NITRC Functional Analysis of Diffusion Tensor Forum: help

FSL multishell DTIFIT and preprocessing topup

bionerd — Tue, 01 Mar 2022 21:12:03 GMT

Hi,

I have 3 questions and was wondering if anybody could help me out please:
1) I have multi-shell DTI data and I had read that FSL's DTIFIT tool isn't ideal for processing this kind of data that has multiple b-values (please see attached image and site: https://fsl.fmrib.ox.ac.uk/fslcourse/201... for source info). However, when I ran it on my data, it somehow did produce FA maps, etc. All I need to know is whether anybody has a good detailed understanding about the background process that FSL performs in order to generate these results and how it exactly did that for my data???
2) Secondly, with respect to the same data, when I tried performing topup on it, it gave me the error: 'Topup: msg=topup_clp::topup_clp: Mismatch between b0_all and acqparams.txt' and I checked my acquisition paramters for the original dti nifti and it said that the phase enconding direction was: j- which I assume means it is A>>P encoded, correct?? The total readout time was 0.038625 so my acqparams looks like this: 0 -1 0.038625
3) Point-2 brings me to my third question: for topup, we merge A>>P (b0 image) and P>>A; how does one get the P>>A image? Is it supposed to be in the raw data I received from the scanner itself or is it something one generates (if so, how)?
I also came across a prebaked topup tool but am confused as to whether this is a file that needs to be downloaded first.
Any and all help would be highly appreciated.
Thank you for your time.
Attachment: Screen Shot 2022-02-24 at 1.05.43 PM.png

RE: Diffusion data & FADTTS

Linglong Kong — Mon, 14 Dec 2015 9:07:52 GMT

k is the number of linear constraints in the test
m is the number of measures.

RE: Diffusion data & FADTTS

Myriam Oliver — Thu, 19 Nov 2015 19:05:50 GMT

Thank you very much for your response!

I have another question.

At the Cdesign and BO, what "k" stands for?
Cdesign = k x mp
B0 = k x Lo

Sorry I could not find this information.
Is k refering to the number of diffusion properties? so in the example will bE 2 (refering to FA & MD?)

Thank you!!

RE: Diffusion data & FADTTS

Chao Huang — Thu, 05 Nov 2015 3:11:45 GMT

Hi Myriam,

Thank you very much for using FADTTS. For your data set, you have 4815 tracts for each subject. If the order of the tracts is consistent across all subjects. You can reform you data structure. For example, if you have 100 subjects, you can form a matrix 1335 x 100 for each tract, then repeatedly apply FADTTS on each tract. Finally, you can get the global p value for each tract.

Please let me know if you have any other questions.

Best,
Chao

Diffusion data & FADTTS

Myriam Oliver — Fri, 30 Oct 2015 18:31:09 GMT

Dear FADTTS users,

I am trying to use FADTTS with my data from DSIstudio, however I am having a problem with my diffusion data.

If I am correct I need a diffusion data matrix which will contain 1 value per subject/per tract. So, for instance a [75 x 64], 75tracts x 64subjects.

However, in my data, I do not have 1 value/per subject. I have different values for each "point" in the tract, and of course, different tracts.
So, I have a matrix for each subject of [4815 x 1335], which means, 4815 tracts and 1335 "points" along the tract. And these for every subject.

So, I am not sure how can I fit these into the diffusionfile that I need to enter to FADTTS. I was thinking to do one file for each point, but that will means I need 1335 files (one file/per "point" along the tract). Is there any better way?

Thank you for your time,
Myriam Oliver

RE: use FADTTS in win7

hongtu zhu — Thu, 11 Sep 2014 3:11:49 GMT

It does not matter. Our code should work in multiple platforms.

use FADTTS in win7

tingting feng — Wed, 13 Aug 2014 8:25:26 GMT

hi,
I read the paper "Local polynomial regression for symmetric positive definite matrices" and want to run the code in win7 .I downloaded the code from http://www.nitrc.org/projects/fadtts/ . But the instructions in "ReadMe.txt" only focus on linux . I wonder whether this code can be run in win7, is there any other detailed instructions for win7?I want to reuse the code ,not just run the code . Any help would be appreciated. Thank you!
Best regards!

Tina

Welcome to Help

Christian Haselgrove — Mon, 24 Jan 2011 14:49:13 GMT

Welcome to Help