Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Volume measurements.
by Goradia, Dhruman D 11 May '06

11 May '06

Hi all, In the aseg.stats file there is a measurement called Brain segmentation volume. Can someone tell me what it is? Is this same as whole brain GM volume? If not is there a way to compute that? -Dhruman

2 1

Ventricular Volume in FreeSurfer?
by anthony gallo 10 May '06

10 May '06

Hello All, I am wondering......... Does FreeSurfer log ventricular volume? -Anthony

2 1

Problems with FSGD file
by Martin.Ystad＠student.uib.no 10 May '06

10 May '06

Hi, I'd like to try out some simple regression analysis on some of my data. I've completed the tutorial until the mri_glmfit step where I get the error message: ERROR: gdfRead: gruppefil.txt is not formated properly I really can't see what's wrong with my file, I've even copy-pasted one of the example files from the tutorial just to check if anything is working at all, but it didn't work either. GroupDescriptorFile 1 Title KognitivAldringTEST21 Class Class1 CLASS Class2 Variables Age Input fs568 Class1 54 Input fs569 Class2 59 Input fs572 Class2 67 Input fs573 Class1 46 Input fs574 Class1 52 Input fs577 Class1 46 Input fs578 Class2 68 Input fs579 Class1 47 Input fs580 Class2 74 Input fs583 Class2 61 Input fs585 Class2 62 Input fs587 Class2 56 Input fs588 Class2 59 Input fs592 Class1 49 Input fs593 Class2 56 Input fs594 Class2 58 Input fs597 Class2 61 Input fs599 Class1 46 Input fs601 Class2 65 Input fs603 Class2 68 Input fs608 Class2 70 DefaultVariable Age I've tried with classes, without classes, with more variables and so on, but nothing seems to work. Any ideas on why I get this error message? I used emacs, vim and open-office to create my FSGD file, gruppefil.txt. It's probably just a trivial mistake somewhere, but I just can't seem to find it... Thanks, MartinYstad University of Bergen, Norway

2 1

Skull Stripping a Macaque
by Faden, Eric (NIH/NIMH) [F] 10 May '06

10 May '06

Hey all, Is anyone using freesurfers mri_watershed to strip macaque skulls? If so what options are you using? I am currently trying to use it but am getting really bad results. I am also open to suggestions of other programs to try. -Eric

1 0

TIV and TBV
by Lee HL 09 May '06

09 May '06

Hi, I was wondering if anyone knows where to extract the values for TIV and TBV after autorecon1? I was planning to compare with and without talairach transformation and how the TIV and TBV, manual and automated methods, would be affected. Thanks. Best regards, HweeLing

2 1

aseg step bypass
by Joao Pereira 09 May '06

09 May '06

I am using freesurfer for an inter-subject cortical thickness analysis. In order to speed things up, I was considering removing the sub-cortical segmentation step with -noaseg in the recon-all command line. I believe this will not affect my results, but I am not sure if some of the subsequent procedures are affected. Is it OK to do this then? Thank you! Joao Pereira

2 1

autorecon2 on rh only
by anthony gallo 08 May '06

08 May '06

Can you please tell me the command line for running recon-all autorecon2 on only the right hemisphere? It isn't entirely clear to me from the wiki. I appreciate it, Anthony

2 1

Noncompletion of autorecon2
by anthony gallo 08 May '06

08 May '06

Hello, I am having some trouble. I have all of the left hemisphere data that autorecon2 makes but not all from the right hemisphere. I have 2 questions: 1. If freesurfer encountered a problem and ended with an "error" would that error appear at the end of the recon-all log? 2. If the computer shut down and that was the problem (some form of auto shutdown) would an error appear in the freesurfer log? Thanks in advance, Anthony

2 1

Re: [Freesurfer] fill stats
by Kevin Teich 08 May '06

08 May '06

Unless Doug has a tool for this, then no; it can't be done within tksurfer. Sorry. On Thu, May 04, 2006 at 06:16:31PM -0400, Chris Baker wrote: > > Yes- we're trying to select labels based on negative regions. If > there's no way to do this, is there a way to change which is the > positive and which the negative contrast in sfa-sess or does it > always take the first condition as being the positive contrast. -- Kevin Teich

2 1

edit surfaces combined with MRI
by Michael Rullmann 08 May '06

08 May '06

hey, i used mri_watershed to produce different surfaces of the brain such as inner/outer skull, outer skin and brain. often the produced surfaces aren't totally correct. tkmedit shows me the surfaces and the MRI at the same time. now i want to edit the shown surfaces with tkmedit. is it possible? for editing i need to see the MRI and the surfaces at the same time. i didn't found an "edit surface tool" there. thanks, michael.

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