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Hi Jon, Thank you a lot for your explanation. Yours sincerely, Rosalia 2016-09-04 15:40 GMT+02:00 Jon Anderson <[log in to unmask]>: > Although some images (e.g. DTI, PET) are more sensitive to the changes in > the acquisition parameters. But this is applicable to all imaging data. > e.g. if you have T1 images acquired with different acquisition parameters > then this will affect the size of the matrix, and the slices thickness. As > a result, you will not be able at the end of the analysis to differentiate > if the differences between the study groups are related to a pathology, or > it is because of the difference in acquisition parameters. > > The reason why I am looking for a method to normalize the images acquired > using different acquisition parameters to include them in the same pipeline. > > > > > Hi Stephen, > > I have been reading the link. Is this applicable to MRI data or just only > for DTI data?...and..why? > > Yours sincerely, > > Rosalia > > 2016-09-03 12:56 GMT+02:00 Stephen Smith <[log in to unmask]>: > Hi - see the FAQ entry: > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/Faq > > Cheers. > > > > > On 3 Sep 2016, at 11:52, Antoine Nasimian <[log in to unmask]> > wrote: > > Hi Steve, > I highly appreciate your response. > I have DTI data aquired using different aquisition parameters ( same b > value, but different TE and TR). > > I was thinking of kind of normalization for the images permits of > including it, regardless the differences in TE, TR in the same analysis > (e.g TBSS) > I know aquision parameters like TE can affect FA value. How can I include > different FA maps (i.e FA maps generated from DWI aquired using different > aquisition parameters) in the same TBSS analysis. > Can intensity normalization be of benifits in here? > > Best, > Ant > > > > Hi > > On 2 Sep 2016, at 12:18, Jon Anderson <[log in to unmask]> wrote: > > Dear FSL experts, > I would like to ask the following questions about " intensity > normalization in FSL": > > 1. In which circumstances, intensity normalization (i.e. the flag -inm in > the command " fslmaths") is urgent? > > I'm not sure what you're asking here, sorry - but maybe the below answer > gives you what you need. > > 2. What type of images can be normalized? Are there any benefits of > intensity normalization in DTI data? > > In general this is NOT done for inputs to TBSS, as the various dtifit > outputs (eg FA, MD) are supposed to already be directly comparable across > subjects as long as all subjects were acquired in the same way. > > Cheers. > > > 3. Can I use the flag "-inm "in the command "fslmaths" in the script > "tbss_3_postreg" to normalize the images "all_FA" then continue with the > rest of the pipeline? I am wondering if the image "all_FA" is 2D or 3D? > > Thanks for any comment and for your help! > > Jon > > > > > ------------------------------------------------------------ > --------------- > Stephen M. Smith, Professor of Biomedical Engineering > Head of Analysis, 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 > ------------------------------------------------------------ > --------------- > > Stop the cultural destruction of Tibet > > > > > > > > > -- > Rosalía Dacosta-Aguayo, Post-Doctoral Researcher. > Biomedicine, PhD > Clinical Neuropsychologist > > Department of Neurosciences. > Group of Neurodegenerative Diseases > Gaixotasun Neuroendekapenezko Taldea > Neurozientziak Arloa > > [log in to unmask] > T. +34 943 006 128 > > IIS BIODONOSTIA - OSI DONOSTIALDEA > Pº Dr. Beguiristain s/n * 20014 Donostia-San Sebastián SPAIN * T.+34 943 > 006 012 * F. +34 943 006 250 * [log in to unmask] * > www.biodonostia.org > > -- Rosalía Dacosta-Aguayo, Post-Doctoral Researcher. Biomedicine, PhD Clinical Neuropsychologist Department of Neurosciences. Group of Neurodegenerative Diseases Gaixotasun Neuroendekapenezko Taldea Neurozientziak Arloa [log in to unmask] T. +34 943 006 128 IIS BIODONOSTIA - OSI DONOSTIALDEA Pº Dr. Beguiristain s/n * 20014 Donostia-San Sebastián SPAIN * T.+34 943 006 012 * F. +34 943 006 250 * [log in to unmask] * www.biodonostia.org