two steps: image transformation, eddy_correction, run fine. In the third stage, the glmfit, the process stops after giving the ERROR message: cannot extra

Re: [Freesurfer] choroid plexus

Hi Jenifer, since everyone else includes choroid as part of their ventricular volumes (and since it's probably pretty partial-volumed with ventricle in any case), I guess I would include it. cheers, Bruce On Thu, 7 Aug 2008, Juranek, Jenifer wrote: Hi, Would like to sum all CSF compar

[Freesurfer] choroid plexus

Hi, Would like to sum all CSF compartments to get a global CSF volume for each subject. Should Choroid plexus (L & R) be included in the summation? I have not seen other "non-freesurfer" apps tease out the choroid plexus. So far, I have the following 8 compartments: [Left-Lateral-Ventricle

[Freesurfer] Re-processing

Hi! Have some subjects processed with 3.0. This version turned out to do wrong ICV-calculations. We therefore want to re-run with 3.0.2. (That version is chosen because the results will be compared with other subjects run with 3.0.2). Just asking this to be sure: If I re-run them now, it´s ok to

[Freesurfer] dt_recon & stage 3

Dear group, i am trying to run dt_recon on some dti data, the first two steps: image transformation, eddy_correction, run fine. In the third stage, the glmfit, the process stops after giving the ERROR message: cannot extract sWiPMemBlock.alFree[8] from .../ dwi-infodump.dat And indeed, there is