Re: [mitk-users] MITK-DI -> import of FSL preprocessed DTI data

Christina Rossmanith Wed, 20 Nov 2013 07:06:24 -0800

Hi Jan,

still no success loading diffusion data. That is what I did so far:

1) MRIconvert to get b0 and b1000 images from Siemens mosaic files

2) gzip *.nii

3) fslmerge -a data.nii.gz *gz

4) a) rename data.nii.gz into data.fslgz

b) rename *bvecs into data.fslgz.bvecs

c) rename *bvals into data.fslgz.bvals

5) start mitk-di and open data.fslgz

6) NiftiImageIO is complaining that temp_dwi.nii.gz is not recognized as a NIFTI file

I guess data.fslgz is renamed to temp_dwi.nii.gz in order to enable NiftiImageIO to read the file. Is there a way to keep temp_dwi.nii.gz to have a closer look at it?

More hints?

Christina

Gesendet: Mittwoch, 20. November 2013 um 15:05 Uhr
Von: "Hering, Jan" <[email protected]>
An: "[email protected]" <[email protected]>
Cc: "Christina Rossmanith" <[email protected]>
Betreff: RE: [mitk-users] MITK-DI -> import of FSL preprocessed DTI data

Dear Christina,

the head-motion and eddy-current correction is provided by the DWI Registration plugin in the latest MITK Diffusion release: Version 2013.09.04

For the import of data in fsl format, the data has to be named as follows :

data.fslgz

data.fslgz.bvecs

data.fslgz.bvals

In this way loading the data.fslgz into MITK will result into a DW image which can then be used for the processing, i.e. starting with the correction. If you have the b0 and b1000 data separately, the fslmerge is a perfect tool for the merge.

Best,

Jan

From: Christina Rossmanith [mailto:[email protected]]
Sent: Donnerstag, 14. November 2013 15:20
To: [email protected]
Subject: [mitk-users] MITK-DI -> import of FSL preprocessed DTI data

Hi,

I'd like to use the fsl import. Which preprocessing is expected to be done with fsl and what will be done within MITK-DI? Just fslmerge all b0 and b1000 volumes into a single data.fslgz? What about eddy current correction? Should bvecs and bvals be renamed to data.{bvecs|bvals}.fsl (because they are plain ASCII files)?

Any hint is welcome,

Christina Roßmanith

Dept. of Neurology

University Hospital Mannheim

------------------------------------------------------------------------------
Shape the Mobile Experience: Free Subscription
Software experts and developers: Be at the forefront of tech innovation.
Intel(R) Software Adrenaline delivers strategic insight and game-changing 
conversations that shape the rapidly evolving mobile landscape. Sign up now. 
http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk

_______________________________________________
mitk-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/mitk-users

Re: [mitk-users] MITK-DI -> import of FSL preprocessed DTI data

Reply via email to