[Freesurfer] Errors in qdec/Analyze

Hi to all, I have been having troubles with qdec and several error messages appear. The first message appeared when clicking 'analyze'. It doesn't matter if i use one or two discrete plus one or two continuos factors, i get the same error message. What does it mean by codno=1e+08? Creati

Re: [Freesurfer] How to rerun recon-all after modifying talairach registration manually?

Hi Nick and all: The talairach_avi can work on my data. In my mind, modifying talairach registration manually should affect the value of talAviQA and z-score. So when we rerun autorecon1, it will give us new talAviQA and z-score, but it outputed the same talAviQA and z-score on my data .This i

Re: [Freesurfer] concerning my posting: curvature file 'lh.area.mid' has wrong magic number - add logfile

Oliver, That's a strange error. Did you run out of disk space? I can only think of that as a reason for a corrupted curvature file. Nick On Mon, 2009-06-22 at 14:00 +0200, Oliver Grimm wrote: > Hi! > > I just mentiones my error > > curvature file 'lh.area.mid' has wrong magic number > > on

Re: [Freesurfer] qdec analyses

Miguel, 1- the 'average' referred to in the display question refers to each vertex on the group average surface, and is the mean of all subjects in a group. Ctrl-right click on a vertex to bring up a data plot to see this raw data. the actual display is the p-value (-log10) of the contrast avgA-

Re: [Freesurfer] how to segment hippocampus using freesurfer

wyang, the recon-all stream will produce a file named aseg.mgz for your subject that contains the segmented hippocampus (and 30+ other structures). you can learn about freesurfer via the tutorials: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial Nick On Mon, 2009-06-22 at 14:43 -0400, Wenl

Re: [Freesurfer] Mris_thickness_diff and FS4.4

Jürgen, the lta file looks right, but your naming of the base subjects looks suspect if you are using the new longitudinal stream. in the new stream, the base subject is composed of all the timepoints, so the names tp1_base and tp2_base look wrong. how were those created? Nick On Mon, 2009-06

[Freesurfer] Mris_thickness_diff and FS4.4

Dear FS experts I run the following command with longitudinal data from FS4.4, but I am not sure whether I specified the files properly (_base files?) and used the right transform (tp1_to_tp2.lta?), because files and transforms changed in FS4.4. mris_thickness_diff -xform tp2.long.tp2_base/mri/tr

[Freesurfer] how to segment hippocampus using freesurfer

Hi all, I want to use freesurfer to segment hippocampus from MR images, but I don't know how to do it because I am a newcomer here. could you give me some advices? thanks. wyang___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

[Freesurfer] qdec analyses

Hi all, I am a little bit confused about the qdec display. I have some simple questions about two groups A and B: 1- In the question, does the average thickness differ between A and B? How this average is calculated? By the difference between the A average and B average (avgA-avgB) ? The negat

Re: [Freesurfer] How to rerun recon-all after modifying talairach registration manually?

Zonglei Zhen, What is the age range of your subjects? You can add -notal-check to the end of the recon-all string to skip the check. We have seen some problems with the talairach_avi processing on some young adult populations though. Nick On Mon, 2009-06-22 at 20:24 +0800, Zhen Zonglei wrote:

Re: R: Re: [Freesurfer] Qdec

Antonio, The Generate Stats Data Table feature was added in the v4.3.0 release of freesurfer. Its not necessary to perform an analysis, only to aid in the import of the morphometric measures from the recon-all stream (like hippocampal volume). You should be able to goto to the Design tab and con

RE: [Freesurfer] error message

Nick, There is no output, I typed that in and got nothing. [...@localhost freesurfer]$ env | grep PERL [...@localhost freesurfer]$ Fatima -Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: 22 June 2009 14:41 To: Ahmed, F, Me Cc: Sita Kakunoori; Freesurf

RE: [Freesurfer] error message

Fatima, Can you send me the output of this command: env | grep PERL Nick On Mon, 2009-06-22 at 09:56 +0200, Ahmed, F, Me wrote: > Nick, > > I tried running fixup_mni_paths and got the following output (see attached). > > Fatima > > > > > -Original Message- > From: freesurfer-b

[Freesurfer] How to rerun recon-all after modifying talairach registration manually?

Hi all: After autorecon1 was done, I corrected the talairach registration manually. Next, I rerun autorecon1 on the data, but tal_check still gave the same talAviQA and z-score as non-corrected. What's the problem? Is it necessary to rerun autorecon1? Can we skip autorecon1 and do autorecon2 dire

[Freesurfer] Problem "curvature file 'lh.area.mid' has wrong number"

Hi! I'm trying some first steps with freesurfer and got the error mris_calc: curvature file 'lh.area.mid' has wrong magic number after I started recon-all all for some nifti MPRage files. I'm running freesurfer on openSUSE 11.1. What does this error mean, what can be done?

RE: [Freesurfer] error message

Nick, I tried running fixup_mni_paths and got the following output (see attached). Fatima -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: 19 June 2009 23:24 To: Ahmed, F, Me Cc: Sita