Hi Matt,
I have repeated measures DTI data of one subject which I want to analyses
with FSL.
So like with the "normal" EPI images, should I realign them first to the
first series of images and than average them to get only one image for the
analysis...???
Do I also have to normalise them for a group analysis?
If so, how should I do this? The average procedure was described in former e
mails, but what about the normalisation and how should I handle the bvecs
files???
Many thanks and sorry, this is my first analysis...
Best wishes
boris
> -----Ursprüngliche Nachricht-----
> Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag
> von Matt
> Gesendet: Dienstag, 7. August 2007 14:31
> An: [log in to unmask]
> Betreff: Re: [FSL] AW: [FSL] Averaging of multiple DTI acquisitions
>
> Boris,
>
> I'm not sure I understand your questions. eddy_correct motion corrects
> the
> data and corrects for eddy currents. The bvecs files are modified based
> on
> the output of DTIFit. Off the list I asked Lars to provide the following:
> please send me a screenshot showing the V1 in all three planes (axial and
> coronal through the corpus callosum, sagittal through the corona radiate)
> of
> both sets of bvecs you have. Make sure you load one V1 for color and one
> with lines so you can see both lines and colors on the screen (use the FA
> to
> modulate the one with colors). From this you can determine any gradient
> directions that need to be swapped or flipped.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of boris suchan
> Sent: Tuesday, August 07, 2007 4:21 AM
> To: [log in to unmask]
> Subject: [FSL] AW: [FSL] Averaging of multiple DTI acquisitions
>
> Hi Matt,
> I am also interested in this topic,
> And I have 2 questions:
>
> Q1: How will the data be realigned?
>
> And Q2: How will the vecs files be modified?
>
> Many thanks
>
> boris
>
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im
> Auftrag
> > von Matt Glasser
> > Gesendet: Sonntag, 5. August 2007 13:51
> > An: [log in to unmask]
> > Betreff: Re: [FSL] Averaging of multiple DTI acquisitions
> >
> > Lars,
> >
> > Q1: The format for avwroi is <first volume> <# of volumes> and in FSL
> > volumes start with number 0.
> >
> > Q2: I thought you were already using a single volume with both averages
> in
> > it. The top of the script that does that would be:
> >
> > avwmerge -t big4d data1 data2
> >
> > where data1 and data2 are your two uncorrected averages.
> >
> > Q3: The script does average each same volume together as we are
> splitting
> > the motion corrected file into two averages with 0-9 b0 and 10-39
> > diffusion
> > weighted images.
> >
> > Peace,
> >
> > Matt
> >
> > -----Original Message-----
> > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> > Of Lars Tjelta Westlye
> > Sent: Sunday, August 05, 2007 5:59 AM
> > To: [log in to unmask]
> > Subject: Re: [FSL] Averaging of multiple DTI acquisitions
> >
> > Hi Andreas and Matt,
> >
> > thanks for your help. It's very helpful indeed. I will follow your
> > suggestions, and get get back to you concerning the bvecs as soon as I
> > have made an average of the two acquisitions.
> >
> > Meanwhile, please apologize my ignorance and allow a couple of more
> > questions.
> >
> > Q1: The third line in your bash script says that avg_2_corr is to be
> made
> > of vol 40-40. Should this read 40-80?
> >
> > Q2: The big4d.nii.gz would be my 80 volume raw data (included 20
> > b0's)concatenated into one nii.gz? In this case, should I use MRIConvert
> > to convert my raw data into NiftiFSL, and then avwmerge/mri_concat into
> > one 4D vol, or would you suggest something else? What I have done is to
> > mri_convert my raw .IMA-files into .bfloat (which I need to something
> > else), and then mri_convert the bfloats to .nii to use with Fsl.
> >
> > Q3: My first thought would be - after motion correction - to average
> > volumes with equal directions (in my case I guess that would be vol 11
> and
> > 51, 12 and 52 etc, resulting in 30 averaged DWI's), then average all 20
> > b0's into one vol and then merge the resulting 31 vols into one 4D using
> > avwmerge or something like that to constitute my data file. My concern
> is
> > that averaging over different gradient directions and even b0 would
> create
> > a mess, but that is maybe not even what you are suggesting or what
> avwroi
> > and avwmaths_32 does?
> >
> > Thanks!
> >
> > Lars
> >
> >
> > > Lars,
> > >
> > > Averaging data with FSL is easy, once you make a script to do it (call
> > your
> > > starting NIFTI_GZ file with both averages big4d.nii.gz):
> > >
> > > bash eddy_correct big4d big4d_corr 0 #motion correct all data to first
> > volume
> > > bash -c "avwroi big4d_corr av1_corr 0 40"
> > > bash -c "avwroi big4d_corr av2_corr 40 40"
> > > avwmaths_32R av1_corr -add av2_corr -div 2 data #average motion
> > corrected
> > > data
> > >
> > > Then preprocess for DTIFIT:
> > > bash -c "avwroi data nodif 0 1" #select first b0 volume
> > > bash -c "/usr/share/fsl/bin/bet nodif nodif_brain -m -f .2" #make mask
> > of
> > > brain from b0 volume
> > > dtifit -k data -o data -m nodif_brain_mask -r bvecs -b bvals
> #calculate
> > DTI
> > > maps
> > >
> > > We can work on getting your gradient directions oriented correctly
> once
> > you
> > > have the data averaged.
> > >
> > > Peace,
> > >
> > > Matt.
> > >
> > > -----Original Message-----
> > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> > Behalf
> > > Of Lars Tjelta Westlye
> > > Sent: Friday, August 03, 2007 5:20 PM
> > > To: [log in to unmask]
> > > Subject: [FSL] Averaging of multiple DTI acquisitions
> > >
> > > Hi, I have a 30-direction DTI data set that is repeated 2 times. The
> > data
> > > is transferred from the Siemens scanner in a mosaic format with a
> total
> > of
> > > 80 volumes. Vols 1-10 is b0, 11-40 is the diffusion weighted images.
> > This
> > > sequence is repeated in vols 41-80.
> > >
> > > The Fdt pipeline says the user is to manually average multiple
> > > acquisitions prior to Eddy current correction.
> > >
> > > Q1: How can I do this with Fsl? Or is the averaging somehow
> > automatically
> > > taken care of within Fdt stream?
> > >
> > > I have not done any averaging, but still performed Eddy current
> > correction
> > > and DTIFit on these data. I'm not sure as to the quality of the output
> > files. Please see the tiny screen dump from Fslview (_V1 RGB's modulated
> > on _FA) and the bvecs attached. I'd be very grateful if someone would
> > have
> > > a quick look and tell me if it looks reasonable and if I'm on the
> right
> > track here before rushing into BEDPOST.
> > >
> > > Thank you very much!
> > >
> > > Best,
> > > Lars
> > >
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