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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 > >