Re: [Freesurfer] Freesurfer Digest, Vol 147, Issue 29 - Freesurfer

19 May 2016


      Dag Jolijn,
Gegenereerd! En ik heb gezien dat nr 13136 wm_lh_g_temp_sup_plan_tempo ertussen staat! (output linux) :)
Groetjes, Caroline
-----Oorspronkelijk bericht-----
Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens freesurfer-request@nmr.mgh.harvard.edu
Verzonden: dinsdag 17 mei 2016 22:50
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Freesurfer Digest, Vol 147, Issue 29
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Today's Topics:
1. Re: 3T flag (Moeller, Sebastian)
   2. Re: FreeSurfer Validation and Longitudinal Analysis of WM
      Hyperintensities (Navena Rebecca Lingum)
   3. Re: ERROR: cannot unpack mosiacs without ASCII header
      (Douglas N Greve)
   4. Re: wm parcellation (Douglas N Greve)
   5. Re: Same coordinates for all labels (Douglas N Greve)
   6. Re: segfault using brainstem module from dev version
      (Martin Reuter)
   7. WM Hyperintensities (Martin Reuter)
   8. errors in wm and pial boundaries (Corinna Bauer)
   9. Re: errors in wm and pial boundaries (Bruce Fischl)
  10. Question on Yeo 2015 cognitive atlas (Josh Gray)
  11. Postdoctoral Position in Infant MRI Analysis at	UNC-Chapel
      Hill (gangli)
  12. Freesurfer (Limachia, Gaurang (NIH/NINDS) [F])
----------------------------------------------------------------------
Message: 1
Date: Tue, 17 May 2016 16:01:19 +0000
From: "Moeller, Sebastian" sebastian.moeller1@rwth-aachen.de
Subject: Re: [Freesurfer] 3T flag
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Message-ID: DAAC6E30-68D8-4C96-A658-1CD19D6A79A7@rwth-aachen.de
Content-Type: text/plain; charset="utf-8"
Hi Kasper,
...
On May 17, 2016, at 17:44 , Kasper Jessen kasper_j@cnsr.dk wrote:
Thanks for the answers :-)
Sebastian: What do you mean with "A somewhat wrong, but intuitive rationale is with array coils the loops are smaller and hence the coil sensitivity profiles as well and these modulate the intensity inhomogeneity. But again that is probably wrong?"
What is it that is probably wrong?
I would be amazed if that rationale was a truthful description of the full physical basis for the changes in inhomogeneities; and to be on the safe side (I never even discussed this with a physicist) I declare that it is incomplete and hence ?wrong?. The last thing I want is to spread half-baked information as ground truth?
Best Regards
    Sebastian
...
Best regards,
Kasper
2016-05-17 14:48 GMT+02:00 Moeller, Sebastian sebastian.moeller1@rwth-aachen.de:
Hi Kasper,
...
On May 17, 2016, at 10:05 , Kasper Jessen kasper_j@cnsr.dk wrote:
I would like to know the following:
a) what is the differences between the 3T Atlas (schwartz atlas) and the standard atlas?
b) what does the 3T-specific NU intensity correction parameters do differently than the standard?
    If I recall correctly this is based on http://www.sciencedirect.com/science/article/pii/S1053811909006703:

Improvement of brain segmentation accuracy by optimizing 
non-uniformity correction using N3
Type    Journal Article
Author  Weili Zheng
Author  Michael W. L. Chee
Author  Vitali Zagorodnov
URL     http://www.sciencedirect.com/science/article/pii/S1053811909006703
Volume  48
Issue   1
Pages   73-83
Publication     NeuroImage
ISSN    1053-8119
Date    October 15, 2009
Journal Abbr    NeuroImage
So most likely it reduces the N# smoothing distance from the default 
200 to 50
Here is the relevant part from recon-all (v5.3):
  if ($DoNuIntensityCor3T) then
    # params from Zheng, Chee, Zagorodnov 2009 NeuroImage paper
    # "Improvement of brain segmentation accuracy by optimizing
    # non-uniformity correction using N3"
    set NuIterations = 1;
    set cmd = ($cmd --proto-iters 1000 --distance 50)
  endif
A somewhat wrong, but intuitive rationale is with array coils the loops are smaller and hence the coil sensitivity profiles as well and these modulate the intensity inhomogeneity. But again that is probably wrong?
Best Regards
        Sebastian
...
Best
Kasper
2016-05-10 8:09 GMT+02:00 Kasper Jessen kasper_j@cnsr.dk:
Dear FreeSurfer group,
Our subject sample has been obtained on a 3 Tesla MR scanner. For this reason we used the -3T flag to enable the 3T-specific NU intensity correction parameters and usage of the special 3T atlas for Talairach alignment.
However, where can i find the documentation for the above?
Best regards,
Kasper
--
Kasper Jessen,
MD, PhD student
Center for neuropsychiatric Schizophrenia Research (CNSR) Mental 
Health Centre Glostrup Nordre Ringvej 29-67
2600 Glostrup
Tlf.: 24430136
E-mail: kasper_j@cnsr.dk eller kasper.jessen@regionh.dk 
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--
Kasper Jessen,
MD, PhD student
Center for neuropsychiatric Schizophrenia Research (CNSR) Mental 
Health Centre Glostrup Nordre Ringvej 29-67
2600 Glostrup
Tlf.: 24430136
E-mail: kasper_j@cnsr.dk eller kasper.jessen@regionh.dk 
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------------------------------
Message: 2
Date: Tue, 17 May 2016 16:37:18 +0000
From: Navena Rebecca Lingum nlingum@uwo.ca
Subject: Re: [Freesurfer] FreeSurfer Validation and Longitudinal
    Analysis of WM Hyperintensities
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Message-ID: 8950AD6C-3FCE-4AA1-AC22-67FEB8ADB675@uwo.ca
Content-Type: text/plain; charset="windows-1252"
Dear Martin,
Thank you kindly for your prompt response.
I am actually having difficulties with the delineation of White Matter Hyperintensities at a single time point. I apologize if my question is redundant and perhaps an answer to it is already mentioned elsewhere.
As it stands, I am finding it difficult to understand the exact ?pipeline? of commands necessary to perform this segmentation and accurate delineation of WMH. I have ran the recon -all command on my T1w images, but I suspect a proper segmentation of WMH would require a T2w Flair (which I have). How do I go about combining the preprocessing data produced by FreeSurfer with my T2w images to produce a WMH mask/volume/stats?
Any help on the matter is much appreciated!
Kindly,
Navena Lingum
On May 16, 2016, at 4:24 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Navena,
There is currently no dedicated stream for longitudinal WM abnormalities (in the sense of joint estimation and modeling). You can, however, make use of the longitudinal stream and it's increase reliability - e.g it is working in the same space across time, which should help get more reliable estimates.
Best, Martin
On 05/16/2016 01:47 PM, Navena Rebecca Lingum wrote:
Dear FreeSurfer experts,
My colleagues and I would like to use FreeSurfer to perform a longitudinal analysis of white matter hyperintensities. Is there an additional add-on for the software to perform this analysis or can this analysis be performed using the recon-all command?
Navena Lingum
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