Re: [Freesurfer] -normalization error

Hi Jeff, I've seen this happen before with the N3 stuff where it reduces the image intensities so much that you start losing dynamic range. Not sure what causes it, but you could cp orig.mgz to nu.mgz and run from there forward. cheers, Bruce On Wed, 24 Sep 2008, Jeff Sadino wrote: Hello

[Freesurfer] -normalization error

Hello all, I am receiving an error when trying to run autorecon1. When trying to step through it manually step-by-step, everything is fine up to -nuintensitycor. After running that command and looking at nu.mgz in tkmedit, the picture starts to fade out pretty bad above 120 intensity. When

[Freesurfer] LGI error in make_outer_surface at 31

Looks like my image processing toolbox from matlab was not properly installed. Now that I have re-installed the image processing toolbox, LGI appears to be working fine. Cheers, Jenifer ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ___ Freesurfer mailing list Fre

Re: [Freesurfer] Warning in recon-all -long

Juergen, I'm pretty sure that message can be ignored. I see it myself in our own -long runs, and I think it results from initializing the tp2 surface with the tp1 surface (which then gets deformed into tp2's volume). Nick On Wed, 2008-09-24 at 16:18 +0200, Juergen Haenggi wrote: > Dear FS expe

Re: [Freesurfer] LGI error in make_outer_surface at 31

Hi Jenifer, I don't know what the error exactly means, but sometimes just re-running the analysis helps. Best, Martin On Wednesday 24 September 2008 19:24:40 Juranek, Jenifer wrote: > Hi, > Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB > v7.6.0.324 (R2008a) install

[Freesurfer] Default LGI settings

Hi, I wonder how are the default FS settings to calculate LGI finetuned? More towards large-scale changes, such as in neonal>pediatric cortex, or would it be possible to study rather focal changes, say on a sulcus/gyrus level? Which parameters should I change to become sensitive to "smaller" LG

[Freesurfer] Cortical thickness differences

Hi, I have a question regarding cortical thickness differences in 2 subject populations. I want to compare the total cerebral and gyral thickness difference in the patient and control groups. Here is what I did for each subject mris_anatomical_stats -t thickness lh > lh_hemistats.txt So, I now

[Freesurfer] Fixing WM intensity normalization via control points

Hello, I have some basic questions with regards to adding control points to fix the WM intensity normalization. I am running some subjects through autorecon 1 and 2 only (we are not concerned with subcortical structures). The reconstructed volumes had a lot of missing grey matter in the lateral

[Freesurfer] LGI error in make_outer_surface at 31

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined fun

[Freesurfer] Warning in recon-all -long

Dear FS experts I run recon-all -long and the following warnings occurred in Smooth2 and Inflation2: WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. Can I ignore this warning? Thanks in advance Regards Juergen

Re: [Freesurfer] error: mris compute white volume

Nick, I am tryng to get the updated executables for mri_segstats and mris_wm_volume that are described in your mail message: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08009.html Christian, Updated mri_segstats and mris_wm_v

Re: [Freesurfer] Count non-zero voxels without matlab

Hi Jeff, we're actively working on the issue of stability of these measures. We have used the non-zero brain voxels, but that's really not ICV, it's more total brain volume. You really can't see the sulcal CSF on a T1, so it will frequently get stripped. If you have global atrophy using this m