Re: [Freesurfer] wm boundries

Hi Amy, what version are you running? This looks really strange. Maybe a huge topological defect that was corrected improperly? Bruce On Thu, 6 Dec 2007, Amy DeLuca wrote: Hi All, I am having difficulties with a subject and would like advice on anything else I can try. I've attached a j

Re: [Freesurfer] wmparc/white matter problems?

Can you send a pic? Ryan Muetzel wrote: Hello, We are running Freesurfer version 4.0.1 and seem to be having problems with the white matter/gray matter parcellation borders. When viewing the pial and the main white surfaces in tkmedit, everything looks good against the t1 brain. However, wh

Re: [Freesurfer] Cluster thresholding

FDR assumes that the collection of values has both positives and negatives. It assumes that the pvalues of the negatives are uniformly distributed between 0 and 1, and this model is used to estimate the total number of positives (both true and false). When you cluster, you are setting all voxel

[Freesurfer] estimated total intracranial volume

Hi All, I'm interested in the relationship between estimated total intracranial volume (eTIV), and the volume measures generated in aseg.stats and lh/rh.aparc.stats. I have used freesurfer v3.0.3 for this data set. Here I am using the output of aseg.stats for all volumes except the cerebral

[Freesurfer] mri_convert

Hello All, I wanted to convert the brainmask volume to analyze format. I'm not very familiar with the analyze format and had two questions. 1) The wiki mentions that converting to SPM-Analyze format could involve converting to multiple or single frames. What exactly are multiple or single frames?

Re: [Freesurfer] estimated total intracranial volume

Paul, The eTIV calc in freesurfer is an estimate of the total intracranial volume based on a scaling factor determined by the alignment with an atlas. The technique is described in the paper referenced here: http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV To my knowledge, its relationship to the

Re: [Freesurfer] mri_convert

Anil Roy wrote: Hello All, I wanted to convert the brainmask volume to analyze format. I'm not very familiar with the analyze format and had two questions. 1) The wiki mentions that converting to SPM-Analyze format could involve converting to multiple or single frames. What exactly are m

Re: [Freesurfer] estimated total intracranial volume

the total will be brain plus ventricles. eTIV also includes sulcal csf, so it won't be the same On Thu, 6 Dec 2007, Nick Schmansky wrote: Paul, The eTIV calc in freesurfer is an estimate of the total intracranial volume based on a scaling factor determined by the alignment with an atlas. The

[Freesurfer] Question about brain masking

Dear FreeSurfers, I'm having some trouble with my brain masks. Below I have inserted a subject's T1.mgz and brain.nii overlay (made with preproc-sess). As you can see, the mask goes well beyond the boundaries of the brain. Any ideas what could cause this-perhaps noisy functional scans? The majo

Re: [Freesurfer] Question about brain masking

I would not worry about it. It is just used to help exclude voxels for whitening. Dan Dillon wrote: Dear FreeSurfers,   I’m having some trouble with my brain masks. Below I have inserted a subject’s T1.mgz and brain.nii overlay (made with preproc-sess). As you can see, the m

[Freesurfer] Recon-all failing at CA Reg

Hello, I am having trouble with one subject during the recon-all process. It has failed twice at CA Reg: status file for recon-all Thu Nov 8 15:11:20 EST 2007 [EMAIL PROTECTED] MotionCor Thu Nov 8 15:11:20 EST 2007 [EMAIL PROTECTED] Nu Intensity Correction Thu Nov 8 15:18:50 EST 2007 [EMAIL

Re: [Freesurfer] Recon-all failing at CA Reg

Hi Caroline, can you send us the end of the recon-all.log when it fails? Bruce On Thu, 6 Dec 2007, Caroline Chapman wrote: Hello, I am having trouble with one subject during the recon-all process. It has failed twice at CA Reg: status file for recon-all Thu Nov 8 15:11:20 EST 2007 [EMAI