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FAQ

The purpose of this FAQ is to provide a Wiki space where users can add the most frequent questions to avoid asking already answered questions in the support list.

TableOfContents

General

How can I help this FAQ?

A: If you are able to edit pages go ahead! If you don't have permission to write on the Wiki send an e-mail to ppj at netfilter dot com dot br

How long does it take to finish a reconstruction?

A: It depends on your processor speed and machine performance (notice that dual core or hyperthead won't speed up one analysis significantly), give a look at the link below in the section "Step-wise directives": http://surfer.nmr.mgh.harvard.edu/fswiki/recon_2dall

How can I reduce the time of recon-all in a group of patients?

A: FreeSurfer run its process in a non-parallel environment, so you won't have benefit from a dual core machine for a single case analysis. However if you have many cases you can start two FreeSurfer recon-all process in the same machine and theoretically you can reduce by half the time to analyze your group of cases. A similar procedure can also be used in quad-core environment. Note that to take benefit of a multi-core environment you need to use a SMP kernel in your OS.

Is it possible to run FreeSurfer in Ubuntu Linux?

A: Yes. Ubuntu Linux is basically a Debian distro, so you should use FreeSurfer RH9 version. Depending on your video card you should disable the DRI using the option NoDRI in the Device section of your X configuration file. Notice that in older Ubuntu version there's a bug that prevents NoDRI from working.

Reconstruction

Q: It seems that there is a 5mm thickness upper limit in my volumes, is it normal? How can I change this?

A: We did this to prevent noncortical regions such as the basal ganglia from corrupting the thickness measure through averaging. With the ?h.cortex.label it is probably no longer needed, however you can use mris_thickness -max <max thick> to generate a thickness with a different max. Take a look in the example below:BRBR mris_thickness -max 10 bert lh newlh.thicknessBRBR The file newlh.thickness will be created inside the surf directory of your subject. But we don't think the true thickness is ever that much except in pathological cases like dysplasia and other disorders of cortical development.

Why in many subjects the insular cortical surface seems so thick? Is the convoluted nature of the Insula that causes that?

A: It's not the convoluted nature of the Insula. It's the fact that extreme capsule is so thin that it frequently isn't very apparent on MR, and so there appears to be continuous gray matter from the basal ganglia into the cortex. We think version 4.0 fixes this.

I am trying to measure the cortical thickness of specific ROI how can I do this?

A: You can save the ROI to a label file and then use:BRBR

FreeSurfer & Matlab

How can I make an histogram of cortical thickness?

A: In Matlab you can use the read_curv() function, as in the example below.BRBR