Hi Nick,
yes I have been trying to use the -noaseg flag, but as recon-all did exit with an error I thought this process might be needed, so I haven't tried anything else.
The error message I received was:
#-------------------------------------------- #@# WM Segmentation Wed Mar 18 10:14:42 CET 2009
cp wm.mgz wm.seg.mgz
mri_segment -keep brain.mgz wm.seg.mgz
preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 106.9 +- 5.8 [80.0 --> 125.0] GM (69.0) : 66.3 +- 11.6 [30.0 --> 96.0] setting bottom of white matter range to 77.9 setting top of gray matter range to 89.4 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... thickening thin strands.... 20 segments, 4813 filled 10270 bright non-wm voxels segmented. 5589 diagonally connected voxels added... white matter segmentation took 2.4 minutes writing output to wm.seg.mgz... ERROR: mri_segment-MRIcheckVolDims: volume1 height=256 != volume2 height=320.
Regards, Falk
-------- Original-Nachricht --------
Datum: Sat, 21 Mar 2009 10:08:24 +0100 Von: "Falk Lüsebrink" falk.luese@gmx.net An: falk.luese@gmx.net Betreff: RE: [Freesurfer] Voxel size smaller than 1x1x1mm?
Falk,
Probably you should try adding the -noaseg flag to recon-all, as the aseg step relies on having 'conformed' volume data to register to the atlas. The -noaseg flag skips creation and usage of the subcortical atlas.
Nick
On Wed, 2009-03-11 at 13:16 +0100, Falk Lüsebrink wrote:
Hi again,
so I did use the -cm flag to conform the voxels to its minimum size of
.8mm
iso (which is also the native size of my data set) during the
mri_convert
process and used the -noconform flag for the mri_normalize stage during autorecon1 to prevent further conformation to 1mm.
But now recon-all exits with an error at stage 12 (http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all). The error message
I
got is as follows: #-------------------------------------------- #...@# Intensity Normalization2 Wed Mar 11 08:38:44 CET 2009 /home/falk/freesurfer/subjects/claus/mri
mri_normalize -f home/falk/freesurfer/subjects/claus/tmp/control.dat -noconform -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using control points from file /home/falk/freesurfer/subjects/claus/tmp/control.dat... not interpolating and embedding volume to be 256^3... using segmentation for initial intensity normalization reading from norm.mgz... mri_normalize: aseg volume aseg.mgz must be conformed using MR volume brainmask.mgz to mask input volume... Linux xxxxxx 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 x86_64 GNU/Linux
recon-all exited with ERRORS at Wed Mar 11 08:38:55 CET 2009
Does anyone know what to do?
Regards, Falk
-----Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, March 06, 2009 1:26 PM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Voxel size smaller than 1x1x1mm?
Hi Falk,
yes, you can use the "conform to min" (-cm I think) switch in recon-all. Can you cover the whole brain at .7mm iso? That's hard. And 7T is hard for whole brain morphometry because of dielectric effects. Good luck.
Bruce On Fri, 6 Mar 2009, Falk Lüsebrink wrote:
Hi Freesurfers,
I'm currently doing my bachelors thesis in medical engineering and I'm trying to measure the cortical thickness of scans acquired by a 7T
MRT.
A colleague of mine has used Freesurfer (v4.0.5) before and mentioned
that
high resolution scans with a voxel size smaller than 1x1x1mm (like .7x.7x.7mm) are converted to 1x1x1mm during a processing stage of
autorecon
- I think during the mri_convert process.
Is it possible to keep the native size or does Freesurfer need to
change
the
voxel size to 1mm in order to do the segmentation correctly?
Regards, Falk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger01
freesurfer@nmr.mgh.harvard.edu
-
"Falk Lüsebrink"