hello experts

i solve the problem

always thanks your reply

2016-04-30 0:18 GMT+09:00 A-reum Min <naniy...@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 <gr...@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 <naniy...@gmail.com
>> > <mailto: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
>> >     <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 <fis...@nmr.mgh.harvard.edu
>> >     <mailto: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
>> >             <mailto: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
>> >             <mailto: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
>> >             <mailto: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
>> >             <mailto: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
>> >             <mailto: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
>> >             <mailto: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>
>> >                                                       >
>> >                         <mailto: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>
>> >
>> >
>> >                         <mailto: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/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:esth...@nate.com>aniy...@gmail.com
>> >     <mailto:aniy...@gmail.com>
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
>
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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
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