Re: [Freesurfer] inter vertex distance

do you mean on along the surface or in the volume? On Mon, 27 Dec 2010, YUMI MAEDA wrote: HI, I am wondering if there is a way to calculate inter vertex distance on fsaverage surface with freesurfer. thanks for your help. YUMI ___ Freesurfer

Re: [Freesurfer] bad output of autorecon2 - is there any way to adjust it?

Hi Paola, that looks pretty bad. What version are you running? You can try using rhe expert opts to set the g/w intensities, or drop the dataset on our site and we'll take a look. cheers Bruce On Tue, 28 Dec 2010, Paola Valsasina wrote: Dear Freesurfer experts, I have tried to analyze

[Freesurfer] R: bad output of autorecon2 - is there any way to adjust it?

Dear Bruce Thank you for your answer. I tried to analyze these data both with FS 4.5 and with FS 5.0. Outputs are similar and bad in both cases. I think that the major problem is the quality of the starting sequence (3D FFE acquired on a Philips 3T), because I am running FS on another dataset

Re: [Freesurfer] R: bad output of autorecon2 - is there any way to adjust it?

Hi Paola we'll need the 001.mgz. You can check our wiki for info on sending stuff to us. cheers Bruce On Tue, 28 Dec 2010, Paola Valsasina wrote: Dear Bruce Thank you for your answer. I tried to analyze these data both with FS 4.5 and with FS 5.0. Outputs are similar and bad in both cases.

[Freesurfer] pial surface in v5.0

I am not able to run recon-all localGI in v5.0 and I suspect this has something to do with the way pial surfaces are produced in v5.0 (the mris_make_surfaces bug) ERROR: compute_lgi did not create output file

Re: [Freesurfer] pial surface in v5.0

Hi Lena, many of us are struggling to get home amid all the snow on the east coast. We'll figure this out in the next few days. cheers Bruce On Tue, 28 Dec 2010, Lena Palaniyappan wrote: I am not able to run recon-all localGI in v5.0 and I suspect this has something to do with the way

Re: [Freesurfer] inter vertex distance

If you run 'mris_curvature_stats' on the surface (see 'mris_curvature_stats -u' for usage help), one of the summary rows in the report is the average inter vertex distance. You could probably just do: $mris_curvature_stats -F smoothwm subjID lh curv given appropriate SUBJECTS_DIR env

Re: [Freesurfer] inter vertex distance

thanks Rudolph and what if you wanted the topological (shortest distance along the surface) between two specific vertices? so, say i have two known locations and i want to know how separated they are over the surface - is there a command where i can input the two vertices and the output is

Re: [Freesurfer] LGI failure

Hi Lena, Sorry for the delay in answering, happy Christmas and new year too! Could you please send me the whole error output? Thanks, Marie On Dec 25, 2010, at 10:37 AM, Lena Palaniyappan wrote: Hi Marie/ list Happy Christmas/New Year!! Any idea why this is happening while I try to

[Freesurfer] FreeSurfer Error(s)

Hello, Below I've copied the information for 1 case that has repeatedly given me the same error; however, I'm receiving the same error for the entire caselist (which has over 30 cases). Any help would be very much appreciated! Thanks, Tali * [bugr output]* FREESURFER_HOME:

[Freesurfer] problem with tksurfer

Dear Freesurfers, I am experiencing a strange problem with tksurfer: lately I seem to be unable to manually enter (using the keyboard) the Vertex Index in the GUI, either on the main window or in the ToolSelect Vertex number window. Oddly enough, while I cannot enter numbers, I can PASTE them

Re: [Freesurfer] FreeSurfer Error(s)

Hi Talis have you visually inspected the talairach transform? How did you get the volume into nifti format? Check the 001.mgz in tkmedit and make sure that it has the directions correct (e.g. coronal is really coronal, etc..) cheers Bruce On Tue, 28 Dec 2010, Tali Swisher wrote: Hello,