Hi Freesurfers,

I’m trying to evaluate the usefulness of high resolution scans acquired at 7T with an isometric voxel size of .6mm for the measurement of cortical thickness. The inhomogeneities are taken care of by dividing the scans with another scan of another sequence, so they are not an issue anymore.

My problem is that Freesurfer usually conforms the voxel size to 1mm which is not desirable. I tried using the –cm and –noaseg flags for the recon-all process to avoid the conformation and to skip the subcortical segmentation, but another problem arises while using these flags.

The error I receive is occurring after the WM Segmentation and states as follows:

#--------------------------------------------

#...@# 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.

The dimensions of the data I’m trying to process is 320 x 320 x 224 and is changed to 320 x 320 x 320 while using the –cm flag. It seems the mri_segment process can’t handle any dimensions above 256 or I’m missing another flag.

Does someone has any ideas about that issue?

Regards,

Falk