Re: [Freesurfer] bbregister aparc+aseg to diffusion space

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: > on behalf of "Michiko H."

Re: [Freesurfer] bbregister aparc+aseg to diffusion space

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

Re: [Freesurfer] bbregister aparc+aseg to diffusion space

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:

[Freesurfer] bbregister aparc+aseg to diffusion space

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

Re: [Freesurfer] Difficulties running tracula

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]

Re: [Freesurfer] Difficulties running tracula

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

Re: [Freesurfer] Freesurfer equivalent to fslmaths?

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

[Freesurfer] Post-Doc position at CAMH, Toronto

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

[Freesurfer] How would one run N4 bias corrected T1 and T2 images through FreeSurfer v6.0

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

Re: [Freesurfer] Difficulties running tracula

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

Re: [Freesurfer] Freesurfer equivalent to fslmaths?

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

Re: [Freesurfer] Freesurfer equivalent to fslmaths?

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

[Freesurfer] Freesurfer equivalent to fslmaths?

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

Re: [Freesurfer] Difficulties running tracula

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

Re: [Freesurfer] Difficulties running tracula

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

Re: [Freesurfer] Difficulties running tracula

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

Re: [Freesurfer] IndexError: list index out of range

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

Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

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

Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit

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

Re: [Freesurfer] Difficulties running tracula

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