Re: [Freesurfer] mris_fix_topology stops with two T1-s

2012-08-12 Thread Garikoitz Lerma Usabiaga
Many thanks Bruce, I will choose the best one in this case. The command line was: recon-all -s B_06 -qcache -measure thickness -all (I already had copied by hand the /mri/orig/001.mgz and 002.mgz) Just in case I repeated the process with the original files, but I had exactly the same results.

[Freesurfer] Averaging overlays/labels across subjects

2012-08-12 Thread raij
Dear Surfers, I have (non-fMRI) .w format surface overlays/labels, computed at the smoothwm surface in each individual subject, in 25 subjects. FS5.1 recon-all has been run for all T1 images. I already managed to convert all individual surface overlays into the surface space of one of the

Re: [Freesurfer] Averaging overlays/labels across subjects

2012-08-12 Thread Douglas Greve
Hi Tommi, to compute an average, all you need to do is run mri_concat file1.mgh file2.mgh ... fileN.mgh --mean --o average.mgh doug On 8/12/12 7:50 PM, r...@nmr.mgh.harvard.edu wrote: Dear Surfers, I have (non-fMRI) .w format surface overlays/labels, computed at the smoothwm surface in

[Freesurfer] (no subject)

2012-08-12 Thread Hugh Pemberton
Hi, How can I get sulcal depth measurements from Freesurfer? Cheers, Hugh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the

Re: [Freesurfer] (no subject)

2012-08-12 Thread Douglas Greve
The values are in the ?h.sulc file doug On 8/12/12 10:12 PM, Hugh Pemberton wrote: Hi, How can I get sulcal depth measurements from Freesurfer? Cheers, Hugh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] (no subject)

2012-08-12 Thread Matt Glasser
What are the units of that measure? Thanks, Matt. _ From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Sunday, August 12, 2012 9:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no

Re: [Freesurfer] (no subject)

2012-08-12 Thread Bruce Fischl
They are the integrated dot product of the surface normal and the movement vector during inflation. On Aug 12, 2012, at 10:28 PM, Matt Glasser m...@ma-tea.com wrote: What are the units of that measure? Thanks, Matt. From: freesurfer-boun...@nmr.mgh.harvard.edu