open-discussion > error with brain extraction tool
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Mar 22, 2016  11:03 AM | Michael Jutras
error with brain extraction tool
I'm using BioImage Suite 3.01 in 32-bit Windows 7, VTK 5.2.0.

When attempting to run the brain extraction tool, popup windows display the messages "Failed to load image C:/BIS/IM_0001_stripped_overlay.hdr", then "No Brain Extraction Results in Memory; Cannot perform Create Mask from BET Output!".

The log displays the following:

-------------------------------------------------------
-d nhdr post-swap: nifti_1_header :
sizeof_hdr = 348
data_type[10] = 0x 0 0 0 0 0 0 0 0 0 0
db_name[18] = 0x 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
extents = 0
session_error = 0
regular = 0x0
dim_info = 0x0
dim[8] = 3 245 134 242 1 0 0 0
intent_p1 = 0.000000
intent_p2 = 0.000000
intent_p3 = 0.000000
intent_code = 0
datatype = 16
bitpix = 32
slice_start = 0
pixdim[8] = 1.000000 0.800000 0.800000 0.800000
1.000000 1.000000 1.000000 1.000000
vox_offset = 0.000000
scl_slope = 1.000000
scl_inter = 0.000000
slice_end = 0
slice_code = 0
xyzt_units = 0x2
cal_max = 255.000000
cal_min = 0.000000
slice_duration = 1.000000
toffset = 0.000000
glmax = 255
glmin = 0
descrip = 'created by vtkbisImageHeader'
aux_file = 'none'
qform_code = 0
sform_code = 1
quatern_b = 0.000000
quatern_c = 0.000000
quatern_d = 1.000000
qoffset_x = 0.000000
qoffset_y = 0.000000
qoffset_z = 0.000000
srow_x[4] = -0.800000, 0.000000, 0.000000, 0.000000
srow_y[4] = 0.000000, -0.800000, 0.000000, 0.000000
srow_z[4] = 0.000000, 0.000000, 0.800000, 0.000000
intent_name = ''
magic = 'ni1'
-------------------------------------------------------
-d nifti_read_header: found header filename 'C:/BIS/IM_0001.hdr'
dt=16
Bad Data Type=16


Thanks,
Michael
Mar 22, 2016  11:03 AM | Larry Olson - Emory University
error with brain extraction tool
Have you ever considered BrainSuite for brain extraction?
http://forums.brainsuite.org/download/
I find it is very easy and flexible, and use it preferably. (Just use Menu:
Cortex->Skull Stripping (BSE)
You can also create a mask easily with Menu: Tools->Mask Tool

I usually do not find the other BrainSuite features as useful, but they are
interesting.
Mar 22, 2016  12:03 PM | Xenophon Papademetris
error with brain extraction tool
On Windows especially this might be a good idea. BioImage Suite just calls FSL here which does not really exist in a native form on Windows any more.