From: zorze...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject:
Date: Thu, 6 Aug 2015 07:42:40 +0200
Hi,
The recon pipeline outputed an apparently correct file, which happen to confuse
freesurfer reading functions.
I attached a slightly-altered file named lh.data_crash which have the same
problem. The other file named lh.data_nocrash seems to be parsed fine, despite
differing by only 1 float-value somewhere in the middle of the data section.
Original file was lh.area
The mri_info command outputs some meaningless values; and the mris_calc command
bails out.
$ mri_info lh.data_crash
WARNING: # of slices=-45 in header - assuming 124...
Volume information for lh.data_crash
type: unknown
dimensions: 3391 x 2677 x 124
voxel sizes: -0.0000, -0.0000, -0.0000
type: SHORT (4)
fov: 0.246
dof: 0
xstart: 548.5, xend: 5149214485235471024091229374082187264.0
ystart: -0.0, yend: -0.0
zstart: -1008284058362807724504196555655348224.0, zend: 0.0
...
$ mri_info lh.data_nocrash
Volume information for lh.data_nocrash
type: curv
dimensions: 124254 x 1 x 1
voxel sizes: 1.0000, 1.0000, 1.0000
type: FLOAT (3)
fov: 124254.000
dof: 0
xstart: -62127.0, xend: 62127.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.0
...
The difference between the two files are a single value change (4 bytes) at
offset 1095 (15+4*1095'th byte), although other alteration are possible which
avoid the crash too.
This happens on Freesurfer version 5.3.0, and also 5.1.0, and 6-beta,
on all arch i could test, which are RedHat 6.6 (64bits), Ubuntu 10.x (32bits),
and MacOSX 10.8 (64bits)
Note: to preserve privacy, the original map values have been replaced by a
dummy 42.0 for most of the file, since i believe actual data is irrelevant here.
I couldn't track the problem further, as i only have (stripped) binaries here.
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