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Thanks for the info, Steve. Here's what I've done. Please let me know if this sounds correct. 1) I've preprocessed all of the DTI data through FDT (eddycorrect, dtifit, and bedpostx) 2) Using the FDT Registration GUI, I aligned dti_FA.nii.gz to both a high-res anatomical image and the default standard brain. 3) Using ApplyXFM_gui, I selected diff2standard.mat as the transform matrix, dti_FA.nii.gz as the input volume, and the MNI brain used in the FDT registration as the reference volume and made a dti_FA_alignstandard.nii.gz file. 4) I opened dti_FA_alignstandard.nii.gz in fslview and using the JHU probabilistic atlas, I added the structure of interest then saved it to file. 5) I used the following command to make a binary mask (What is the rationale for using 25 as a threshold?) fslmaths tract_mask -thr 25 -bin binary_tract_mask 6) Here's where I'm unsure of what to do. Before I had used the following commands to get the average FA of a mask: avwmaths_32R binary_tract_mask -mul dti_FA_alignstandard FA_tract avwstats FA_tract -M Now those commands don't exist, so I'm not sure how to use the fslmaths command to get the same result. Any thoughts? Also, is there any way to pull out the individual labels of the JHU white matter label atlas? If I add one structure, it seems like it adds the whole atlas. Thanks so much for your help! Kristen -----Original Message----- From: FSL - FMRIB's Software Library on behalf of Steve Smith Sent: Sat 2/23/2008 2:12 AM To: [log in to unmask] Subject: Re: [FSL] DTI-based White Matter Atlas Hi, Yes, you can do this; it's particularly easy if you have run the registration to highres and standard space in the FDT GUI. You can then go into FSLView, turn on atlas viewing, open 'structures', select the atlas and the structure of interest, press '+' to move that structure permanently into the image list, and then save that image to file. In general this will be a probabilistic mask so you may want to threshold it using fslmaths before using it as a mask in tracking, e.g. fslmaths thalamus_mask -thr 25 -bin binary_thalamus_mask Cheers. On 21 Feb 2008, at 12:34, Lindgren, Kristen, Ann wrote: > Thanks for the response, Steve. Really what I'd like to do is > directly identify a particular tract on the FA maps as opposed to > relying on tractography to identify it. Right now I'm getting > results by identifying two seeds in anatomical space and connecting > them, and I'm getting good results on some subjects but sometimes no > track on others. I thought the atlas was something like the > freesurfer atlas but for DTI data where I could create a label and > use that as a mask to get an average FA. I will look more carefully > at the atlas and see if it maybe would inform me of how to identify > my seed points in my FA maps for tractography. Thanks! > > Kristen > > > -----Original Message----- > From: FSL - FMRIB's Software Library on behalf of Steve Smith > Sent: Thu 2/21/2008 2:45 AM > To: [log in to unmask] > Subject: Re: [FSL] DTI-based White Matter Atlas > > Hi - the atlases are there as a guide for what structures are where - > but they may not exactly related to a given new individual's scan. > Using the masks directly in the context of TBSS results makes some > sense, but for tractography, if you have already got your tracts, this > implied that you chose your seed/target voxels/masks carefully and so > presumably already have a strong idea of what tracts you are looking > for? So I'm not quite sure how you are wanting to then use the > atlases? > > Cheers. > > > On 19 Feb 2008, at 21:18, Lindgren, Kristen, Ann wrote: > >> Hello. I am interested in using the JHU DTI-based white-matter >> atlases >> to obtain the average FA values of various tracts. I've created >> masks >> and gotten average FAs from our DTI using tractography, but I'm >> wondering if there is documentation on how to use the available >> atlases >> to do this. Thanks and hopefully I explained that clearly! >> >> Kristen >> > > > --------------------------------------------------------------------------- > 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 > --------------------------------------------------------------------------- > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------