> Dear David,
Hi Mr. Jesper,
> if you take a look at https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/Faq you should be able to figure out what your acqparams.txt and your index.txt should look like.
There's a lot of information about this file. I understand. Because exists a lot of possibilities for all those parameters. But on my case, I really not using different phase encodings. Images are acquired with 1.5 Tesla GE Scanner. I will send informations obtained when DICOM to Nifiti conversion are made, could you help me to find how these informations are correlated with I need to put in --acqp file:
Series UID : 1.2.840.113619.2.336.6945.4265474.16724.1381140642.151
Study date : 07/10/2013
Study time : 181533
Series date : 07/10/2013
Series time : 183053
Subject : XXXX^XXXX X
Subject birth date : DD/MM/YYYY
Series description : Ax DTI
Image type : ORIGINAL\PRIMARY\OTHER
Manufacturer : GE MEDICAL SYSTEMS
Model name : DISCOVERY MR750
Software version 24\LX\MR Software release : 23\LX\MR Software releaseDV23.1_V02_1317.c
Study id : 3711
Series number : 5
Repetition time (ms) : 9500
Echo time[1] (ms) : 82,2
Inversion time (ms) :
Flip angle : 90
Number of averages : 1
Slice thickness (mm) : 2,9
Slice spacing (mm) : 2,9
Image columns : 256
Image rows : 256
Phase encoding direction : COL
Voxel size x (mm) : 0,9375
Voxel size y (mm) : 0,9375
Number of volumes : 35
Number of slices : 65
Number of files : 2275
Number of frames : 0
Slice duration (ms) : 0
Volume interval (s) : 0
Orientation : tra
on this case with 35 volumes (first 3 volumes are b0's but with bvectors [0 0 0] (same encoding directions) and bvals 0) and just one phase encoding direction for all, I will need a --index file with 35 number 1's?, like:
1 1 1 1 1 1 1 1 1 .... (35 times)?
> I am afraid I don’t see anything there that looks like a fieldmap. In order to get a fieldmap you need to explicitly run a fieldmap sequence as part of your experiment.
Could create this artificially?
> I see. The first dtifit is run _only_ to make sure that the bvecs are in the correct format for FSL. You only use it to visualise the V1 file in fslview and ensure that the lines line up between voxels. Once you have done that you can throw away the output from the first run of dtifit and proceed as if you had never run it.
Nice! Its like more a Quality control step. Cool.
Thank you very much
Best Wishes
David
> Jesper
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