Dear Mahshid,
Thanks, you are right. But it seems that the .json of my data does not contain the information I need!
which vendor’s scanner are you using?
Jesper
From: "Glasser, Matthew" <[log in to unmask]<mailto:[log in to unmask]>>
To: [log in to unmask]<mailto:[log in to unmask]>
Date: Mon, 31 Dec 2018 19:37:27 +0000
Subject: Re: [FSL] How to create slspec.txt file for eddy correction
That json lists the NIFTI files provided, not the acquisition parameters of a given diffusion dataset.
Matt.
From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Mahshid Fouladivanda <[log in to unmask]<mailto:[log in to unmask]>>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>>
Date: Monday, December 31, 2018 at 1:34 PM
To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>>
Subject: Re: [FSL] How to create slspec.txt file for eddy correction
Hi Mahmoud,
Thanks for your help. I am using WU-Minn HCP Lifespan Pilot Data<https://db.humanconnectome.org/data/projects/WU_L1A_Cur>, it is accessable from ttps://db.humanconnectome.org/app/template/Login.vm;jsessionid=257EDCA0E14F7FB84BF4A63D79636744<https://db.humanconnectome.org/app/template/Login.vm;jsessionid=257EDCA0E14F7FB84BF4A63D79636744>. The data is in nifti format with .json file (attached in this email). But as I have tried to use it in your mfile, it had not the desired information. So that an error occurred, seen bellow:
Error using textscan
First input can not be empty. Expected a non-empty string or a valid file-id.
Error in slspec_mz (line 12)
slicetimes = textscan(cslicetimes,'%f','Delimiter',',');
Error in demo (line 2)
slspec_mz('LS4036_3T_Diffusion_unproc.json')
Regards,
Mahshid
From: Mahmoud <[log in to unmask]<mailto:[log in to unmask]>>
To: [log in to unmask]<mailto:[log in to unmask]>
Date: Mon, 31 Dec 2018 09:44:32 -0500
Subject: Re: [FSL] How to create slspec.txt file for eddy correction
Hi Mahshid,
If the MB factor information is saved in the header file of your dicom images, then using the newer version of dcm2niix you will have a json file that stores some of the header information.
You may feed that json file to the attached m-file (that I got from the FSL forum or wiki) and it creates a slspec.txt for you that you may use it for eddy.
Hope this helps.
Mahmoud
On Mon, Dec 31, 2018 at 4:06 AM Mahshid Fouladivanda <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear Experts,
I want to apply eddy correction including Correcting slice-to-volume movement on dMRI data. So I need to create slspec.txt file, in order to use the command:
eddy --imain=data --mask=my_hifi_b0_brain_mask --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --topup=my_topup_results --niter=8 --fwhm=10,8,4,2,0,0,0,0 --repol --out=eddy_corrected_data --mporder=6 --slspec=my_slspec.txt --s2v_niter=5 --s2v_lambda=1 --s2v_interp=trilinear
But I don know how I can calculate the multiband (MB) factor? and what is the number of slices? is it (MB factor) the value of the z dimension of the images???
Regards,
Mahshid
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