Hi Colin
have you tried mri_convert? We did support bshort as a format (such as it
is!), although it hasn't gotten much use for years. Try something like:
mri_convert file.bshort file.nii
cheers
Bruce
On Sun, 5 Aug 2012,
Colin Reveley wrote:
also -
I'm assisting someone with a dti analysis.
the data I have is a martinos centre .hdr .bshort file, acquired at martinos
I think, in 2005.
I'm having trouble figuring out how to covert this (mainly for use with FSL)
I'd like a 4d nifti ultimately (or analyse).
I was thinking of writing code (probably matlab) to read in the data with
fread, reslice the matrix, write to nifti.
I'm no expert in nifti headers, certainly not the format below.
by bshort we mean 2 bytes unsigned integer?
could I even use mri_convert to make a 4d nifti from the bshort? or else a
3d nifti I can load simply into matlab and re-arrange?
the header (people's names blanked out, just to be on safe side) of the
bshort is below
mainly we simply want
line1: 256 128 2816 1
to become
line1: 256 128 128 22
right?
just getting the data into 3d nifti is fine. 4d a bonus.
obviously the dwi scan parameters need not be in the nifti header, included
for completeness
also: to my unexpert eye this looks like a single shot sequence probably,
would that be right?
help appreciated
Colin
---
256 128 2816 1
MonkBrain_425mic3Ddti
fovx=57.599998 fovy=115.199997 fovz=57.599998
name=xxxxxx
id=xxxxx
dob=
sex=female
study name: 34667 macaque brain
purpose: xxxxx
Institution=MGH Biospec 47/40
date=21:17:49_10_Sep_2005
Operator=******
Software=PV 3.0.1
Protocol/descr=A*******C/MonkBrain_425mic3Ddti
pulse prog=gdDiffSE.ppg
SW=29761.9048 Hz
acq_rare_factor=1 acq_inter_echo_time=28.000 acq_echo_time=28.000
acq_repetition_time=250
Method is PVM
exam=33 series=5
slices=1 coronal, readout=H_F, thickness=57.60 mm separation=57.60 mm
offset=0.00 mm
TE=28.00 TR=250.00 TI=0.00
NEX=1, acq time 25h1m52s0ms
ExcPulse 1.580ms, 3417.7Hz, flip=90.0, 18.4dB, <hermite.exc>
RefPulse 1.001ms, 3416.6Hz, flip=180.0, 8.4dB, <hermite.rfc>
$GDDIFF_BigDelta=10.400000$GDDIFF_BigDelta=10.400000
$GDDIFF_LittleDelta=6.925000
$GDDIFF_DiffGrad=0.000 0.000 379.787 379.836 379.879 379.690 379.868 379.823
379.730 379.688
379.729
379.716 379.732 379.905 379.867 379.667 379.702 379.809 380.000 379.984
379.734
379.868
$GDDIFF_DiffGradB=0.000 0.000 4004.836 4005.877 4006.782 4002.793 4006.554
4005.596 4003.634
4002.761
4003.606 4003.338 4003.686 4007.327 4006.534 4002.317 4003.058 4005.309
4009.333
4009.005 4003.722 4006.558
$GDDIFF_PathName=/home/a********c
$GDDIFF_DiffGradFileName=Jones20B.txt
$GDDIFF_DiffGradRead=0.000 0.000 0.979 0.329 -0.396 0.807 0.006 -0.794 0.834
-0.235 0.817 0.009
-0.062
-0.263 -0.413 -0.588 -0.505 -0.773 0.713 0.259 -0.549 -0.396
$GDDIFF_DiffGradPhase=0.000 0.000 0.000 0.922 0.593 -0.502 -0.355 -0.281
-0.313 0.939 0.266 -0.885
-0.795
-0.382 -0.611 0.762 0.084 -0.594 -0.177 -0.094 -0.686 0.618
$GDDIFF_DiffGradSlice=0.000 0.000 0.000 0.000 0.670 -0.231 0.912 0.499 0.405
0.146 0.468 0.418
-0.568
-0.862 0.644 -0.173 -0.834 0.085 -0.647 -0.940 -0.431 -0.648
ImageType=MAGNITUDE_IMAGE
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