2016-04-30 0:21 GMT+09:00 A-reum Min <naniyaah@gmail.com>:

hello experts

i solve the problem

always thanks your reply

2016-04-30 0:18 GMT+09:00 A-reum Min <naniyaah@gmail.com>:
hi experts

i have some problem using qdec

when i enter the qdec and then 'Generate Stats Data Tables'

show up these sentences

asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/HCP_sleep/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects con_1 con_2 con_3 con_4 con_5 con_6 con_7 con_8 con_9 con_10 con_11 con_12 con_13 con_14 con_15 con_16 con_17 con_18 con_19 con_20 con_21 con_22 con_23 con_24 con_25 con_26 con_27 con_28 con_29 con_30 con_31 con_32 con_33 con_34 con_35 con_36 con_37 con_38 con_39 con_40 con_41 con_42 con_43 con_44 dep_1 dep_2 dep_3 dep_4 dep_5 dep_6 dep_7 dep_8 dep_9 dep_10 dep_11 dep_12 dep_13 dep_14 dep_15 dep_16 dep_17 dep_18 dep_19 dep_20 dep_21 dep_22
SUBJECTS_DIR : /usr/local/freesurfer/subjects/HCP_sleep
Parsing the .stats files
ERROR: The stats file /usr/local/freesurfer/subjects/HCP_sleep/con_12/stats/aseg.stats is not found or is too small to be a valid statsfile
Use --skip flag to automatically skip bad stats files

and show up error box(fig1.jpg)

how can i to do.. plz help me.

my data information is

1 diagnosis discrete 2
1 Control
2 Deprivation
2 age continuous 0
Continuous Factors: Mean: StdDev:
------------------- ----- -------
age 28.167 3.280

Number of subjects: 66
Number of factors: 2 (1 discrete, 1 continuous)
Number of classes: 2
Number of regressors: 4

rh--Avg-thickness-age-Cor.mtx and lh-Avg-thickness-age-Cor.mtx contain (1 -1 0 0)

2016-03-05 0:36 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>:
for asymmetryc, see
https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi

On 03/04/2016 09:28 AM, 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 <naniyaah@gmail.com
> <mailto:naniyaah@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
> <http://en.citizendium.org/wiki/Brain_disorder>: While Alzheimer's
> disease <http://en.citizendium.org/wiki/Alzheimer%27s_disease>,
> even very early on, is characterized by pronounced cortical
> thinning^[4]
> <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Dickerson2009-4>
> , Williams syndrome
> <http://en.citizendium.org/wiki?title=Williams_syndrome&action=edit&redlink=1> patients
> exhibit an increase in cortical thickness of about 5-10% in some
> regions ^[5]
> <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Thompson2005-5>
> , and lissencephalic
> <http://en.citizendium.org/wiki/Lissencephalic> patients show
> drastic thickening, up to several centimetres in occipital
> regions^[6]
> <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Guerrini2006-6>
> . from wiki
>
> i wonder increased or reduced cortex depended on disorder?
>
> plz answer me
>
> 2016-02-06 0:27 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@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 <naniyaah@gmail.com
> <mailto:naniyaah@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
> <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@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
> <fischl@nmr.mgh.harvard.edu

> <mailto:fischl@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
> <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@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
> <naniyaah@gmail.com

> <mailto:naniyaah@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
>
> <greve@nmr.mgh.harvard.edu
> <mailto:greve@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
>
> <naniyaah@gmail.com <mailto:naniyaah@gmail.com>
> >

> <mailto:naniyaah@gmail.com

> <mailto:naniyaah@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
> >
> <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
>
>

> <mailto:fischl@nmr.mgh.harvard.edu

> <mailto:fischl@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/orig
> /
> 0
> 0
> 1-iscale.txt
> >
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale
> .
> 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 (
> >
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu

> <mailto: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.
>
>
>
>
> --
> *------------------------------------------------------------*
> *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 : n <mailto:esthekr@nate.com>aniyaah@gmail.com
> <mailto:aniyaah@gmail.com>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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