Hi there, A lot of people go by Jones et al 1999 (http://www3.interscience.wiley.com/journal/62500520/abstract) who suggested 1 b0 image for every 8-10 DWIs. You can easily add another scan with these extra b0s on the trio. Just go to the diffusion tab of the sequence and set only a single diffusion weighting (b=0) and then set the number of averages you want to acquire. Just be sure you keep the other parameters the same between the two sequences. Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Russ Poldrack Sent: Wednesday, June 04, 2008 12:21 AM To: [log in to unmask] Subject: Re: [FSL] AW: [FSL] Optimizing DTI sequences another issue with this 64 direction sequence on the trio is that it only collects one image at b=0 - I would be interested to hear whether others think that it is important to oversample this image (as most other sequences seem to do) cheers russ On Tue, Jun 3, 2008 at 2:16 PM, Peter Kochunov <[log in to unmask]> wrote: Interestingly, I've never see this artifact on either of our trios. But we do keep the TE below 90ms and this limits our b values to 700. pk ----- Original Message ----- From: "Matt Glasser" <[log in to unmask]> To: <[log in to unmask]> Sent: Tuesday, June 03, 2008 4:03 PM Subject: Re: [FSL] AW: [FSL] Optimizing DTI sequences In my personal experience, changing the phase encoding direction to R/L reduced the vibration somewhat (as felt from inside the scanner), and we haven't had the parietal artifact in those scans (though we also switched to the gradient table be got from Tim Behrens). Also, I have some 30 direction data I am tracking the arcuate in and it seems to have fewer terminations in anterior IFG (BAs 45 and 47) than the 60 direction data I have previously tracked. This suggests that the second fiber direction is not being modeled as well (aIFG arcuate terminations must pass through a region of crossing fibers, and are often not detected at all in methods that do not make use of a second fiber direction). Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Andreas Bartsch Sent: Tuesday, June 03, 2008 3:25 PM To: [log in to unmask] Subject: [FSL] AW: [FSL] Optimizing DTI sequences The vive artefact is still there under VB15 and actually related to the gradients. So far the best you can do to minimize it is to put a water cushion under the head and possibly remove the side restraints. The MGH sequence by Thomas is cool but also has limitations (TE, max ADC...). Nothing is perfect;) Cheers- Andreas -----Ursprüngliche Nachricht----- Von: FSL - FMRIB's Software Library im Auftrag von David Gutman Gesendet: Di 03.06.2008 20:18 An: [log in to unmask] Betreff: Re: [FSL] Optimizing DTI sequences Yeah I'll have to look into that as well. I've gotten a strong sense the vibration artifact didn't seem to be unique to our system and was known about-- just wasn't sure how people had worked around it. Appreciate the advice! dg On Tue, Jun 3, 2008 at 2:14 PM, Markus Gschwind < [log in to unmask]> wrote: Hi! However when it is present, it just looks like a signal void, particularly in the axial, towards the parietal/occipital junction--- based on where it is I think it may partially related to the person's head actually shaking around a bit. Please see our several mails about the "vibration artifact" on Siemens TrioTIM system in the Siemens own DTI sequence on the list. We finally changed the Sequence to the Stejskal-Tanner Sequence (ask your Siemens Physicist about it). With a good effect so far. But I downt know how things are with the Siemens sequence under the VB15 software update. Interested in your experience! Cheers, Markus Quoting Peter Kochunov <[log in to unmask]>: Well, everytime the baseline software is upgraded it removes all the sequences from the /MriCustomer/seq directory. pk ----- Original Message ----- From: David Gutman To: [log in to unmask] Sent: Tuesday, June 03, 2008 12:44 PM Subject: Re: [FSL] Optimizing DTI sequences I'll have to check. In the past we had used the MGH sequence, however after a scanner "upgrade" it went away, and we started using the 64 direction sequence built into the scanner. However I've never been super happy with the actual built in sequence-- we appear to get an artifact in the temporal/parietal region in some, but not all of the subjects and on some, but not all gradient directions. Obvioulsy this type of thing is a real joy to sit down and troubleshoot, since it's only there sometimes and only in some patients. However when it is present, it just looks like a signal void, particularly in the axial, towards the parietal/occipital junction--- based on where it is I think it may partially related to the person's head actually shaking around a bit. Anyone else have a similar issue with the built in Siemens sequence? On Tue, Jun 3, 2008 at 1:37 PM, Peter Kochunov <[log in to unmask]> wrote: My first suggestion would be to upgrade siemens product sequence to the MGH sequence. MGH sequence signficantly extends the capabilities in terms of number of directions, etc. You can contact Thomas Benner to get this sequence. [log in to unmask] ----- Original Message ----- From: David Gutman To: [log in to unmask] Sent: Tuesday, June 03, 2008 12:33 PM Subject: [FSL] Optimizing DTI sequences I am currently helping optimize a DTI sequence on a 3T siemens scanner for human work, and also beginning a foray into small animal DTI sequences. I was wondering if anyone could give me some pointers or point me towards some good papers on optimizing sequence parameters (# of echoes, # of averages, # of B0's to collect, # of directions, etc, etc..) Obviously we want the best resolution and best image quality we can get in the shortest amount of time while getting good single to noise and contrast to noise (we're quite ambitious). Just eyeballing the images and saying "looks good" lacks a certain amount of academic rigor, and based on the recent discussion on the list about measuring PHI angles,etc.,etc. simply eyeballing it won't do it. Also the question of what images to even look at-- analyzing all 65+ images by eye is obviously not accurate. Is there a particular way of measuring signal to noise and also contrast to noise, in particular as it applies to tractography? Would looking at the standard deviation of a region outside the brian, and then comparing it to a relatively homologous intracranial region (pick some big hunk of gray matter) be a useful metric? Also do you take a sampling of a certain # of gradients to generate an average SNR across your entire DTI acquisition. Sorry I am relatively naive to all of this, it's just hard to get the sense of what's "good enough". Also can anyone comment on the use of a 30 gradient sequence vs a 64 gradient sequence. Some of my colleagues are trying to integrate DTI in one of their existing protocols and would like it to be as brief as possible, since it's not their main focus. Obviously 30 gradients would take about half as much time as 64 gradients; however I've been using 60+ gradient data now and feel quite compelled to strongly suggest not getting any less than this. Any comments or pointers would be greatly appreciated. DG -- David A Gutman, M.D. Ph.D. Department of Psychiatry & Behavioral Sciences Emory University School of Medicine -- David A Gutman, M.D. Ph.D. Department of Psychiatry & Behavioral Sciences Emory University School of Medicine -- Dr. med. Markus Gschwind, M.D. Laboratory for Neurology and Imaging of Cognition Dept of Neurosciences University Medical Center (CMU) 1 Michel-Servet - 1211 GENEVA - CH Tel 0041 (0) 22 379 5324 Fax 0041 (0) 22 379 5402 email: [log in to unmask] http://labnic.unige.ch -- David A Gutman, M.D. Ph.D. Department of Psychiatry & Behavioral Sciences Emory University School of Medicine -- Russell A. Poldrack, Ph.d. Associate Professor UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563 phone: 310-794-1224 fax: 310-206-5895 email: [log in to unmask] web: www.poldracklab.org