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Subject:

AW: [FSL] AW: [FSL] Pre-Processing in FDT

From:

Andreas Bartsch <[log in to unmask]>

Reply-To:

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

Date:

Tue, 7 Dec 2004 21:24:03 +0100

Content-Type:

text/plain

Parts/Attachments:

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text/plain (1 lines)

Hi,

 

just use avwmerge for creating the 4D-file. The bvecs are intrinsic to the pulse sequence you use. You should either be able to obtain the values from your scanner or the person who has implemented that particular sequence.

Hope that helps-

Andreas



	-----Urspr√ľngliche Nachricht----- 

	Von: Amrapali Arshanapalli [mailto:[log in to unmask]] 

	Gesendet: Di 07.12.2004 20:39 

	An: [log in to unmask] 

	Cc: 

	Betreff: Re: [FSL] AW: [FSL] Pre-Processing in FDT

	

	



	Hi,

	

	I am a novice in DTI Analysis and FSL. According to the following

	mail, I converted my data into NIFTI/Analyze so that FSL can read it.

	But how do I create the 4D-file? How do I get the fourth dimension -

	bvecs? Do we get the bvecs at the scanner/magnet? If not, how do we

	calculate? Please advise.

	

	Thank you,

	Amrapali.

	

	On Fri, 26 Nov 2004 21:06:23 +0100, Andreas Bartsch

	<[log in to unmask]> wrote:

	> Hi Rhuang,

	>

	> just convert the data into a format FSL can read and create a proper 4D-file (where the fourth dimension is your bvecs so to say). If you have multiple acquisitions the image reconstruction of your scanner may either spit these out averaged or (/and) seperately. In the latter case, you may want to create the appropriate average yourself (to increase SNR). Finally, it is always a good idea to look at the data you have acquired, i.e. by using fslview (here, the movie option comes in handy!). This may give you the option to discard volumes afflicted from strange artefacts. Then, just go ahead for ECC.

	> Best regards-

	> Andreas

	>

	>         -----Urspr√ľngliche Nachricht-----

	>         Von: R Huang [mailto:[log in to unmask]]

	>         Gesendet: Fr 26.11.2004 16:43

	>         An: [log in to unmask]

	>         Cc:

	>         Betreff: [FSL] Pre-Processing in FDT

	>

	>         Dear Group

	>

	>         Using FDT, there is one recommended processing pipeline which can

	>         be found on the website

	>           <http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_pipeline.html>.

	>         The first item is the scanner-specific pre-processing.

	>

	>         In our Lab, we use Siemens Sonate 1.5T scanner to acquire

	>         diffusion weighted images. I would like to ask your suggestions about the

	>         necessary procedures for the pre-processing (besides  of the motion

	>         correction and BET) ?

	>

	>         Thanks in advance

	>

	>         rhuang

	>

	>

	



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