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/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 (
>>>                               >
>>>
>>>
>>>
>>>  /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
>>>                               >             )
>>>                               >                       to      TP
>>>             1 (
>>>                               >
>>>
>>>
>>>
>>>  /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
>>>                               >             )
>>>                               >
>>>                               >                    -- Original :
>>>             (0.4688,
>>>                         0.4688,
>>>                               0.800001) mm size
>>>                               >             and (512, 512, 244)
>>>                               >             voxels.
>>>                               >                    -- Resampled:
>>>             (0.4688,
>>>                         0.4688,
>>>                               0.4688) mm size and
>>>                               >             (512, 512, 417)
>>>                               >             voxels.
>>>                               >                    -- Reslicing
>>>             using cubic
>>>                         bspline
>>>                               >             MRItoBSpline degree
>>>             3
>>>                               >                    -- Original :
>>>             (0.4688,
>>>                         0.4688,
>>>                               0.800001) mm size
>>>                               >             and (512, 512, 244)
>>>                               >             voxels.
>>>                               >                    -- Resampled:
>>>             (0.4688,
>>>                         0.4688,
>>>                               0.4688) mm size and
>>>                               >             (512, 512, 417)
>>>                               >             voxels.
>>>                               >                    -- Reslicing
>>>             using cubic
>>>                         bspline
>>>                               >             MRItoBSpline degree
>>>             3
>>>                               >
>>>                               >                - Max Resolution
>>>             used: 3
>>>                               >                  -- gpS ( 64 ,
>>>             64 , 52 )
>>>                               >                  -- gpT ( 64 ,
>>>             64 , 52 )
>>>                               >                - running loop to
>>>             estimate
>>>                         saturation
>>>                               parameter:
>>>                               >               Sigma too small: 0
>>>             (identical
>>>                         images?)
>>>                               >               Sigma too small: 0
>>>             (identical
>>>                         images?)
>>>                               >               Sigma too small: 0
>>>             (identical
>>>                         images?)
>>>                               >               Sigma too small: 0
>>>             (identical
>>>                         images?)
>>>                               >               Sigma too small: 0
>>>             (identical
>>>                         images?)
>>>                               >               Sigma too small: 0
>>>             (identical
>>>                         images?)
>>>                               >               Sigma too small: 0
>>>             (identical
>>>                         images?)
>>>                               >               Sigma too small: 0
>>>             (identical
>>>                         images?)
>>>                               >               Sigma too small: 0
>>>             (identical
>>>                         images?)
>>>                               >               Sigma too small: 0
>>>             (identical
>>>                         images?)
>>>                               >             Killed
>>>                               >             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
>>>                               >
>>>                               >             recon-all -s sub002
>>>             exited with
>>>                         ERRORS at
>>>                               Thu Nov  5
>>>                               >             02:37:57 PST 2015
>>>                               >
>>>                               >             For more details,
>>>             see the log
>>>                         file
>>>                               >
>>>
>>>
>>>
>>>  /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log
>>>                               >             To report a problem,
>>>             see
>>>                               >
>>>
>>>
>>>              http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>                               >
>>>                               >
>>>                               >             2015-10-19 11:05
>>>             GMT+09:00
>>>                         A-reum Min
>>>                               <naniy...@gmail.com
>>>                         >
>>>              <mailto:naniy...@gmail.com>>:
>>>                         >                   hello experts.
>>>                         >             i have a question to
>>>             you..
>>>                         >
>>>                         >             i'm doing recon-all stage,
>>>             but errors
>>>                         show up like
>>>                         this
>>>                         >
>>>                         >
>>>                         >
>>>                         >
>>>                         >
>>>              ects/OSA/14/subj014/mri/orig/002.mgz
>>>                         --average 1
>>>                         --template
>>>                         >
>>>
>>>              /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz
>>>                         >             --satit
>>>                         >             --inittp 1 --fixtp --noit
>>>             --iscale
>>>                         --iscaleout
>>>                         >
>>>
>>>
>>>  /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt
>>>                         >
>>>
>>>
>>>  /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt
>>>                         >             --subsample 200 --lta
>>>                         >
>>>
>>>
>>>  /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta
>>>                         >
>>>
>>>
>>>  /usr/local/freesurfer/subjects/OSA/14/subj014/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/14/subj014/mri/orig/001.mgz
>>>                         >             as
>>>                         >             movable/source volume.
>>>                         >             --mov: Using
>>>                         >
>>>
>>>
>>>  /usr/local/freesurfer/subjects/OSA/14/subj014/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/14/subj014/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/14/subj014/mri/orig/001.mgz'...
>>>                         >             converting source
>>>                         >
>>>
>>>
>>>  '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
>>>                         >             to
>>>                         >             bspline ...
>>>                         >             MRItoBSpline degree 3
>>>                         >             reading source
>>>                         >
>>>
>>>
>>>  '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
>>>                         >             converting source
>>>                         >
>>>
>>>
>>>  '/usr/local/freesurfer/subjects/OSA/14/subj014/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 (
>>>                         >
>>>
>>>
>>>  /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
>>>                         >             )
>>>                         >                       to      TP 1 (
>>>                         >
>>>
>>>
>>>  /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
>>>                         >             )
>>>                         >
>>>                         >                    -- Original :
>>>             (0.4688, 0.4688,
>>>                         0.800001) mm
>>>                         size
>>>                         >             and (512, 512,
>>>                         >             244) voxels.
>>>                         >                    -- Resampled:
>>>             (0.4688, 0.4688,
>>>                         0.4688) mm
>>>                         size and
>>>                         >             (512, 512,
>>>                         >             417) voxels.
>>>                         >                    -- Reslicing using
>>>             cubic
>>>                         bspline
>>>                         >             MRItoBSpline degree 3
>>>                         >                    -- Original :
>>>             (0.4688, 0.4688,
>>>                         0.800001) mm
>>>                         size
>>>                         >             and (512, 512,
>>>                         >             244) voxels.
>>>                         >                    -- Resampled:
>>>             (0.4688, 0.4688,
>>>                         0.4688) mm
>>>                         size and
>>>                         >             (512, 512,
>>>                         >             417) voxels.
>>
>>
>> _______________________________________________
>> 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.
>>
>>
>
>
> --
> *------------------------------------------------------------*
> *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 <esth...@nate.com>aniy...@gmail.com
>



-- 
*------------------------------------------------------------*
*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 <esth...@nate.com>aniy...@gmail.com
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