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Hi Matt, could you please explain me: you take one flirt matrix and you use it to rotate components of the whole bvecs? While this could be correct for rotating gradient component of, say 5th DTI image with respect to the reference, the 10th image may be rotated differently than the 5th one. Thanks, Martin On Sat, Sep 6, 2008 at 6:26 PM, Matt Glasser <[log in to unmask]> wrote: > It is attached. > > > > Matt. > > > ------------------------------ > > *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On > Behalf Of *vin > *Sent:* Saturday, September 06, 2008 11:18 AM > > *To:* [log in to unmask] > *Subject:* Re: [FSL] correcting dti bvecs after registration > > > > Hi Matt, > > I would like to try this script. how I can get it ? > > reg, vin > > On Sat, Sep 6, 2008 at 7:40 AM, Matt Glasser <[log in to unmask]> wrote: > > It is currently extra, but will be included in FSL in the future. > > > Peace, > > > > Matt. > > > ------------------------------ > > *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On > Behalf Of *vin > *Sent:* Friday, September 05, 2008 6:17 PM > > > *To:* [log in to unmask] > *Subject:* Re: [FSL] correcting dti bvecs after registration > > > > also mriconvert software(dicom--fsl nifti converstion) will give you the > desired format as Matt wrote. > > I want to ask , is this script to rotate the gradients using FLIRT > transform is included in FSL ? or extra. > > vin > > On Fri, Sep 5, 2008 at 9:08 PM, Matt Glasser <[log in to unmask]> wrote: > > Like I said, you need to convert your bvecs file to be of the form: > > > > x1 x2 x3 … x12 > > y1 y2 y3 … y12 > > z1 z2 z3 … z12 > > > > The script I wrote will not work with the gradient table in the format you > have. If you want to convert the gradient table to the correct format > quickly, highlight the cells in excel, select paste special, and transpose. > > > > > Peace, > > > Matt. > ------------------------------ > > *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On > Behalf Of *Michela Pievani > *Sent:* Friday, September 05, 2008 8:33 AM > > > *To:* [log in to unmask] > *Subject:* Re: [FSL] correcting dti bvecs after registration > > > > Hi, I'm not sure if I'm correctly interpreting the output of Tbvecs. > My bvecs file looks like this: > > 0.89440000 0.00000000 -0.44730000 > -0.00010000 0.44730000 -0.89450000 > 0.44720000 0.89450000 0.00000000 > 0.89400000 0.44830000 0.00000000. > ..... > ..... > -0.44730000 0.00000000 -0.89450000 > > where the rows are n=12. The output I get is: > > 0.8951819 0 0 > -0.001100128 0.4473 0 > 0.4456314 0.8945 0 > > What's the meaning of this 3x3 matrix? I expected the output to contain 12 > (new) directions...I got no warning nor errors. > Thanks, > Michela > > > On 9/5/08, *Matt Glasser* <[log in to unmask]> wrote: > > An FSL formatted bvecs file contains x, y, and z rows, and a number of > columns that equals the number of directions + number of b0 images > acquired. > The code won't work unless the bvecs file is formatted in this way. > > Peace, > > > Matt. > > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf > Of Michela Pievani > Sent: Friday, September 05, 2008 5:23 AM > To: [log in to unmask] > Subject: Re: [FSL] correcting dti bvecs after registration > > Hi, > I'm using your script to rotate the gradients using FLIRT transform. I have > a question about the input/output files: > > Q1. Should the input file (original bvecs) be formatted as a bvecs FSL > file? > > If so, there's something wrong with my files: I provided a bvecs file > containing 12 directions, but the output contains only three rows. What's > wrong in it? > > Thanks! > Michela > > > > > > >