If you have the raw data stored, you may as well be able to redo the image reconstruction.
Cheers-
Andreas

________________________________

From: FSL - FMRIB's Software Library on behalf of Tim Behrens
Sent: Thu 2/1/2007 8:59 PM
To: [log in to unmask]
Subject: Re: [FSL] AW: [FSL] AW: [FSL] bedpost running time


My guess is the same as Saad's, but I also don't have any direct experience.  

T

On 1 Feb 2007, at 18:13, Saad Jbabdi wrote:


	hi,
	my guess is that it is not a good idea to interpolate upsampled data. 
	If you do this, the value in each voxel will slightly change, because of the interpolation, compared to the original signal.
	now if you do this for each volume, corresponding to each gradient direction, the signal in each voxel will go slightly up, or slightly down, for each direction volume, and this might miss up with your orientation information and anisotropy values.
	having said that, I don't know if it does change things that much..

	cheers,
	saad



	On 1 Feb 2007, at 17:19, Hedok Lee wrote:


		Dear FSLers.

		I also have a dataset which has been upsampled.  Has anyone tried downsampling a data set (like sinc interpolation) and run bedpost?

		thanks in advance,

		Hedok


		Andreas Bartsch wrote:

			Yeah, probably Tim is right. I noticed the resolution but it is true that this is unlikely to reflect the "real sampling". On the other hand, depending on your system you may in fact have acquired the data at 256x256? But you better check on it as this is a indeed a fairly big data set to process...
			Andreas 
			-----Ursprüngliche Nachricht-----
			Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Tim Behrens
			Gesendet: Donnerstag, 1. Februar 2007 18:11
			An: [log in to unmask]
			Betreff: Re: [FSL] AW: [FSL] bedpost running time

			Your sacnner has upsampled the resolution of your image to <1mm in- plane. This is what is causing it to be slow, and it will also cause huge problems at later stages.

			You should turn this feature off on your scanner, so that your data is analysed at the resolution that it is acquired. Then everything will run much faster.

			cheers

			T

			On 1 Feb 2007, at 17:07, Andreas Bartsch wrote:

			  
			

				Hi,
				Be patient. On cygwin such a data set make take 36 hours or so.
				Cheers-
				Andreas

				-----Ursprüngliche Nachricht-----
				Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von [log in to unmask]
				Gesendet: Donnerstag, 1. Februar 2007 17:33
				An: [log in to unmask]
				Betreff: [FSL] bedpost running time

				Hi,

				I'm fairly new to FSL.  I'm trying to run bedpost.  I have a data set with
				34 volumes, 32 diffusion weighted, and 2 withouth the weighting.   It has
				56 slices, and 56 slices.  It has been running for over 18 hours now, and so far it's only analyzing the 10th slice.  Should I be concerned that it's taking so long?  I got images that looked ok when I ran DTI fit.
				when I ran the datacheck, everything was fine.  I'm running it on windows XP with 2GHz pentium processor, with 2GB of ram.  The bedpost_datacheck output is below.  Any ideas anyone?  Or is it just a large dataset?

				data_type      INT16
				dim1           256
				dim2           256
				dim3           56
				dim4           34
				datatype       4
				pixdim1        0.8280000091
				pixdim2        0.8280000091
				pixdim3        2.2000000477
				pixdim4        1.0000000000
				cal_max        4095.0000
				cal_min        0.0000
				file_type      NIFTI-1+

				/home/mark/Kelly/UBC_3T_DTI_32dir_data/BEDPOST/nodif
				data_type      INT16
				dim1           256
				dim2           256
				dim3           56
				dim4           1
				datatype       4
				pixdim1        0.8299999833
				pixdim2        0.8299999833
				pixdim3        2.2000000477
				pixdim4        3.0000000000
				cal_max        4095.0000
				cal_min        0.0000
				file_type      NIFTI-1+

				/home/mark/Kelly/UBC_3T_DTI_32dir_data/BEDPOST/nodif_brain_mask
				data_type      INT16
				dim1           256
				dim2           256
				dim3           56
				dim4           1
				datatype       4
				pixdim1        0.8299999833
				pixdim2        0.8299999833
				pixdim3        2.2000000477
				pixdim4        3.0000000000
				cal_max        1.0000
				cal_min        0.0000
				file_type      NIFTI-1+

				 num lines in /home/mark/Kelly/UBC_3T_DTI_32dir_data/BEDPOST/bvals
				1
				 num words in /home/mark/Kelly/UBC_3T_DTI_32dir_data/BEDPOST/bvals
				34
				 num lines in /home/mark/Kelly/UBC_3T_DTI_32dir_data/BEDPOST/bvecs
				3
				 num words in /home/mark/Kelly/UBC_3T_DTI_32dir_data/BEDPOST/bvecs
				102

				thanks

				~Kelly
				    
				


	
	---------------------------------------------------------------------------
	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
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