[Freesurfer] FDR button

Dear FS experts When using the FDR button in the Configure Overlay Display, there appear the FDR corrected new threshold in the terminal after pressing the Set Threshold Using FDR button. However, when changing the rate from 0.05 to e.g. 0.1, the FDR corrected threshold does not change. Why? Furth

Re: [Freesurfer] cortical thickness

Hi 李日, 1) Is the cortical thickness of the area where you passed the mouse over. 2) Is the index of the vertex in the cortical model. 3) Red line select the threshold limit for red color in the map, green line select the interface between red/yellow coloring. Regards, Pedro Paulo Jr. 2008/8/1

[Freesurfer] downloadable manual

Hello folks - I recently downloaded freesurfer and am slowly becoming more familiar with it. However, having to search through the myriad of pages on the wiki every time I have a question is very cumbersome, and more often than not, fruitless. Is there a downloadable manual available anyw

Re: [Freesurfer] downloadable manual

Hello, I would definitely be interested as well if such a thing exists, thanks!!! Jake On 8/13/08 12:13 PM, "Eliezer Kanal" <[EMAIL PROTECTED]> wrote: > Hello folks - > > I recently downloaded freesurfer and am slowly becoming more familiar > with it. However, having to search through the my

Re: [Freesurfer] cortical thickness

Take a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/ppaulo/qdec-coord PPJ 2008/8/13 Al-Radaideh Ali <[EMAIL PROTECTED]> > Hi Pedro, > > I have seen in one email that using mri_surf2vol can map the

Re: [Freesurfer] downloadable manual

I think the manual is spread among the wiki pages. However I think to start up the best way is using the tutorials: http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials Pedro Paulo Jr 2008/8/13 Eliezer Kanal <[EMAIL PROTECTED]> > Hello folks - > > I recently downloaded freesurfer and am slowly be

Re: [Freesurfer] downloadable manual

Just to emphasize the point, while the wiki (and the tutorials within it) are good for getting started, its proving (for me, at least) to be very poor as a reference. The wiki search functionality is not so hot. If such a manual doesn't exist, are there plans for one? Thanks - Eliezer Kanal

Re: [Freesurfer] downloadable manual

Hi Eliezer We changed the search system couple of months back but sometimes the search takes a bit of time, yes. Could you give me an example query you gave, the page you expected and what the search results turned out to be? Also, use the "Text" search function rather than Title search bec

Re: [Freesurfer] FDR button

This will sometimes happen when there is no or little activation (it get's stuck at it's highest threshold). Truncation removes vertices from the list of values used to compute the FDR threshold (effectively reducing your search space). Use "Only marked" if you want to reduce your search spac

Re: [Freesurfer] downloadable manual

If you are just getting started, this is the best place. http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction Once you have the basics the wiki is much more manageable. I think manual is at the bottom of the list because functionality is at the top. Anthony Eliezer Kanal wrote:

[Freesurfer] error while loading shared libraries:libtiff.so.3

I'm using 64 bit Ubuntu and installed freesurfer-Linux-rh9-stable-pub-v4.0.5-full.tar.gz Everything worked fine when I tested the installation with tkmedit and tksurfer. I then ran recon-all and got error

Re: [Freesurfer] downloadable manual

Hi Eliezer, we had a manual some years ago, but found the wiki was much easier to keep current. What form would the manual take? A list of commands and usages? cheers, Bruce On Wed, 13 Aug 2008, Eliezer Kanal wrote: Hello folks - I recently downloaded freesurfer and am slowly becoming more

Re: [Freesurfer] error while loading shared libraries:libtiff.so.3

Ian, Your best bet is to install the libtiff.so.3 rpms. Nick On Wed, 2008-08-13 at 12:35 -0700, lan lin wrote: > I'm using 64 bit Ubuntu and installed freesurfer-Linux-rh9-stable- > pub-v4.0.5-full.tar.gz > > Everything worked fine when I tested the installation with tkmedit and > tksurfer.

Re: [Freesurfer] downloadable manual

Well, I'm no editor, but in my mind a comprehensive manual would contain the following: 1) installation instructions 2) a walkthrough for the test dataset 3) descriptions for each program: a) a summary of each program b) acceptable program input c) a description of the o

Re: [Freesurfer] downloadable manual

Eliezer, Thank you for the input. We'd like to automate the generation of documentation when we can get some work-cycles to do so. I agree the wiki can be a bit of a hunting expedition to get information (but isn't that half the fun :). About a year ago, we started using Doxygen-style commentin

Re: [Freesurfer] error while loading shared libraries:libtiff.so.3

libtiff.so.3 is typically provided by the ia32-libs package in Ubuntu and Debian (and presumably any other Debian-derived distros) So you can install using the following command: sudo aptitude install ia32-libs I'm not sure which binary is doing the complaining, I don't see anything in $FRE

Re: [Freesurfer] error while loading shared libraries:libtiff.so.3

My system is also 64 bit Ubuntu and met the same problem. while doing ln -sf usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3 It works ok, so I guess you can try to create soft link instead of hard link~~ bin lv 2008-08-14 bin.lv 发件人： lan lin 发送时间： 2008-08-14 03:37:38 收件人： freesurfer@n