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Hi, 1st, thanks so much for helping me out. So, the corr_data file seems to be fine to me, please see the attached output for fslsplit corr_data.nii.gz. I even see all the 33 volumes in fslview of the corr_data.nii.gz. I got this to work out so far. But when I run DTIFIT program and get the FA, MD, files, then I see nothing. The intensity is zero. see the attached files. when I run the command fslstats dti_FA.nii.gz -R, I get min/max intensities of 0.000000 0.000000 again, thanks for your time. aj --- On Fri, 1/8/10, Markus Gschwind <[log in to unmask]> wrote: > From: Markus Gschwind <[log in to unmask]> > Subject: Re: [FSL] DTIFIT problems-please help > To: FSL@JISCMAIL.AC..UK > Date: Friday, January 8, 2010, 2:30 AM > Hi, > > It seems everything all right. Both files have the sime > dimensions: > dim0 4 > dim1 256 > dim2 256 > dim3 32 > dim4 33 > > Which means you should find the 33 volumes in both files. > > > How did you find that there was nothing? You can try > fslsplit corr_data.nii.gz > > this will split up the 4D file in its 33 volumes. You can > have a look at them separately. > fslstats vol....nii.gz -R > > Did you have a look at data.nii.gz? Is it really all > right? > > > Best, > Markus > > > > > > 2010/1/8 Adil Javed <[log in to unmask]> > > Hi, > > here's the output you requested for the files. > > thanks so much for your help. > > aj > > > > > > > > Hi! > > > > > > > > > > > > Seems that your eddy correct was a little hungry ;-). > > > > > > What does it say when you do > > > > > > fslhd > <your_data_file_before_eddy_correct>.nii.gz > > > > > > fslhd > <your_data_file_after_eddy_correct>.nii.gz > > > > > > > > > > > > Best, > > > > > > Markus > > > > > > > > > > > > > > > > > > > > > > > > 2010/1/7 Adil Javed <[log in to unmask]> > > > > > > > > > > > > > Hi, > > > > > > > I am trying to analyze DTI data to get the FA and > MD > > > images by running > > > > > > > DTIFIT. After running the DTIFIT I do get FA, > > > MD, etc images but when I > > > > > > > look at them in FSL view, all these images have > > > intensities of 0. There are > > > > > > > no images to look at. I even played around with > > > min/max itensity from 0-1 or > > > > > > > -1 to 1 and again nothing. I've tried > other > > > programs to analyze the same > > > > > > > data, such as DTI tool in MedINRIA, and it works > fine > > > there. > > > > > > > > > > > > > > > > > > > > > > > > > > > > also after I run Eddy current correction, the > > > generated file has only 1 > > > > > > > volume which looks like b0 file and the remaining > 32 > > > volumes of various > > > > > > > directions are gone? > > > > > > > > > > > > > > any ideas? > > > > > > > > > > > > > > Thanks for your help, > > > > > > > > > > > > > > aj > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > > > > > > > Dr. med. Markus Gschwind, M.D. > > > > > > Laboratory for Neurology and Imaging of Cognition - > Dept of > > > Neurosciences > > > > > > University Medical Center (CMU) > > > > > > 1, Michel-Servet > > > > > > CH-1211 GENEVA - Switzerland > > > > > > > > > > > > Tel 0041 (0) 22 379 5324 > > > > > > Fax 0041 (0) 22 379 5402 > > > > > > email: [log in to unmask] > > > > > > http://labnic.unige..ch > > > > > > > > > > > > > > > > > > > > > > > > > > > This email is intended only for the use of > the individual > > > or entity to which it is addressed and may contain > > > information that is privileged and confidential. If > the > > > reader of this email message is not the intended > recipient, > > > you are hereby notified that any dissemination, > > > distribution, or copying of this communication is > > > prohibited. If you have received this email in error, > please > > > notify the sender and destroy/delete all copies of > the > > > transmittal. Thank you. > > > > > > > > > >