Could you give me something about the transpsition here? I checked the code flip4fsl and found there are two kinds of sign. line 59. set sign = `echo $inorient | sed "s/[LAS]/+\ /g; s/[RPI]/-\ /g"` line 99. set sign = `echo $inorient | sed "s/[RAS]/+\ /g; s/[LPI]/-\ /g"` e.g. When the orientation of DWI is LPS, we have to transform data to RAS. ($fslplipx=1) The first sign = +-+ and the second sign = --+. So I have to multiple the bvecs(extracted from DICOM) by [-1 -1 +1], but NOT [+1 -1 +1]. Why are they different?
Thanks!
2012-02-04
Xiangzhen Kong
发件人： Anastasia Yendiki 发送时间： 2012-02-04 00:48:58 收件人： Xiangzhen Kong 抄送： freesurfer 主题： Re: [Freesurfer] What does trac-all do on the file 'bvecs'? When the DWIs are transformed to LAS and processed with eddy_correct, the same transformations are applied to the respective bvecs. On Fri, 3 Feb 2012, Xiangzhen Kong wrote:
Hi, all~ ? I use trac-all with .nii data, not dicom. So I have to specify the bvecs and bvals in the config file. Trac-all requires a bvecs file in 3 columes, but FSL need that in 3 raws. I wonder what does trac-all do on the bvecs file that I specify. And I have check the code 'trac-preproc' and the log, but found nothing, except copy and Eddy-current "correction". ? ps: The orientation of my dicom and .nii fils are both LPS, and the bvecs is read from the DICOM header via nibabel. But FSL requires LAS. I thinks trac-all have done the transposition on the bvecs somewhere. What orientation of bvecs does trac-all need when run with .nii files? ? Thanks! ? Xiangzhen ? 2012-02-03 ?
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