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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 >> >> +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >> 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 >> W http://web.iitd.ac.in/~sghosh/ >> >> >> 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 >> >> >> >> >> >> --------------------------------------------------------------------------- >> 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 >> --------------------------------------------------------------------------- >> >> >> >> >> >> >> > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > (+44)1865-222466 (fax 717) > www.fmrib.ox.ac.uk/~saad > > > > > > > > > >