On Fri, 4 Mar 2016, A-reum Min wrote:
hello experts
i have some question to you
Question 1.
i want to compare two groups(patients group VS control groups) for cortical
thickness asymmetry.
so.. am i using a lh.thickness.fsaverage.mgh and
rh.thickness.fsaverage.mgh for each group subjects right..?
Question 2.
Left hemisphere whole vertices were extracted using a matlab. ( i read
lh.thickness.fsaverage.mgh)
i was wondering why vertex# 9(cortical thickness) value is zero? (fig1.png)
what is that mean? plz answer me.
2016-02-13 5:19 GMT+09:00 A-reum Min <naniy...@gmail.com>:
hello experts
i have some question to you
What is the meaning about cortical thickness alteration (increase or
decrease)
a few days ago i read these sentences
Deviations from these patterns can be used as diagnostic indicators
for brain disorders: While Alzheimer's disease, even very early on, is
characterized by pronounced cortical thinning[4], Williams
syndrome patients exhibit an increase in cortical thickness of about
5-10% in some regions [5], and lissencephalic patients show drastic
thickening, up to several centimetres in occipital regions[6]. from
wiki
i wonder increased or reduced cortex depended on disorder?
plz answer me
2016-02-06 0:27 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
Hi A-reum
we use average Euclidean distance from gray to white and
visa-versa. There are other (variational) techniques that
we have messed around with, but none of our experiments
have shown that they are any better, so we have stuck with
the simplest thing.
cheers
Bruce
On Fri, 5 Feb 2016, A-reum Min wrote:
hello experts
i have some question to you
What method do you use when measuring the cortical
thickness?
(ex. Euclidean distance of a Danielsson Distance Map
or 3D Eikonal
equation?)
plz answer me.
2016-01-17 0:53 GMT+09:00 A-reum Min
<naniy...@gmail.com>:
Thank you for u r answer.
I have some question to you.
i compared two groups(patients VS control)
How can i extract the total vertices(ex.#1 vertex :
cortical thickness
value) to 1 subject(patient) and average of patients
?
I want to compared asymmetry of brain
(lateralization). So, i really
necessary above value(cortical thickness value of
vertex).
plz answer me.
Thank you.
2016-01-17 0:22 GMT+09:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi Areum
every brain will have a somewhat different
number of
vertices depending on size and geometry. If
you want them
to be comparable you need to map them into the
fsaverage
space using e.g. the -qcache switch to
recon-all (or
mri_surf2surf directly if you prefer).
cheers
Bruce
On Sat, 16 Jan 2016, A-reum Min wrote:
Hello expert.
I'm Areum.
I have some question to you.
A weeks ago, i compared two groups (OSA
patients VS control) and then the
number of vertices were confirmed.
Each group has the same number of
vertices.(176416) -experiment 1.
And yesterday, i compared two
groups(partial
sleep deprivation:PSD VS
control) and then the number of vertices
were
confirmed.
Each group has the same number of
vertices(169548) -experiment 2.
1) Why isn't the same number of total
vertices? is it related rain size?
2) How can i extract the number of total
vertices(ex.#1 vertex : cortical
thickness value) to 1 subject(PSD) and
average
of PSD ?
I want to compared asymmetry of brain
(lateralization). So, i really
necessary above value(cortical thickness
value
of vertex).
plz answer me.
Thank you.
2016-01-07 3:52 GMT+09:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi A-reum
did you talk to the Wash U group?
If you
have nifti files they
can be processed using recon-all
(i.e.
recon-all -i <full path
to nifti file> -s <subject id> -sd
<directory to contain all
subjects> -all)
cheers
Bruce
On Tue, 29 Dec 2015, A-reum Min
wrote:
hello experts!my name is
areum.
i have some question to
you.i have
never seen before
these NIFTI
format(fig.1.png)
I want to see these data
subjects's cortical
thickness using qdec.
how can i to do? plz answer
me
2015-12-25 2:16 GMT+09:00
Bruce
Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi A-reum
you should probably
ask the
Wash U HCP group.
I'll cc Matt
Glasser who might be
able to
answer your
question
cheers
Bruce
On Thu, 24 Dec 2015,
A-reum
Min wrote:
hello experts!my
name
is areum.
i have some
question
to you.
a few days ago i
was
down load HCP(human
connectom
project) data.
but.. how can i
use
these HCP format.
i have never
seen
before these
format(fig.1.png)
I want to see
HCP data
subjects's
cortical thickness
using qdec.
how can i to
do?
plz answer me
2015-11-10 7:49
GMT+09:00 A-reum Min
<naniy...@gmail.com>:
Hello
experts!
I have some
question
to you..
I don't need to
show
up so small blue
regions(fig.1
blue region)
How can i
control
these?
2015-11-10 7:41
GMT+09:00 Douglas N
Greve
<gr...@nmr.mgh.harvard.edu>:
Hi, please
create a new thread
since this is a
new topic.
Also, I
don't
understand
your
question so please
elaborate.
On
11/09/2015
05:34 AM, A-reum Min
wrote:
> Hello
experts!
>
> i have
some
question to you..
>
> How can
i
control the cluster
size?
>
> My
cluster
threshold is 1.
>
> then,
too many
blue regions (as
shown
fig.1).
>
> so, i
want to
control cluster
threshold 1-->
cluster
threshold
5.
>
>
2015-11-08
20:44 GMT+09:00
A-reum Min
<naniy...@gmail.com
>
<mailto:naniy...@gmail.com>>:
>
>
Hello
bruce!
>
> I
solve
the problem for your
answer.
>
>
And.. i
have some question
to you..
>
> How
can i
control the
cluster size?
>
> My
cluster
threshold is 1.
>
>
then, too
many blue regions
(as shown
fig.1).
>
> so,
i want
to control
cluster threshold
1--> cluster
threshold
5.
>
> How
can i
to do?
>
>
>
>
>
>
2015-11-05
22:22 GMT+09:00
Bruce Fischl
>
<fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>>:
>
>
are
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
>
and
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
>
images
from *different*
series or
from the
*same*
series?
If
>
they
are in the same
series than
that explains
what is
>
happening. You should
only give
recon-all a
single
file from
>
any
one acquisition - it
will figure
out the
rest of
the
files
>
that
are part of it.
>
>
cheers
>
Bruce
>
>
>
On
Thu, 5 Nov 2015,
A-reum Min
wrote:
>
>
hello experts.
>
i
have some question
to you...
>
>
when i enter the
recon-all -i
/paht~
>
>
error showed up....
like below
one..
>
>
how can i to fix it?
>
>
[areum@localhost
0165766_1]#
recon-all -i
>
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
-i
>
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
>
-all -s sub002
>
Subject Stamp:
>
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>
Current Stamp:
>
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>
INFO: SUBJECTS_DIR
is
>
/usr/local/freesurfer/subjects/OSA/0165766_1
>
Actual
FREESURFER_HOME
/usr/local/freesurfer
>
Linux
localhost.localdomain
2.6.32-504.el6.x86_64 #1 SMP
>
Wed Oct 15 04:27:16
>
UTC 2014 x86_64
x86_64 x86_64
GNU/Linux
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002
>
>
mri_convert
>
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
>
>
>
mri_convert
>
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
>
>
$Id: mri_convert.c,v
1.179.2.7
2012/09/05
21:55:16
mreuter
>
Exp $
>
reading from
>
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm...
>
Starting
DICOMRead2()
>
dcmfile =
>
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
>
dcmdir =
/usr/local/freesurfer/subjects/OSA/0165766_1
>
Ref Series No = 3
>
Found 247 files,
checking for
dicoms
>
Found 244 dicom
files in series.
>
First Sorting
>
Computing Slice
Direction
>
Vs: -0.8 0 0
>
Vs: -1 0 0
>
Second Sorting
>
Counting frames
>
nframes = 1
>
nslices = 244
>
ndcmfiles = 244
>
PE
Dir = ROW (dicom
read)
>
TransferSyntaxUID:
--1.2.840.10008.1.2.1--
>
Loading pixel data
>
TR=7.70, TE=3.37,
TI=400.00,
flip
angle=12.00
>
i_ras = (0, -1, 0)
>
j_ras = (0, 0, -1)
>
k_ras = (1, -0, 0)
>
writing to
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz...
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002
>
>
mri_convert
>
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
>
>
>
mri_convert
>
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
>
>
$Id: mri_convert.c,v
1.179.2.7
2012/09/05
21:55:16
mreuter
>
Exp $
>
reading from
>
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm...
>
Starting
DICOMRead2()
>
dcmfile =
>
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
>
dcmdir =
/usr/local/freesurfer/subjects/OSA/0165766_1
>
Ref Series No = 3
>
Found 247 files,
checking for
dicoms
>
Found 244 dicom
files in series.
>
First Sorting
>
Computing Slice
Direction
>
Vs: -0.8 0 0
>
Vs: -1 0 0
>
Second Sorting
>
Counting frames
>
nframes = 1
>
nslices = 244
>
ndcmfiles = 244
>
PE
Dir = ROW (dicom
read)
>
TransferSyntaxUID:
--1.2.840.10008.1.2.1--
>
Loading pixel data
>
TR=7.70, TE=3.37,
TI=400.00,
flip
angle=12.00
>
i_ras = (0, -1, 0)
>
j_ras = (0, 0, -1)
>
k_ras = (1, -0, 0)
>
writing to
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz...
>
#--------------------------------------------
>
#@# MotionCor Thu
Nov 5
02:27:17 PST
2015
>
Found 2 runs
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
>
Checking for
(invalid)
multi-frame
inputs...
>
Checking for
(invalid)
multi-frame
inputs...
>
#-----------------------------------------------
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002
>
>
mri_robust_template
--mov
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
>
--average 1
--template
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
>
--satit
>
--inittp 1 --fixtp
--noit
--iscale
>
--iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/ori
g
/
0
0
1-iscale.txt
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscal
e
.
t
x
t
>
--subsample 200
--lta
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
>
>
>
$Id:
mri_robust_template.cpp,v
1.37.2.2
2012/10/10
>
19:59:06 mreuter Exp
$
>
>
--mov: Using
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
>
as
>
movable/source
volume.
>
--mov: Using
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
>
as
>
movable/source
volume.
>
Total: 2 input
volumes
>
--average: Using
method 1 for
template
computation.
>
--template: Using
>
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
>
as
>
template output
volume.
>
--satit: Will
estimate SAT
iteratively!
>
--inittp: Using TP 1
as target
for
initialization
>
--fixtp: Will map
everything to
init TP!
>
--noit: Will output
only first
template (no
iterations)!
>
--iscale: Enableing
intensity
scaling!
>
--iscaleout: Will
perform
intensity
scaling
and output
results
>
--subsample: Will
subsample if
size is
larger
than 200
on
>
all axes!
>
--lta: Will output
LTA
transforms
>
reading source
>
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'...
>
converting source
>
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'
>
to
>
bspline ...
>
MRItoBSpline degree
3
>
reading source
>
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'...
>
converting source
>
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'
>
to
>
bspline ...
>
MRItoBSpline degree
3
>
>
MultiRegistration::initializing
Xforms (init
1 , maxres
0
>
,
iterate 5 ,
>
epsit 0.01 ) :
>
>
[init]
=========================
TP 2 to TP
1
>
==============================
>
Register TP
2 (
>
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The information in this e-mail is intended only for the person
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--
------------------------------------------------------------
Areum Min
Medical Image Processing Lab.
Department of Biomedical Engineering, Yonsei Univ.
218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon,
Korea
Office : +82-33-760-2499
Mobile : +82-10-3428-0608
E-Mail : naniy...@gmail.com
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
