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Hi Steve, I just wanted to confirm that you have received my previous email (see below) saying that I have uploaded these files. Thanks Nic Thank you for responding to my email. I have uploaded the file as requested. The ID is 886269. My concern is that some non-brain is being included in one of the paired scans and I am not sure how to deal with it. I have had a look at the course notes. Thanks, every bit helps. Is there something similar for the surface-based analysis in siena which will be my next challenge after resolving the scan quality/segmentation issue. Is there an intensive fsl/freesurfer course coming up? Being based in Australia I cannot attend short courses on the other side of the world but I would consider week-long courses particularly if they had a strong structural component. I am very grateful for fsl software and support. Nic -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Steve Smith Sent: Tuesday, February 13, 2007 8:39 PM To: [log in to unmask] Subject: Re: [FSL] siena and assessing quality of output Hi Nic, You can upload the files in a single compressed tarfile to http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi and then email me the upload ID. I would send the full results of running SIENA, including the inputs, and use the "-d" option to keep the intermediate stages. The number output by SIENA is described in the second para of the manual - it's the percentage brain volume change (PBVC) between two input images, taken of the same subject, at different points in time. There isn't a huge amount more detail, but you might find it informative to look through the course lecture slides: http://www.fmrib.ox.ac.uk/fslcourse/ Cheers, Steve. On 13 Feb 2007, at 03:33, Nicolas Cherbuin wrote: > Dear FSLers, > > I want to run siena to compare a clinical group and a control group > with > scans four years apart. The scans were of lesser quality in the first > than in the second wave. As a first test, as I am no expert, I have > run > siena on two subjects. I had attached the gifs of the results but > it did > not make it to the list since the message was too large. > > > My questions are: > 1. I would like to know if my results look reasonable, is there a drop > folder for somebody to have a look at them? and is the red outline the > second scan overlayed on the first one (or the reverse)? > 2. What should I do to improve the results and apart from looking > at the > GIF what is the best way to assess the quality of the registration? > 3. At the end of processing siena spits out -6.332, is it the volume > difference in mm3? (where can I find all the volumes?) > 4. I have looked at the siena website, searched for > tutorials,looked at > the mailing list, read the attached pdfs, and browsed the wiki but it > seems that there is not enough detailed step-by-step information for a > new user like me. Is there a detailed tutorial somewhere dealing not > just with process but with quality of output and what to do to improve > it? > > Thanks very much for your continuing support > > Nic ------------------------------------------------------------------------ --- 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 ------------------------------------------------------------------------ ---