That doesn’t sound like you solved the alignment problem (it will still be
misaligned in the volume) and I wouldn’t expect specifying the T2w as the T1w
will work without some pipeline modifications.
Matt.
From: Kelli Cannon mailto:kecanno...@gmail.com>>
Date: Thursday, October 6, 2016 at 1:17
I think if you start doing a lot of HPF you start picking up structured
artifacts in the data, which may make distinguishing between signal and noise
more difficult for the ICA. I'm not aware of any other tests than the one that
Steve and I did between hp2000 (essentially linear detrend) and hp
Hi Greg/all,
It turns out the "bad" PULS.log time stamps are off by 24 hours.
Subtracting 24 hours worth of ticks from the time stamps solves the problem
for those runs.
Andrew
On Thu, Oct 6, 2016 at 1:45 PM, Burgess, Gregory wrote:
> We have not had enough experience with these yet. You may w
Steve,
Have you found an obvious downside to a shorter HPF cutoff of, say, 200
seconds? Would the HCP FIX training data still apply or would the
classifier need to be retrained?
-Keith
On Thu, Oct 6, 2016 at 12:43 PM, Xu, Junqian wrote:
>
> > On Oct 4, 2016, at 9:03 PM, Ely, Benjamin wrote:
Hi Matt,
Thanks for the information! I was able to successfully run the PreFreeSurfer
pipeline by specifying the T1w image as the T2w image. The FreeSurfer pipeline
is running now, and I expect to be able to run the PostFreeSurfer pipeline
next, since I have the output files from the PreFreeSur
We have not had enough experience with these yet. You may want to check the
CMRR MB support page, or post an issue
https://github.com/CMRR-C2P/MB/issues
--Greg
Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washi
> On Oct 4, 2016, at 9:03 PM, Ely, Benjamin wrote:
>
> Thanks Steve, that's good to keep in mind. Our acquisition is a single
> "HCP-like" 15 minute run at MB6, 2.1mm isotropic resolution, TR=1s, AP phase
> encoding, 32-channel head coil on a 3T Skyra; hopefully that gives us a
> similar temp
> On Oct 4, 2016, at 9:03 PM, Ely, Benjamin wrote:
>
> Thanks Steve, that's good to keep in mind. Our acquisition is a single
> "HCP-like" 15 minute run at MB6, 2.1mm isotropic resolution, TR=1s, AP phase
> encoding, 32-channel head coil on a 3T Skyra; hopefully that gives us a
> similar temp
Hi Greg,
Thanks for your reply, I was not aware of the 'readCMRRPhysio.m' function
or that repo. That code is similar to mine, and I'm glad to see that the
ACQ_START_TICS are indeed 2.5 ms / tic. My first concern was that I was
misinterpreting the time stamp values.
The issue is that the window
I haven’t had a chance to look at those new files, so I’d be interested to hear
more about your experience.
If you’re not familiar with it, you should check out
https://github.com/CMRR-C2P/MB/blob/master/readCMRRPhysio.m .
One thing to note, at least with the legacy files, the time stamp in the
Hi all,
Has anyone had issues with the "new" format of the physio files, which end
in PULS.log? For some of our scans, I have found that the 'ACQ_START_TICS'
time stamps do not align with any of the time stamps found in our dicom
headers.
Andrew
--
Andrew Bock, PhD
Postdoctoral Researcher
Depar
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