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Sorry, when I said it "works" for me, I was only looking at the interactive ability to selects different N's, number of shells, etc. When I actually tried to "Download" the vector set nothing happened. Sounds like you might need to contact the author of the tool. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [log in to unmask] From: Michael Harms <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Monday, May 6, 2013 10:26 AM To: FSL - FMRIB's Software Library <[log in to unmask]> Subject: Re: [FSL] free mode in Siemens DTI Works for me with Firefox 20.0 with Java 7 Update 17 on OSX 10.8.3 , and Firefox ESR 10.0.7 with Java 1.7.0_07 on CentOS 5.5. good luck, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [log in to unmask] From: Andreas Bartsch <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Monday, May 6, 2013 10:19 AM To: FSL - FMRIB's Software Library <[log in to unmask]> Subject: Re: [FSL] free mode in Siemens DTI Hi Michael, it doesn't for me (OSX 10.6.8, Firefox / Safari). Which OS are you on, what Java? Cheers, Andreas Von: Michael Harms <[log in to unmask]> Antworten an: FSL - FMRIB's Software Library <[log in to unmask]> Datum: Montag, 6. Mai 2013 17:09 An: <[log in to unmask]> Betreff: Re: [FSL] free mode in Siemens DTI Not sure what you tell you regarding the web site -- it works for me :) It does seem to resolve to a new address now, so perhaps try this address instead? http://www.rad.upenn.edu/sbia/Emmanuel.Caruyer/q-space-sampling.php cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [log in to unmask] From: Andreas Bartsch <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Saturday, May 4, 2013 8:05 AM To: FSL - FMRIB's Software Library <[log in to unmask]> Subject: Re: [FSL] free mode in Siemens DTI Hi Michael, thanks für sharing the link. However, it does not seem to work for me. I tried Safari & Firefox. Is there anything special to pay attention to when trying to download? Cheers, Andreas Von: Michael Harms <[log in to unmask]> Antworten an: FSL - FMRIB's Software Library <[log in to unmask]> Datum: Freitag, 3. Mai 2013 15:30 An: <[log in to unmask]> Betreff: Re: [FSL] free mode in Siemens DTI Hi Martin, There is a literature on optimizing diffusion directions -- see for example publications by Derek K Jones from the early 2000's. For multiple shell protocol design, the HCP used a tool available at the following website: http://www-sop.inria.fr/members/Emmanuel.Caruyer/q-space-sampling.php 'eddy' requires either diffusion directions sampled sufficiently on the whole sphere, or a given set of directions acquired with "blip-up, blip-down" (i.e., reversed) phase encoding polarity. The key in the latter approach is that the diffusion gradient directions themselves don't change in the two scans. I think the latter approach with "blip-up, blip-down" is probably a little more robust as regards 'eddy', because you end up with pairs of images with opposing eddy current induced distortions. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [log in to unmask] From: Martin Reiss-Zimmermann <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Thursday, May 2, 2013 4:54 PM To: FSL - FMRIB's Software Library <[log in to unmask]> Subject: [FSL] free mode in Siemens DTI Dear all, in the applytopup-posts <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;92db18fa.1305> it was suggested to rather use the "Free mode" for DTI protocols in Siemens scanners instead of MDDW. I also thought about this and searched the internet without luck. Can someone tell me, what needs to be taken into account, when creating a set of diffusion directions? Is there a page that lists example protocols / direction settings - or is it that everybody does it differently? I also have a question about blip up / blip down scanning. It seems to me that I have to scan the sequence twice in opposite readout directions, meaning that I have a (minimal) chance of screwing up the positioning of the second dataset. So, is it be possible to create a "free mode" direction set with two sets of directions with opposite values or are readout-direction and dw-directions two totally different pair of shoes (showing my lack of basic MR physics). Also: are the eddy current distortions different not only for the readout direction but also for the variable gradient directions? Or could I also scan a couple of b0-images in AP and PA direction (saving some scanning time)? As always, thank you for your help. Martin