Re: [Freesurfer] mkhaedsurf error

Hi, What's in T1-neuromag/slices? Just an error.log file. What version are you using? I am not aware of the version of the FreeSurfer. How can I check the version ? Shriks SHRIKANTH KULASHEKHAR wrote: Hi all, When I attempt to create a high-resolution head surface tessellation using

Re: [Freesurfer] mkhaedsurf error

Hi To check the version of FS If you are usinfg a tcsh shell then use the following commandsource $FREESURFER_HOME/SetUpFreeSurfer.csh If you're using sh shell then useexport FREESURFER_HOME=/Applications/freesurfersource $FREESURFER_HOME/SetUpFreeSurfer.sh bestRaka --- On Wed, 6/3/09,

[Freesurfer] temporal lobe segmentation

Hi all, I am interested in automated segmentation of temporal lobe using freesurfer. I understand that it is possible to add up the individual regions of a specific lobe, create one massive label for that lobe, and get statistics on those. But I am not sure about the practicality of this

[Freesurfer] smooth sulc on only part of the surface

Hi,all   I am interested in only the positive sulc  and would like to make group analysis of the postive sulc values. Hence I would like to mask off the negative values (as the lh.sulc file has both positive and negative value). Before making group analysis, I have to resample and smooth the

[Freesurfer] substantia nigra's segmentation

Hello! How I do for make segmentation of substantia nigra using freesurfer? Thanks! -- == Paula Rejane Beserra Diniz Bacharel em Informática Biomédica Mestre em Neurociências Doutoranda em Neurociências Universidade de São Paulo Hospital das Clínicas - Ribeirão

Re: [Freesurfer] substantia nigra's segmentation

sorry, we don't do substantia nigra at the moment. On Wed, 3 Jun 2009, Paula Diniz wrote: Hello! How I do for make segmentation of substantia nigra using freesurfer? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] smooth sulc on only part of the surface

You can use make a mask out of the sulc using mri_binarize. This will result in a surface value file with 1s and 0s. You can then run mris_fwhm to smooth the sulc, passing it the sulc mask. Note: mri_surf2surf and mris_fwhm are redundant in that they can both smooth (and will yield the same

[Freesurfer] multiple subjects on Linux

Experts, I have 13 subjects on which I have to run autorecon-all processes to do cortical reconstruction. I work on an Ubuntu machine, dual core, each with 2.8 GHz and 4 MB RAM. Can I run more than one subject simultaneouly? If yes, how many and in what way? Would that affect process time?

[Freesurfer] Re: 'Max' in sig.cluster.summary

Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output. Is the Max in column 2 below a measurement of thickness? If it is thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal

Re: [Freesurfer] multiple subjects on Linux

you should be able to do 2 at a time On Wed, 3 Jun 2009, Barnali Basu wrote: Experts, I have 13 subjects on which I have to run autorecon-all processes to do cortical reconstruction. I work on an Ubuntu machine, dual core, each with 2.8 GHz and 4 MB RAM. Can I run more than one subject

Re: [Freesurfer] Re: 'Max' in sig.cluster.summary

Hi Judith, Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster. Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output. Is the Max in column 2 below a measurement of thickness? thickness, is the correct