[Freesurfer] Fwd: FW: XNAT update: Processing failed for PrenatalMA_13_MR_1

.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386 recon-all exited with ERRORS at Mon Apr 6 15:19:36 EDT 2009 How do we scale the nu.mgz images? Our 001.mgz are looking fine... thanks! -- Forwarded message -- From: Nurun

[Freesurfer] atlas use

Hi, if I want to use an alternative subcortical atlas (and I only have the equivalent of GCA_ALL but not GCA_SKULL), can I just add -gca GCA_ALL to the command line? Is there anything else I need to do? thanks, Nurunisa ___ Freesurfer mailing list Fr

[Freesurfer] Segmentation fault

Hi I am getting the following error while running auto-recon2. ... Reporting on 49 segmentations # [EMAIL PROTECTED] Cortical ribbon mask Tue Nov 11 01:32:03 EST 2008 /localA/nneyzi/MLS2/PedBirnPipeline_20081103_014127/mri mris_volmask --label_left_w

[Freesurfer] mri_ca_normalize

Hi, I am getting an error with the command: mri_ca_normalize -mask /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/brain.mgz -seg /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/cma_seg_noAA.mgz /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/nu.mgz -noatlas -noxform /Users/N

Re: [Freesurfer] volumes in wmparc.stats vs. aparc.stats

Hi, for subcortical segmentations, is it then better to use the volumes in wmparc.stats than those in aseg.stats? On Tue, Jul 22, 2008 at 2:54 PM, Doug Greve <[EMAIL PROTECTED]> wrote: > > Actually, the construction of aparc+aseg and wmparc do use info about where > the surface is to refine the

[Freesurfer] orientation

Hi, I have these analyze files with wrong orientation I can change their orientation using fslswapdim but when I convert them to mgz files using mri_convert, the orientation is wrong again. i tried the following reading from 001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, 0, -1) j

[Freesurfer] mri_convert: IMA

Hi, I am getting an error message while trying to convert the SIEMENS IMA to MGZ: siemensRead(): file rows (30067) not divisible by image rows (18771) It looks like i managed to do a similar conversion before, so I wonder if there is something I need to add to the command line for this special ca

[Freesurfer] ICV / brain volumes

Hi. does it matter whether I use the total brain volumes or the ICVs from the aseg. stats in order to normalize individual brain structure volumes? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

[Freesurfer] WM vol

Hi, when I use mri_anatomical stats - I get a total WM value 503450 for left and right hemispheres that's the same number in the stats file in the stats folder. but when I use mris_wm_volume - I get 174896 and 178464 which one is the accurate one? also, is the GM volume I get from mris_anatomica

[Freesurfer] (no subject)

Hi, I am trying to color code my labels according to the stats associated with each label. I was playing with the colortable but that did not work. I will appreciate any guidance/ help on that. How can I give to a given label the color I want to? thanks, Nurunisa __

[Freesurfer] Re: labels in matlab

) = ct.table(5, j). On 2/9/07, Nurunisa Neyzi <[EMAIL PROTECTED]> wrote: Hi, just a quick question, I am reading my annotation files into matlab following: [v, L, ct] = read_annotation(annotation_filename); Suppose N is the number of vertices. Then, (1) v = N x 1 vector, v(i) = i-1 (y

[Freesurfer] labels in matlab

Hi, just a quick question, I am reading my annotation files into matlab following: [v, L, ct] = read_annotation(annotation_filename); Suppose N is the number of vertices. Then, (1) v = N x 1 vector, v(i) = i-1 (you can usually ignore v) (2) L = N x 1 vector, L(i) = label of ith vertex of mesh

[Freesurfer] glibc detected

Hi, when I try to redo the parcellation with another gcs file, and type the command: mris_ca_label 2560_4 lh lh.sphere.reg gcs_jan07/lh.outputclassifier.gcs lh.renewparc.annot I get the following error/log: $Id: mris_ca_label.c,v 1.16 2006/02/14 20:25:59 nicks Exp $ $Id: mrisurf.c,v 1.441 200

[Freesurfer] retinotopy

Hi, during retinotopic mapping, still at the beginning, when I run the analysis (with the command sfa-sess), I get the error: ERROR: meanimg for mean image failed meanimg -i rtopy/eccen/h-offset -i rtopy/polar/h-offset -o rtopy/h-offset and I have h.bdhr and omnibus in my eccen and polar folder

[Freesurfer] Re: freesurfer

Hello, I have whole brain T1 maps and the pseudo T1-weighted images that I created out of them (so they are perfectly aligned). The are all brain extracted using fsl and I am doing my own tissue segmentation (again, using fsl), but in both steps there is much optimization involved, because I wan