ok thanks...I was wondering how you guys handle errors like these? Or are your
data so awesome that it never happens? ;-)
__
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
On Oct 24, 2014, at 2:46 PM, Harms, Michael wrote:
>
> Hi Gaurav,
&g
Thanks...we'll be bring the subject back so we'll reacquire anatomy then and
see what happens
______
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
> On Oct 24, 2014, at 3:04 PM, Harms, Michael wrote:
>
>
> It's not that errors
t sure but I'll check with our
sequence programmer. Do you?
______
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
> On Oct 24, 2014, at 3:04 PM, Glasser, Matthew wrote:
>
> Is that image you initially sent one of the down sampled FreeSurfer
>
s for the help
__
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
> On Oct 24, 2014, at 3:19 PM, Harms, Michael wrote:
>
>
> FWIW, the surface error at the crosshair position in your original
> snapshot seemed relatively minor from that sing
well
for us. If your scanner can only give you complex/imaginary images, then the
script I've written won't work unfortunately.
______
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
On Mar 31, 2015, at 5:35 AM, Benjamin Garzon wrote:
>
> Dea
real fieldmap, so
there's no need to use those parameters in the HCP scripts. Sorry for the
error, its been a while since I've thought about this. Let me know if you need
any other details
______
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
On A
Any help would be appreciated. Thanks!
_____
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
> On May 22, 2015, at 3:00 PM, Glasser, Matthew wrote:
>
> It helps to reply to the previous e-mail chain so that all of the info on a
> question is in one plac
Hmmm...no I don't think so. Will do and let you know
__
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
> On May 22, 2015, at 3:32 PM, Glasser, Matthew wrote:
>
> Hi Gaurav,
>
> Did you look at all 3 warpfield volumes (the second volum
to be roughly
inverted versions of 4-6. Would it help for me to attach the images in a
separate email? Thanks
__
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
On May 26, 2015, at 3:19 PM, Glasser, Matthew wrote:
> Are there only two of those files?
erences so far. Any help or insight would be appreciated. Thanks!
______
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
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.
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gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
> On May 31, 2015, at 4:21 PM, Glasser, Matthew wrote:
>
> Hi Barbara,
>
> I agree that the main heavily myelinated areas are found, the issue is with
> that lateral cortex (e.g. the diff
ll see if I can get a transmit field map--i'm fairly certain we have
those sequences
__
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
> On May 31, 2015, at 7:48 PM, Glasser, Matthew wrote:
>
> I wouldn’t recommend using FAST to try to deal with t
I also spoke to our sequence programmer about getting B1 receive and transmit
field measurements here, and he said he thought we had the necessary sequences.
I'll let you know what happens
__
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
On Jun 1,
Yeah, upon hearing about PURE correction I had high hopes, but it works less
well than it sounds. The B1 field mapping sequence on DV24 is a bit funny
apparently; I'll let you know what our sequence programmer is able to come up
with
__
gaurav patel
gau
FYI we're still working on this problem; I'm hoping for a meaningful update soon
_____
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
> On Jun 21, 2015, at 3:04 PM, Harms, Michael wrote:
>
>
> I don't know. If the myelin mapping isn&
do and are able to run some
tests, we'll post the results
______
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
On Nov 19, 2015, at 11:27 AM, Barbara Kreilkamp wrote:
> Dear all,
>
> We've now been able to acquire a sagittal B1-Map from the
f the MPRAGE on our
scanner, so hopefully soon we'll see if that solves the problem.
______
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
On Nov 27, 2015, at 1:15 PM, Harms, Michael wrote:
>
> Please cc the list, so that others can respond and
We've been noticing similar masking issues with our non-HCP data acquired on a
GE MR750, and have found that fat sat in our sequence was turned off, so we
will attempt to do the same and report whether that changes things.
__
gaurav patel
gauravpa...@gmai
ike "Error reading column 1, row 1". Is this the way that
cifti-roi-average is supposed to behave, only accepting metric ROI files?
Thanks!
______
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
___
HCP-Us
Ok thanks!
_
gaurav patel
gauravpa...@gmail.com
www.neurofreak.com
> On May 2, 2014, at 4:24 PM, "Glasser, Matthew"
> wrote:
>
> This feature has already been requested for this command.
>
> Peace,
>
> Matt.
>
>>
essed
__
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
On Apr 27, 2017, at 9:44 AM, Harms, Michael wrote:
>
> The number of windows you use to launch the processing is irrelevant. But if
> you only have 8 cores on your machine, and only want to use 7 of them, you
The fMRIVolume pipeline also takes advantage of SGE through fslsub, and we
hacked it to use condor as well--that allows for significant time savings on
our end
_
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
> On Apr 27, 2017, at 2:29 PM, Glasser, Matt
Yes that fits with what Juan and I have seen so far—no problems with our 2mm
data, but sudden weirdness with 2.4mm data. We’ll try version 3.22 and let you
know if we have further issues. Thanks
__
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
>
Yes…we’ve been 3.4 for many years without problems, and 3.22 only required
those minor changes. We recently verified that it was easy to install and run
on macs when we expanded the network of mac pros we use to run the HCP pipelines
gaurav patel
gauravpa...@gmail.com
Well, I guess that would be us every time we update our local installation.
We’ll let you know how it goes
gaurav patel
gauravpa...@gmail.com
pateldsclab.net
> On Mar 2, 2018, at 2:30 PM, Glasser, Matthew wrote:
>
> Hi Gaurav,
>
> I guess they are s
GRE image
comes from in the new pipelines; we stopped collecting b0 fieldmaps in this new
protocol, chossing to rely only on topup for distortion correction. Juan will
send you a copy of the fmrivolume batch script if that helps.
gaurav patel
gauravpa...@gmail.com
Well, that explains a lot. Ok, we’ll try it with SBRef set to NONE. Thanks
gaurav patel
gauravpa...@gmail.com
pateldsclab.net
> On Mar 29, 2018, at 4:32 PM, Glasser, Matthew wrote:
>
> You would need to use a mean image SBRef then (which should be the def
, so that setting
doesn’t make a difference. Thanks
gaurav patel
gauravpa...@gmail.com
pateldsclab.net
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In the borders menu? Changing that changes the size of the final border, but
not the border as I draw it
_
gaurav patel
gauravpa...@gmail.com
pateldsclab.net
> On Oct 9, 2018, at 12:42 PM, Dierker, Donna wrote:
>
> Check the diameter of your spher
. I am drawing
this on the tutorial surface
gaurav patel
gauravpa...@gmail.com
pateldsclab.net
> On Oct 9, 2018, at 1:07 PM, Harwell, John wrote:
>
> How huge is huge? When drawing a new border, the symbol size should be about
> 3% of the longest surface
this is the tutorial 1.0 brain (Q1-Q6_R440.R.veryinflated.32k_fs_LR.surf.gii).
2mm was actually much smaller than the current 3% standard for the adult brain.
Are you able to reproduce the issue with the same surface?
gaurav patel
gauravpa...@gmail.com
Thanks; drawing borders will be easier and more accurate with smaller sphere
sizes
_
gaurav patel
gauravpa...@gmail.com
pateldsclab.net
> On Oct 10, 2018, at 6:45 PM, Timothy Coalson wrote:
>
> To clarify the phrasing: the existing release doesn't
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