Dear Bruce,
Thank you for answering my question. However, I'm still in a bit confused...
Therefore, I have one more question:
Would it then be best to choose a particular WM intensity value to rely upon
for adding control points or to rely upon sight?
Thank you very much!
Kind regards, Caroline Beelen
-----Oorspronkelijk bericht-----
Van: freesurfer-boun...@nmr.mgh.harvard.edu
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Verzonden: donderdag 18 mei 2017 18:00
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Freesurfer Digest, Vol 159, Issue 31
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Today's Topics:
1. Postdoctoral position in psychosis studies - Oslo, Norway
(Tiril Pedersen Gurholt)
2. manuel edits (Caroline Beelen)
3. Re: Question of longitudinal processing (jahanvi patel)
4. Re: Mean gray-white contrast for each ROI (Douglas N Greve)
5. Re: manuel edits (Bruce Fischl)
6. Re: Freesurfer white matter outer edge to volume (Douglas N Greve)
7. Re: mri_mcsim for individual subjects and references
{Disarmed} (Douglas N Greve)
8. Improving the brainmask.mgz using aseg.mgz for getting rid of
dura (Karteek Popuri)
9. Re: Improving the brainmask.mgz using aseg.mgz for getting
rid of dura (Douglas N Greve)
10. Re: Improving the brainmask.mgz using aseg.mgz for getting
rid of dura (Bruce Fischl)
----------------------------------------------------------------------
Message: 1
Date: Thu, 18 May 2017 12:04:49 +0000
From: Tiril Pedersen Gurholt <t.p.gurh...@medisin.uio.no>
Subject: [Freesurfer] Postdoctoral position in psychosis studies -
Oslo, Norway
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <9e8a081e-d148-4b08-b276-dd5b58c20...@medisin.uio.no>
Content-Type: text/plain; charset="utf-8"
Dear All,
At the NORMENT ? K.G. Jebsen Research Centre for Psychosis Research, a Centre
of Excellence, Institute of Clinical Medicine, University of Oslo, Oslo
University Hospital and Diakonhjemmet Hospital, Norway, there is a position
available as a postdoctoral student with employment at Diakonhjemmet hospital.
The research area is psychiatric neuroimaging with focus on obstetric
complications and the analysis of structural and functional, DTI and ASL MR
imaging datasets with regard to developmental trajectories and genetic,
environmental and phenotypic variation. Applicants should have a doctoral
degree (PhD) in psychiatry or a related medical discipline, neuroimaging,
computer science, bioinformatics, psychology, or equivalent. Applicants who
have handed in their dissertation for evaluation are also encouraged to apply,
caveat the dissertation is approved. Application deadline is June 15th, 2017.
For further information and to submit an application please see the website of
Diakonh jemmet H ospital, Oslo, Norway:
https://www.webcruiter.no/WcMain/advertviewpublic.aspx?oppdragsnr=3420277973&company_id=201412&Link_source_id=0&use_position_site_header=0&culture_id=NB-NO
Best regards,
Tiril Gurholt
---
Tiril Gurholt
Postdoctoral Fellow
Psychosis Research Centre, NORMENT
Institute of Clinical Medicine, University of Oslo, Norway
http://www.med.uio.no/norment/
[cid:image001.png@01D21DA0.544E82D0]
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Message: 2
Date: Thu, 18 May 2017 12:40:12 +0000
From: Caroline Beelen <caroline.bee...@kuleuven.be>
Subject: [Freesurfer] manuel edits
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<02267843e84c41ad9d0490fc5939f...@icts-s-exmbx25.luna.kuleuven.be>
Content-Type: text/plain; charset="us-ascii"
Dear FS team,
I have two questions regarding manuel editing. We were looking at inter-rater
reliability, but noticed it was not too high... However, during editing we used
different criteria. Therefore I would like to ask:
1. Does the order of pial correction, topological deficit, wm corrections
and control points editing matters? You seem to assume on your website for
instance that pial corrections would come before wm corrections/control points,
but is this necessarily the case?
2. When the wm intensity value is below 110, voxel inclusions might be needed. On
the website is written: "when you feel like there is wm underneath you can add
control points (...)". How to make a decision on this matter: based on sight or on
wm intensity values?
For instance, often the WM values are either 0 or 80 or above... Would it be
good to assume that wm intensity values above 80 are actually wm, regardless of
how it visually would look like? Likewise, would it be good to assume that
areas where it says the wm intensity value is 0, that these areas are actually
not wm, regardless of whether it might look like wm? So, basically, it is
correct to make your decision only based on wm intensity values?
Thank you for your reply.
Kind regards,
Caroline Beelen
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Message: 3
Date: Thu, 18 May 2017 14:45:30 +0200
From: jahanvi patel <jahanvipatel...@gmail.com>
Subject: Re: [Freesurfer] Question of longitudinal processing
To: Martin Reuter <mreu...@nmr.mgh.harvard.edu>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<cac0h5b4urb6gr1suotxqwpn0e0ou6dlukxg5rmxasqya+s8...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Martin,
Thanks a lot.
So it is uncorrected. Can one use the following cmd to do multiple comparison
correction?
mri_glmfit-sim \
--glmdir lh.testretest.thickness-pc1.fwhm15 \
--cache 4 neg \
--cwp 0.05\
--2spaces
I tried to run above cmd, it shows
ERROR: thresh = 4,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 done
Not sure if there is a bug or if my input is wrong.
Any suggestions is appreciated!
Best,
Jahanvi
On Thu, May 18, 2017 at 9:46 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu>
wrote:
Hi Jahanvi,
there should be a way to display the bar, but I don?t know how (others
will know)!
sig is not FDR corrected.
Best, Martin
On 18 May 2017, at 08:56, jahanvi patel <jahanvipatel...@gmail.com> wrote:
Hi Martin,
Thanks a lot for the reply. Is there a way to display the bar in
effect size?
And is this sig.mgh already statistically corrected? (FDR?)
Best,
Jahanvi
On Thu, May 18, 2017 at 1:55 AM, Martin Reuter <
mreu...@nmr.mgh.harvard.edu> wrote:
Hi Jahanvi,
I think red is positive (some people invert the colors, then
red=hot=dangerous ). But I think default is blue negative, red
positive, so there is an average increase in thickness. You should
also look at the effect size (gamma).
The p -values are in log 10 space, so 2 = 0.01 and 5 = 0.00001
Best, Martin
On 17 May 2017, at 22:17, jahanvi patel <jahanvipatel...@gmail.com>
wrote:
Hi Martin,
Thanks a lot. It had worked nicely.
I got one question about this following cmd
tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fw
hm15/osgm/sig.mgh
I got a red to yellow sig.mgh, does it mean I got a increased percent
thickness change (pc1)? and the color bar showing 2 to 5 means?
Best,
Jahanvi
On Sun, May 14, 2017 at 10:11 PM, Martin Reuter <
mreu...@nmr.mgh.harvard.edu> wrote:
Hi Jahanvi,
1. yes, you need to create this table to then perform the stats 2.
no, the format is as I described it below
fsid fsid-base
tp1_subA templatesubA
tp2_subA templatesubA
tp1_subB templatesubB
tp2_subB templatesubB
this is assuming that you called your base templatesubA and
templatesubB for the two subjects. It will automatically look in the
tp1_subA.long.templatesubA etc. directories.
Best, Martin
On 12 May 2017, at 16:55, jahanvi patel <jahanvipatel...@gmail.com>
wrote:
Hi Martin,
Do you mean by creating this long.testretest.qdec file, one can then
perform the stats for the longitudinal2StageModel?
So for a 2 timepoints analysis, eg. TP1 & TP2.
the long.testretest.qdec will be looking like this ?
fsid fsid-base
tp1_subA.long.TemplatesubA tp2_subA.long.TemplatesubA
tp1_subB.long.TemplatesubB tp2_subB.long.TemplatesubB
tp1_subC.long.TemplatesubC tp2_subC.long.TemplatesubC
.
.
.
Thanks,
Jahanvi
tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fw
hm15/osgm/sig.mgh
Hi Jahanvi,
long.testretest.qdec is a qdec table in the longitudional format
(with the fsid-base as the second column).
For test-retest (e.g. same session with subject removal), you
usually don't need a time column, that is why --generic-time is
specified. the qdec table would just look like
fsid fsid-base
me me_test
me me_retest
you you_test
you you_retest
...
Best, Martin
On 05/08/2017 04:10 PM, jahanvi patel wrote:
Hello list,
I have a simple question about the LongitudinalTwoStageModel
tutorials on freesurfer website.
It is from this link
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel
long_mris_slopes --qdec long.testretest.qdec \
--meas thickness \
--hemi lh \
--sd $SUBJECTS_DIR \
--do-pc1 --do-label \
--generic-time \
--fwhm 15 \
--qcache fsaverage \
--stack-pc1 lh.testretest.thickness-pc1.stack.mgh \
--isec-labels lh.testretest.fsaverage.cortex.label
My question is, what is the content of long.testretest.qdec ?
I understood till 1st stage was done, we got only one file which is
long.qdec.table.dat.
Could anyone help to clarify my question?
Thanks a lot
Jahanvi
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Message: 4
Date: Thu, 18 May 2017 10:33:07 -0400
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Mean gray-white contrast for each ROI
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <4fbc7b5a-06c8-da45-b5eb-82dee6a5d...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
You will want the "Mean" column. The value is
100*(W-G)
GWC = ---------
0.5*(W+G)
The area is the surface area of the label. The "SNR" is the spatial mean gwc
divided by the spatial stddev gwc, probably not very useful
On 05/17/2017 01:43 PM, Yaakub, Siti Nurbaya wrote:
Hi,
I read from a previous post that the "{lh,rh}.w-g.pct.stats files in
$SUBJECTS_DIR/subject/stats ? will have the mean gray-white contrast
for each ROI in the aparc."
I've looked at the lh.w-g.pct.stats file and am not sure which values
I should be looking at if I am interested in the ratio of grey to
white matter averaged over each of the ROIs? What are the area in mm2
and the SNR in this w-g context?
Thank you,
Siti
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