Hello, I began to use mrtrix on my Mac and quite new to diffusion MRI, I got some dMRI data from dipy dataset from here http://nipy.org/dipy/examples_built/quick_start.html#example-quick-start the data have one image with .nii.gz format and also .bvalue, .bvector files And i tired my first command…

The main issue is hinted at here: [image] Junhao_Wen: [ERROR] Number of volumes in gradient table does not match input image dwipreproc needs to know what diffusion encoding was used to acquire the data, and this information can’t be included within the NIfTI images themselves. So you need t…

Thanks for the rapid answer, right now, i am quite clear. You are right, the dMRI data is download from dipy, and they dont give the info like PE direction, and really i dont know if i put 2 here is correct or not, that is why I suggest you put some tutorial data in the tutorial section, because if…

Tutorial data is a good suggestion, and has been proposed before. In fact, we have an open issue for it … We just haven’t had the time to do anything about it unfortunately. Hopefully we’ll get round to this eventually!

Yes, but you have done a good job already, thanks for your reply:) Good day

One final note: are you sure your PE direction should be 2? That corresponds to the z (inferior-superior) axis, which is quite unusual. It’s more common for it to be along y (anterior-posterior) axis, in which case you’d want a 1 here. I suspect users more frequently use the ‘LR’ / ‘RL’ / ‘AP’ / …

Dear All: I have some similar issue, but for my case I used a .mif file as an input, here is script: dwipreproc -rpe_none 2 ./Downloads/anger/anger_mrconverted.mif ./Downloads/anger/anger_out.mif and I got this error: dwipreproc: [ERROR] Number of volumes in gradient table does not match input i…

Hi, Donald, I try to use ACT followed the instruction of " http://community.mrtrix.org/t/beginner-connectome-pipeline-updated/373 "My commands are as follows: I run dwidenoise command: $ dwidenoise DTI/ DTI_denoise.mif I generate the DTI.mif file as well as DTI.bvecs and DTI.bvals files wit…

Yes, eddy can take a while, it’s quite an intense process. If you have a CUDA-capable graphics card (i.e. NVIDIA with up to date drivers), then you could try running with the -cuda option to run the much faster GPU-accelerated version. Otherwise you should expect relatively long run times. Also, yo…

Dear @SuperClear , for your information, my dwipreproc (which internally invokes eddy) without CUDA took about 4 hours to finish (it could also use openmp to speed up the process somewhat). The CUDA version on nVIDIA TESLA K20 card takes about 8 minutes. Antonin

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jdtournier February 28, 2017, 11:09am 8

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