also - <div><br></div><div>I&#39;m assisting someone with a dti analysis.</div><div>the data I have is a martinos centre .hdr .bshort file, acquired at martinos I think, in 2005.</div><div>I&#39;m having trouble figuring out how to covert this (mainly for use with FSL)</div>
<div>I&#39;d like a 4d nifti ultimately (or analyse).</div><div><br></div><div>I was thinking of writing code (probably matlab) to read in the data with fread, reslice the matrix, write to nifti.</div><div><br></div><div>
I&#39;m no expert in nifti headers, certainly not the format below.</div><div><br></div><div>by bshort we mean 2 bytes unsigned integer?</div><div><br></div><div>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?</div>
<div><br></div><div>the header (people&#39;s names blanked out, just to be on safe side) of the bshort is below</div><div><br></div><div>mainly we simply want </div><div><br></div><div>line1: 256 128 2816 1</div><div><br>
</div><div>to become </div><div><br></div><div>line1: 256 128 128 22</div><div><br></div><div>right?</div><div><br></div><div>just getting the data into 3d nifti is fine. 4d a bonus.</div><div><br></div><div>obviously the dwi scan parameters need not be in the nifti header, included for completeness</div>
<div><br></div><div>also: to my unexpert eye this looks like a single shot sequence probably, would that be right?</div><div><br></div><div>help appreciated</div><div><br></div><div>Colin</div><div><br></div><div>---</div>
<div><br></div><div><div>256 128 2816 1</div><div>MonkBrain_425mic3Ddti</div><div>fovx=57.599998 fovy=115.199997 fovz=57.599998</div><div>name=xxxxxx</div><div>id=xxxxx</div><div>dob=</div><div>sex=female</div><div>study name: 34667 macaque brain</div>
<div>purpose: xxxxx</div><div><br></div><div>Institution=MGH Biospec 47/40</div><div>date=21:17:49_10_Sep_2005</div><div>Operator=******</div><div>Software=PV 3.0.1</div><div>Protocol/descr=A*******C/MonkBrain_425mic3Ddti</div>
<div>pulse prog=gdDiffSE.ppg</div><div>SW=29761.9048 Hz</div><div>acq_rare_factor=1 acq_inter_echo_time=28.000 acq_echo_time=28.000 acq_repetition_time=250</div><div>Method is PVM</div><div>exam=33 series=5</div><div>slices=1 coronal, readout=H_F, thickness=57.60 mm separation=57.60 mm offset=0.00 mm</div>
<div>TE=28.00 TR=250.00 TI=0.00</div><div>NEX=1, acq time 25h1m52s0ms</div><div>ExcPulse 1.580ms, 3417.7Hz, flip=90.0, 18.4dB, &lt;hermite.exc&gt;</div><div>RefPulse 1.001ms, 3416.6Hz, flip=180.0, 8.4dB, &lt;hermite.rfc&gt;</div>
<div>$GDDIFF_BigDelta=10.400000$GDDIFF_BigDelta=10.400000 $GDDIFF_LittleDelta=6.925000</div><div>$GDDIFF_DiffGrad=0.000 0.000 379.787 379.836 379.879 379.690 379.868 379.823 379.730 379.688 </div><div>379.729 </div><div>379.716 379.732 379.905 379.867 379.667 379.702 379.809 380.000 379.984 </div>
<div>379.734 </div><div>379.868</div><div>$GDDIFF_DiffGradB=0.000 0.000 4004.836 4005.877 4006.782 4002.793 4006.554 4005.596 4003.634 </div><div>4002.761 </div><div>4003.606 4003.338 4003.686 4007.327 4006.534 4002.317 4003.058 4005.309 </div>
<div>4009.333 </div><div>4009.005 4003.722 4006.558</div><div>$GDDIFF_PathName=/home/a********c</div><div>$GDDIFF_DiffGradFileName=Jones20B.txt</div><div>$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 </div>
<div>-0.062 </div><div>-0.263 -0.413 -0.588 -0.505 -0.773 0.713 0.259 -0.549 -0.396</div><div>$GDDIFF_DiffGradPhase=0.000 0.000 0.000 0.922 0.593 -0.502 -0.355 -0.281 -0.313 0.939 0.266 -0.885 </div><div>-0.795 </div><div>
-0.382 -0.611 0.762 0.084 -0.594 -0.177 -0.094 -0.686 0.618</div><div>$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 </div><div>-0.568 </div><div>-0.862 0.644 -0.173 -0.834 0.085 -0.647 -0.940 -0.431 -0.648</div>
<div>ImageType=MAGNITUDE_IMAGE</div></div><div><br></div>