Hi Santanu,

thanks for uploading the data. I tried eddy_correct on your data and it seems to work fine: 

eddy_correct PA001 data_cor 0

As Saad pointed out, your input should be a 4D file.

Cheers,
Stam 



On 4 May 2010, at 10:54, Saad Jbabdi wrote:

You should be using a command line that looks like this:
eddy_correct data corrected_data 0

where data is a 4D file (your use of dti* suggests to me that you are feeding many volumes rather than just one 4D volume, causing the program to crash)
0 here means your reference volume is the first one

Cheers,
Saad.


On 4 May 2010, at 09:36, shantanu ghosh wrote:

Matt,
I tried the command line to do the analysis but i get the following error

[root@SunUltra20CogSci newtrial_PA001]# eddy_correct dti* data 6
/usr/local/fsl/bin/eddy_correct: line 86:  7893 Floating point exceptionfslroi $input $output $ref 1
/usr/local/fsl/bin/eddy_correct: line 88:  7894 Floating point exceptionfslsplit $input
/usr/local/fsl/bin/eddy_correct: line 97:  7949 Floating point exceptionfslmerge -t $output $full_list
/bin/rm: cannot remove `vol????.*': No such file or directory
[root@SunUltra20CogSci newtrial_PA001]#

can you tell what the problem is and how to solve it?
I am stuck with this (a previous analysis worked fine), befor i ask the technician to use 2 x 2 x 2 mm isotropic voxels.

thanks in advance,
shantanu
From: shantanu ghosh <[log in to unmask]>
To: [log in to unmask]
Sent: Tue, 4 May, 2010 9:07:08 AM
Subject: Re: [FSL] FDT query:upload ID: 897282

I am trying to set up the possible pipeline and compare the non-isotropic and isotropic outputs. Once the pipeline works without problems, my advisor asked me to reslice the data to 2 x 2 x 2 mm^3 isotropic voxels. Will that be sufficient? I am planning to do the conversion to isotropic voxels using spm2/8. i am a fsl newbie, so please guide me- is there a way to do it within fsl?
Thanks,
Alka

From: Matt Glasser <[log in to unmask]>
To: [log in to unmask]
Sent: Mon, 3 May, 2010 9:25:38 PM
Subject: Re: [FSL] FDT query:upload ID: 897282

With data that is that far from isotropic, I would be suspicious of your tractography results (particularly for pathways that have a significant superior/inferior component).

 

Peace,

 

Matt.  

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of shantanu ghosh
Sent: Monday, May 03, 2010 7:21 AM
To: [log in to unmask]
Subject: Re: [FSL] FDT query:upload ID: 897282

 

Hi Stam,
I have uploaded the file for you <dti.tar.gz>. The session ID for  the file upload is 897282. It has one patients data (pediatric scan) taken on a 3.0 Tesla GE HDx scanner <PA001.nii.gz>, the bvecs and bvals files created by MRICroN (done in Windows), nodif image, nodif_brain, nodif_brain_mask. The imaging parameters are : 23 slices, 2 x 2 x 5 mm^3 non-isotropic voxels, 65 encoding directions along with 5 b0 images.
Our processing pipeline includes :
1. Getting DTI scans from a hospital scanner written onto a CD
2. Using MRICroN (Windows version) converting the diffusion images into 4D-NIfTI, without reorientation
3. Importing the nii.gz and bvals/bvecs files to our Sun workstation (running CentOS4_32_FSL 4.1.4 on RedHat Enterprise 4 update 5)
Then, as per Gwen's suggestion, continued as follows:
4. BET (no problems running this)
5. Eddy current correction
6. BedpostX
7. DTIfit to get FA map
8. flirt FA to FMRIB58
9. flirted FA to create study-specific template
10. fnirt FA to study-specific template (for kids)
11. ProbtrackX

Thanks in advance,
Shantanu/Alka

 

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P Please consider the environment before printing this e-mail
 
Shantanu Ghosh, PhD
Assistant Professor
Department of Humanities and Social Sciences
Indian Institute of Technology Delhi
Hauz Khas
New Delhi 110 016
INDIA
T +91.11.2659.1382
F +91.11.2659.2277

 

 

From: Stephen Smith <[log in to unmask]>
To: [log in to unmask]
Sent: Thu, 29 April, 2010 3:10:03 PM
Subject: Re: [FSL] FDT query

One quickie - Shantano did you tell eddy_correct which timepoint to use as the reference image?
Cheers.

 

 

On 29 Apr 2010, at 10:26, Stamatios Sotiropoulos wrote:


Hi,

 

we will need to take a look at your data, could you please upload them on www.fmrib.ox.ac.uk/cgi-bin/upload.cgi and let me know the upload session ID?

 

Cheers,
Stam

 

 

On 27 Apr 2010, at 05:50, shantanu ghosh wrote:


Dear Fslers,
i am trying to do eddy current correction on a diffusion volume with 65 encoding directions, and i get the following error message:
"Errors:/root/Desktop/fsl/bin/eddy_current: line 85: 5993 Floating point exception fslroi $ input"
Incidentally i can do bet on the same input volume and can display them using fslview.
I don't know what i am doing wrong.
Does anyone have any idea about what is happening?
Thanks in advance,
Alka

 

 

 

 


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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
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--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)