Hi Anastasia and John,
This looks like the glibc issue that was fixed in more recent versions of
FSL. Given that you are running Ubuntu 16.04, if you are using an older
version of FSL, you will get FLIRT matrices saved in hexadecimal format. If
you upgrade your FSL to a more recent version, you sho
Hi,
To make the mask:
mri_binarize --i aseg.mgz --match 17 --o Lhipp.mgh
Run glmfit:
cmdline mri_glmfit.bin --osgm --glmdir
lh.testretest.volume-rate.fwhm10_LHipp --y
lh.testretest.volume-spc-10.stack.mgh --mask fsaverage/mri/Lhipp.mgh --surf
fsaverage lh
sysname Linux
FixVertexAreaFlag = 1
UseM
Dear Anastasia -
Yes, I noticed the added mri_convert capability in the release notes for
Freesurfer 6.0 - that will save some work - thank you.
It sounds like there is no big down side to running tracula on a scan obtained
with higher b-value. At present, I am primarily interested in using tra
Resolved - thank you Andrew!
Solution: operator error, needed to cat file w/ input list for --inputs instead
of just specifying file w/ input list
From: Hoopes, Andrew
Sent: Thursday, February 15, 2018 4:43:18 PM
To: Makaretz, Sara Johanna; Freesurfer support li
Thanks for the tip! I hope that diff2anatorig.bbr.mat looks fine, however,
because that one in particular comes from bbregister. Perhaps this glitch
affected later steps.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Niels Bergsland
Sent: Friday,
Anastasia,
Q: Do the other registration files look like this too?
I'm glad you asked. I looked at the .mat files. Two of the mat files have
regular numbers. The rest have hex. Also, many of the numbers in these
files seem quite huge to me. The two mat files that look normal are
anatorig2anat.mat an
OK, so the ones that come from bbregister (a freesurfer tool) are fine. Then
it's possible that this is related to the FSL glitch. It's worth trying. Sorry
about this, I hope to reduce dependencies in the future.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on
Hi all,
Is there an equivalent of fslmaths in Freesurfer? I would like to add two
scalar value images (.mgh files) that are registered to the fsaverage6 surface
but I’m not seeing an obvious way to do it. Right now I’m reading the images
into Matlab to add them, but this is a bit inconvenient
Hi Jared
I think mris_calc does at least some of what you want.
cheers
Bruce
On Fri, 16 Feb 2018,
Zimmerman, Jared wrote:
Hi all,
Is there an equivalent of fslmaths in Freesurfer? I would like to add two
scalar value images (.mgh
files) that are registered to the fsaverage6 surface bu
Or fscalc
On 2/16/18 11:22 AM, Bruce Fischl wrote:
Hi Jared
I think mris_calc does at least some of what you want.
cheers
Bruce
On Fri, 16 Feb 2018, Zimmerman, Jared wrote:
Hi all,
Is there an equivalent of fslmaths in Freesurfer? I would like to
add two scalar value images (.mgh
file
Anastasia,
Great - this is awesome (knock on wood). Version 5.0.9 looks stable, but I
should probably ask IT department for the recommended. Is that the latest
stable version?
John
On Fri, Feb 16, 2018 at 8:56 AM, Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:
> OK, so the ones that come f
We are using N4 to correct some large inhomogeneities in some samples and
wanted to insert these images into the v6.0 pipeline and bypass the N3 bias
correction done within. What would be the correct sequence of freesurfer
commands to achieve this? Thanks
Eric
_
Sent on behalf of Dr. Nathan Kolla:
The Violence Prevention Neurobiological Research Unit (VPNRU) at the Centre for
Addiction and Mental Health (CAMH) in Toronto, Ontario, Canada, which is fully
affiliated with the University of Toronto, seeks a motivated and enthusiastic
post-doctoral fellow t
Thanks Doug and Bruce,
Fscalc is great because I can do maths with multiple inputs, like a mean. I’m
noticing, however, that when I do a mean with fscalc I get different values
than when I do the mean in Matlab, any idea why? In some regions the
differences are as much as 5-10% so I don’t thi
Hi again,
The latest version is 5.0.10 but the issue was definitely fixed in 5.0.9
(possibly one point release earlier, I can't recall). Regardless, I don't
think there were any changes to flirt between 5.0.9 and 5.0.10.
Good luck!
Niels
On Fri, Feb 16, 2018 at 5:40 PM, John Davis wrote:
> Anas
Thanks for the info, Niels.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Niels Bergsland
Sent: Friday, February 16, 2018 3:38:56 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Difficulties running tracula
Hi again,
The latest version is
Hi,
I understand that bbregister can be used to register diffusion to T1 space
but I'm a lot less certain how this can be done in the reverse way, i.e.
registering the entire aparc+aseg file to diffusion B0? Do I also do:
bbregister
--s $subject --mov bo_brain.nii.gz --reg registration2b0.dat --dt
Hi M - You generally want to register the lower-res to the higher-res image. In
this case, that’s diffusion to T1. Check the diffusion processing tutorial on
the freesurfer wiki for how you can apply the inverse transform to the
aparc+aseg to get it into diffusion space.
Best,
a.y
From:
mailt
Hi Anastasia,
Thank you for the quick response. I did not preprocess my diffusion data
using dt_recon, so I suppose the way to do it would be to first run:
bbregister --s $subject --mov bo_brain.nii.gz --reg register2b0.dat --dti
--init-fsl
and then:
mri_vol2vol --mov lowb.nii --targ $subject/mri/
Yes, same idea as in the tutorial. It doesn’t matter that you didn’t use
dt_recon, if you had it would’ve just run bbregister for you.
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Michiko H." mailto:michiko...@gmail.com>>
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