Hi,
Just one word of caution: changing A>>P to R>>L phase encoding will to some extent disrupt the symmetry of the object due to thegeometric distortions.
Cheers-
Andreas
-----Ursprüngliche Nachricht-----
Von: FSL - FMRIB's Software Library im Auftrag von Matt Glasser
Gesendet: Mi 04.06.2008 06:45
An: [log in to unmask]
Betreff: Re: [FSL] AW: [FSL] Optimizing DTI sequences
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
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