You don't have to multiply the bvecs with anything yourself, it will do it for you. Of course you should check that it does it correctly, check the help of the flip4fsl script for how to do that.
> 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 > > > > ·¢¼þÈË£º Anastasia Yendiki > ·¢ËÍʱ¼ä£º 2012-02-04 00:48:58 > ÊÕ¼þÈË£º Xiangzhen Kong > ³ËÍ£º freesurfer > Ö÷Ì⣺ 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 >> ? >> >> > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
