Re: [Freesurfer] [EXTERNAL] Freesurfer Digest, Vol 188, Issue 32

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Thank you

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of freesurfer-request@nmr.mgh.harvard.edu Sent: Monday, October 21, 2019 10:33 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Freesurfer Digest, Vol 188, Issue 32

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Today's Topics:

1. Re: FreeSurfer transforms (Bruce Fischl) 2. Re: Learning dti processing tutorial (Yendiki, Anastasia) 3. Re: can?t open an image in Freeview (fsbuild) 4. Re: aseg.stats format FreeSurfer 5 versus 6 (Tim Sch?fer) 5. Re: FSGD file formatting for Xhemi (Jose Graterol) 6. Re: FreeSurfer transforms (Vinny K) 7. tracula FA question - 2 cohorts/2 scanners (Krieger, Donald N.) 8. Incorrect/Negative Hippocampal subfields volumes (Jayachandra Raghava) 9. subcortical volume-based pet analysis (miracle ozzoude) 10. Re: imperfect segmentation in the occipital lobe in epilepsy patient (Diamond, Bram Ryder)

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Message: 1 Date: Sun, 20 Oct 2019 15:10:37 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer transforms To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.21.1910201509440.26358@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"

I see. Yes, a bunch of those are on our to-do list for segmentation but we don't have anything distributable at the moment. You are probably better off running some other nonlinear warping like ANTS or VoxelMorph to propagate the labels.

cheers Bruce On Sat, 19 Oct 2019, Vinny K wrote:

????????External Email - Use Caution????????

Hi Bruce, I'm looking at diencephalic and midbrain structures and their various subdivisions for application to tractography.? I used the thalamic nuclei segmentation feature in the development version of FreeSurfer to obtain labeling of individual thalamic nuclei that is run in addition to aseg, which has worked out great.? However, for other deep brain structures such as the subthalamic or pontine nuclei (e.g. pedunculopontine), to my knowledge, aseg does not parcellate these out; however, they are available MNI space.? FreeSurfer gives an excellent registration?of labeled atlas structures in patients with big ventricles, which I've had difficulty with using other registration tools.? I was wondering if there was a way that I could bring some of these labeled nuclei in MNI space into the patient's T1 space using FreeSurfer.

Thanks,

Vinny??

On Sat, Oct 19, 2019 at 12:16 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Vinny

  why do you need to brain structures from MNI space? Isn't the
  aseg
  sufficient? Or are there structures that are not in the aseg?

  cheers
  Bruce
  On Sat, 19 Oct
  2019, Vinny K wrote:

  >
  > ????????External Email - Use Caution????????
  >
  > Hi,
  > FreeSurfer does a great job in registering atlas structures to
  patients with
  > big ventricles.? I'd like to use the calculated FreeSurfer
  transforms in
  > bringing additional subcortical structures from MNI space
  (either MNI305 or
  > MNI2009b) into native T1 space.? Can you please advise on how
  to do this?
  >
  > Thanks,
  >
  > Vinny??
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu

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Message: 2 Date: Sun, 20 Oct 2019 19:23:06 +0000 From: "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu Subject: Re: [Freesurfer] Learning dti processing tutorial To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: BL0PR04MB4833D9194632CC48243F2F488A6E0@BL0PR04MB4833.namprd04.prod.outlook.com Content-Type: text/plain; charset="windows-1252"

Hi, you need to run recon-all on the T1, not on the diffusion scan. This will produce an anatomical segmentation of each subject based on the T1s, which TRACULA will then use to extract anatomical priors on white matter tracts, to aid tractography. When you run trac-all to do the actual tractography, then you run it on the diffusion scan. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Renew Andrade andraderenew@yahoo.com Sent: Friday, October 18, 2019 5:02:35 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Learning dti processing tutorial

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I am using a database of NITRC repository https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nitrc.org_projects_... . This images have a nifti file for 1000s/mm^2 and 2500s/mm^2. I don?t know if it is MPRAGE or not. Can you help me?

What is the input file that you are supplying? Often this happens when the input it a multi-echo MPRAGE. If so, you can run mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz then use mprage.mgz as the input to recon-all

On 10/12/2019 4:48 PM, Renew Andrade wrote:

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Dear freesurfer experts: I am trying to learn dti processing. For using Tracula it appears there is a need for running "recon-all -all -i -s? on every subject before starting to run Tracula. But there seems to be a problem. I have a Parkinson dwi images database and every subject gives me an error of the type ?input(s) cannot have multiple frames!?. I am a little bit stuck on this step. Is it a problem of the file as input? Am I putting the wrong file? Can it be done a recon-all analysis to a dwi image? With trackvis I can obtain the results without any problem. My doubt comes from FreeSurfer only and may be my little knowledge about it. Thanks for your help! Sincerely, Andrade.

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