Re: [Freesurfer] Script to get recon processing time

no, but if you add the flag -time to recon-all, you will get lines like this in the recon-all.log: time:: 0:11.49 cmd:: mris_anatomical_stats where you can grep on 'time::' to get command run times, although you'd have to add together some commands to get times for a stage. note: runtimes c

Re: [Freesurfer] recon-all error

you will need to get a fixed version of mri_ca_label from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc n. On Wed, 2010-07-28 at 22:40 -0400, Watson, Christopher wrote: > I was running a subject, and got this error: > recon-all exited with ERRORS at Wed Jul 28 21:50:47 EDT 2010

Re: [Freesurfer] Script to get recon processing time

fyi, attached is the grep "time:: " output from a recent run (which took 27.5 hours). this should at least spare you from having to run recon-all -time yourself. it was run on a 2GHz amd opteron. n. On Thu, 2010-07-29 at 11:38 -0400, Nick Schmansky wrote: > no, but if you add the flag -time

[Freesurfer] Overlay Thickness Files in tkmedit

Hi, is there a way to visualize the lh.thickness or rh.thickness files as an overlay in tkmedit. Thanks, Michael ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

Re: [Freesurfer] recon-all error

Thanks, that did the trick. Chris Nick Schmansky wrote: > you will need to get a fixed version of mri_ca_label from here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc > > n. > > On Wed, 2010-07-28 at 22:40 -0400, Watson, Christopher wrote: > >> I was running a subject, and got

[Freesurfer] skull strip

I have a question regarding the skull stripping process. I ran my data through recon-all but still had much skull intact. I then followed the recommended process per the freesurfer wiki to change the watershed threshold levels on the recon process. I did so at the 20, 15, 10, 5, and 0 threshold w

Re: [Freesurfer] Overlay Thickness Files in tkmedit

you could sample it into the volume then visualize that I guess. On Thu, 29 Jul 2010, Michael Scheel wrote: > Hi, is there a way to visualize the lh.thickness or rh.thickness files > as an overlay in tkmedit. > > Thanks, Michael > > ___ > Freesurfer ma

Re: [Freesurfer] monkey brain recon outputs

Hi Ali, On Jul 27, 2010, at 12:00 PM, Arslan, Ali wrote: > Hi, > I finished reconstructing a monkey's surface following the scripts on > the wiki. The output surfaces seems to be a bit distorted and rough > around the edges. > This reconstruction is done with a volume normalized by using ~400 >

Re: [Freesurfer] tkmedit scripting question

Hi Sebastian I was able to manipulate the dialogue like this %set gEditBrush(1,cloneSource) 1 %set gEditBrush(1,mode) 1 Try a combination of 0 or 1 for the last argument. And spaces ( or lack of them ) are absolutely important. Don't leave any space in gEditBrush(1,mode) The first argument

[Freesurfer] [fsfast]: temporal overlap of stimuli and concurrent presentation

Dear fellow Surfers, is it possible to model several independent event streams for fs-fast? That is, using the 5 column paradigm file, is it okay to have different condition ID codes that have identical stimulus onset time (well only some of the time)? Or would I have to model that by specifyin

Re: [Freesurfer] tkmedit scripting question

Hi Krish, thanks a lot. Unfortunately that only sets the values for the dialog but does not actually activate them. I will try my luck, now that you showed me how to set more involved tcl structures :). I will report back (once our computer system works again). Best Sebastian On Jul