Hi!

how can I view a .mgz file? How do I fix a skull stripping error?

________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, June 19, 2013 3:33 PM To: Sudhin A. Shah Subject: RE: [Freesurfer] recon-all error MRIthickenThinWMStrands

Hi Sudhin

did you look at the brain.mgz? Much of the brain is stripped so there is a skull stripping error you need to fix.

Bruce

On Wed, 19 Jun 2013, Sudhin A. Shah wrote:

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From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, June 19, 2013 2:58 PM To: Sudhin A. Shah Subject: RE: [Freesurfer] recon-all error MRIthickenThinWMStrands

can you send me the brain.mgz?

On Wed, 19 Jun 2013, Sudhin A. Shah wrote:

...

Hi, Here it is

#@# WM Segmentation Fri Jun 14 16:06:46 EDT 2013

mri_segment brain.mgz wm.seg.mgz

doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (109.0): 110.8 +- 7.7 [80.0 --> 125.0] GM (67.0) : 64.9 +- 12.1 [30.0 --> 96.0] setting bottom of white matter range to 77.0 setting top of gray matter range to 89.1 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... 22510 sparsely connected voxels removed... thickening thin strands.... ERROR: MRIthickenThinWMStrands: invalid x,y,z!

Numerical result out of range

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From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, June 19, 2013 1:42 PM To: Sudhin A. Shah Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error MRIthickenThinWMStrands

nope, never seen that error. Probably from mri_segment. If you send me the input volume I'll take a look (check the recon-all.log and see what command was running when that happened). Also, definitely check it before sending to make sure it's reasonable

On Wed, 19 Jun 2013, Sudhin A. Shah wrote:

...

Hi

ERROR: MRIthickenThinWMStrands: invalid x,y,z!

Numerical result out of range

Any tips? S

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