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FSL  May 2007

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Subject:

AW: [FSL] AW: [FSL] TBSS Pipeline

From:

Andreas Bartsch <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 29 May 2007 23:50:07 +0200

Content-Type:

text/plain

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text/plain (250 lines)

Hi,
first you could check if the volumes are indeed scaled differently. Alternatively, you could write a little matlab or R code to rescale your volumes uniformely - see a previous post of mine. But I guess you are asking for a converter: see the quite recent postings to this list. Freesurfer comes with mri_convert which is quite neat, and Jolinda has written the fast and cool converter MRIConvert (coincidential naming;).
Cheers-
Andreas

________________________________

Von: FSL - FMRIB's Software Library im Auftrag von David Kideckel
Gesendet: Di 29.05.2007 22:24
An: [log in to unmask]
Betreff: Re: [FSL] AW: [FSL] TBSS Pipeline


hi. thanks.  that's interesting... how do i switch to that?
david


On 5/29/07, Andreas Bartsch < [log in to unmask] <mailto:[log in to unmask]> > wrote: 

	Hi,
	I haven't seen your data but this can in fact be a problem due to the volume specific scaling SPM99 introduces. Switch to DICOM -> NIFTI and give it a second trial to see if it still looks weird. 
	Cheers-
	Andreas
	
	________________________________
	
	Von: FSL - FMRIB's Software Library im Auftrag von David Kideckel
	Gesendet: Di 29.05.2007 19:16
	An: [log in to unmask] 
	Betreff: Re: [FSL] TBSS Pipeline
	
	
	hi, the ref number is 913750 (it seems to be taking a while to upload due to the file size) . it is the 4D volume. I wonder if it is the fact that I made my headers with SPM99, then created a 4D image using FSL commands (avwmerge -a <output> <input> and then ran the eddy correct script: eddy_correct <input> <output>. This shouldn't be a problem though, right? 
	Thanks again!
	David
	
	
	On 5/29/07, Saad Jbabdi <[log in to unmask]> wrote:
	
	        what is the difference between the two FA images you sent?
	
	        the most likely explanation for your results is that the data you have do not correspond to the bvecs you provide to dtifit. 
	        could you upload the actual data (not the result of dtifit) ?
	
	
	        saad.
	
	
	
	        On 29 May 2007, at 17:40, David Kideckel wrote:
	
	
	                hi. i uploaded another FA image that looks slightly better, but still pretty bad. the reference number is 886189. 
	                Thanks again!
	                David
	
	
	                On 5/29/07, David Kideckel <[log in to unmask]> wrote:
	
	                        hi. thank you. the ref number is 713292. i sent the FA image after DTIFIT. Do you want me to send any other ones? 
	                        David
	
	
	
	                        On 5/29/07, Saad Jbabdi < [log in to unmask] <mailto:[log in to unmask] > > wrote:
	
	                                they should work fine.
	                                i don't know why your FA image looks like you describe.
	                                maybe you could upload your tar-gzipped data onto our server: www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
	                                and send the reference number. we will have a look.
	
	                                cheers, 
	                                saad
	
	
	                                On 29 May 2007, at 17:18, David Kideckel wrote:
	
	
	                                        hi. when i run dtifit, and view the FA image, it look like a non-diffusion weighted image. do these bvecs and bvals look okay? 
	
	                                        Thank you.
	
	                                        David
	
	                                        On 5/28/07, David Kideckel < [log in to unmask] <mailto:[log in to unmask]> > wrote:
	
	                                        hello. i have tried your previous suggestions, and think that the problem may be in the bvecs file, but i do not know for sure. how would i check for this? 
	                                        thanks again.
	                                        David
	
	
	
	                                        On 5/25/07, Tim Behrens < [log in to unmask] <mailto:[log in to unmask]> > wrote:
	
	                                        Hi - if you run bedpost_datacheck on your directory it might tell you what's wrong - 
	                                        for example make sure the number of entriess in bvals and bvecs is the same as the number of volumes in your data.
	
	                                        T
	
	
	                                        On 24 May 2007, at 00:17, David Kideckel wrote: 
	
	
	                                        hi. thank you for your support. once i run bet from the command line (using cygwin), it does not seem to be working properly. but when i use the gui, it does...
	                                        anyway, i am trying to rum dtifit from the command line and get the following message: 
	                                        0 256 0 256 0 50
	                                        0 slices processed
	                                        Aborted <core dumped>
	
	                                        Any idea why this is happening? Did I enter something wrong? 
	
	                                        Thanks.
	                                        David
	
	
	                                        On 5/23/07, Tim Behrens < [log in to unmask] <mailto:[log in to unmask]> > wrote:
	
	                                        If you select dtifit from the drop down menu on the same page, all` the information about file specifications is there. Don't forget to end your bvecs and bvals files with carriage returns. 
	
	                                        Cheers
	
	                                        T
	
	
	                                        On 23 May 2007, at 18:53, David Kideckel wrote:
	
	
	                                        Hi. That was one of the firs things I did do. I will try to be more specific with my question. I want to do TBSS, and no tractography. So, would I do the following in this order: 
	                                        Eddy Correct
	                                        BET
	                                        DTI Fit
	
	                                        If so, where is it in the manual specified how to create and input the bvecs and bvals files? I follow the link it gives in the FAQ section, but I can't seem to find this info. 
	
	                                        Thanks again for your help.
	                                        David
	
	
	                                        On 5/23/07, Tim Behrens < [log in to unmask] <mailto:[log in to unmask]> > wrote:
	
	                                        Hi - if you go to
	                                         http://www.fmrib.ox.ac.uk/fsl/fdt/index.html
	
	
	                                        and select "processing pipeline", all should be clear.
	
	
	                                        T
	
	
	                                        On 23 May 2007, at 17:22, David Kideckel wrote:
	
	
	                                        Hi. Thank you for your response. Can you please send me this information. I can't seem to find it on the FSL website. 
	                                        Thanks you.
	                                        David
	
	
	                                        On 5/23/07, Steve Smith < [log in to unmask] <mailto:[log in to unmask]> > wrote:
	
	                                        Hi,
	
	                                        Indeed - you should run eddy_correct and then bet and then dtifit to 
	                                        produce the FA image - see the FDT manual pages for more details.
	                                        Sorry the TBSS page isn't clearer about that - we'll fix that shortly. 
	
	                                        Cheers.
	
	
	
	                                        On 22 May 2007, at 18:51, David Kideckel wrote:
	
	                                        > Dear FSLers, 
	                                        >
	                                        > I am new to TBSS and am wondering what the preprocessing steps are
	                                        > to do prior to TBSS. This information seems to be different on the 
	                                        > FAQ section of the FSL website and the technical report on TBSS.
	                                        >
	                                        > Is it correct to assume that to compare 2 groups with diffusion 
	                                        > data, I would need to run:
	                                        > Eddy correct
	                                        > Registration
	                                        > DTIFit 
	                                        > TBSS
	                                        >
	                                        > I am unclear as to whether I need to run BET (brain extraction
	                                        > tool) and/or BEDPOST. 
	                                        >
	                                        > Any guidance would be much appreciated.
	                                        >
	                                        > David Kideckel, PhD Candidate 
	
	
	                                        ------------------------------------------------------------------------
	                                        ---
	                                        Stephen M. Smith, Professor of Biomedical Engineering 
	                                        Associate Director,  Oxford University FMRIB Centre
	
	                                        FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
	                                        +44 (0) 1865 222726  (fax 222717) 
	                                        [log in to unmask]     http://www.fmrib.ox.ac.uk/~steve < http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> >
	                                        ------------------------------------------------------------------------
	                                        ---
	
	
	
	
	
	
	
	
	
	
	
	                                        <bvecs>
	
	                                        <bvals>
	
	
	
	                                --------------------------------------------------------------------------- 
	                                Saad Jbabdi,
	                                Postdoctoral Research Assistant,
	
	                                Oxford University FMRIB Centre
	
	                                FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK 
	                                +44 (0) 1865 222545  (fax 222717)
	                                [log in to unmask]     http://www.fmrib.ox.ac.uk/~saad 
	                                ---------------------------------------------------------------------------
	
	
	
	
	
	
	
	
	
	        --------------------------------------------------------------------------- 
	        Saad Jbabdi,
	        Postdoctoral Research Assistant,
	        Oxford University FMRIB Centre
	
	        FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
	        +44 (0) 1865 222545   (fax 222717) 
	        [log in to unmask]     http://www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/~saad >
	        ---------------------------------------------------------------------------
	

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