Sometimes, depending on the manufacturer and software version of the scanner, dcm2nii will include an "isotropic diffusion" volume at the end which is the average of the diffusion weighted volumes. Check your images, b values, and most importantly, directions, to see if you have a volume with a nonzero b value but a 0 direction. You can excise it with fslsplit, fslmerge, and/or fslroi.
Rob
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Robert I. Reid, Ph.D. | Sr. Analyst/Programmer, Information Technology
Aging and Dementia Imaging Research | Opus Center for Advanced Imaging Research
Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Howayda Mrad
> Sent: Wednesday, October 01, 2014 6:23 AM
> To: [log in to unmask]
> Subject: [FSL] DTI FA analysis
>
> I'm learning how to analyze DTI data with FSL(FDT), and I'm wondering if any
> one can make comments about my procedures described below.
>
> My DTI data were acquired with a Simens Trio 3T scanner. 32 directions.
> b=800
>
> I Used dcm2niigui to convert the DICOM data of one patient into NIFTI
> format for DTI. The conversion created 1. one image file with b0 + 32 image
> files with b800.
> 2. one image file with b0 + 33 image files with b800.
> why i don't obtain the b0 file as single image alone , and since we are using 32
> direction why by converting we obtain 33 and 34 ??
>
> How to proceed .. any suggestion ??
>
> Thanks
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