Re: [Freesurfer] reusing mri_surf2surf transformation

I would have thought that it would have crashed without the right files. Or does it go out of the container to get the files it needs? btw, you can use reprozip to see all the files that a process touches to know exactly what it needs

On 11/10/2016 04:10 PM, Chris Filo Gorgolewski wrote:

I found the problem. To save space I only included the surf/{l,r}h.white and surf/{l,r}h.white.reg files in the ICBM2009c_fs6 subejct folder (to save space in my container). After including everything the corregistration run under 10s.

Do you have some ideas which files are speeding up the process?

Best, Chris

On Thu, Nov 10, 2016 at 12:37 PM, Chris Filo Gorgolewski <chris.gorgolewski@gmail.com mailto:chris.gorgolewski@gmail.com> wrote:

There is only one frame in rh.sig.mgh file (see below). Most time
seems to be spent in calculating forward and reverse loops. Ideas?

root@36ddc1c5be86:/code# mri_info
/d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
Volume information for
/d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
          type: MGH
    dimensions: 163842 x 1 x 1
   voxel sizes: 1.000000, 1.000000, 1.000000
          type: FLOAT (3)
           fov: 163842.000
           dof: 0
        xstart: -81921.0, xend: 81921.0
        ystart: -0.5, yend: 0.5
        zstart: -0.5, zend: 0.5
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
angle: 0.00 degrees
       nframes: 1
       PhEncDir: UNKNOWN
 FieldStrength: 0.000000
ras xform present
    xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000,
c_r =     0.0000
              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000,
c_a =     0.0000
              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000,
c_s =     0.0000

talairach xfm :
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
 -1.0000   0.0000   0.0000 81921.0000
0.0000   0.0000   1.0000    -0.5000
0.0000  -1.0000   0.0000     0.5000
0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
 -1.0000  -0.0000  -0.0000 81921.0000
 -0.0000  -0.0000  -1.0000     0.5000
 -0.0000   1.0000  -0.0000     0.5000
 -0.0000  -0.0000  -0.0000     1.0000


On Thu, Nov 10, 2016 at 12:34 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    16min is a very long time. How many frames are in rh.sig.mgh?
    For a
    single frame it should only take 10 or 20 sec


    On 11/10/2016 03:25 PM, Chris Filo Gorgolewski wrote:
    > Thanks for a prompt reply. The command takes ~16 minutes per
    > hemisphere in my setting. Are those realistic numbers or is
    it longer
    > than it should take?
    >
    > mri_surf2surf --s fsaverage --hemi rh --sval
    > /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
    > --trgsubject ICBM2009c_fs6 --tval /tmp/out.mgh
    >
    > sysname  Linux
    > hostname 36ddc1c5be86
    > machine  x86_64
    > user     root
    > srcsubject = fsaverage
    > srcval     =
    /d/drive/workspace/brainbrowser/examples/models/rh.sig.mgh
    > srctype    =
    > trgsubject = ICBM2009c_fs6
    > trgval     = /tmp/out.mgh
    > trgtype    =
    > srcsurfreg = sphere.reg
    > trgsurfreg = sphere.reg
    > srchemi    = rh
    > trghemi    = rh
    > frame      = 0
    > fwhm-in    = 0
    > fwhm-out   = 0
    > label-src  = (null)
    > label-trg  = (null)
    > OKToRevFaceOrder  = 1
    > UseDualHemi = 0
    > Reading source surface reg
    > /opt/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
    > Loading source data
    > Reading target surface reg
    > /opt/freesurfer/subjects/ICBM2009c_fs6/surf/rh.sphere.reg
    > Done
    > Using surf2surf_nnfr()
    > Mapping Source Volume onto Source Subject Surface
    > surf2surf_nnfr: building source hash (res=16).
    > Surf2Surf: Forward Loop (157000)
    >
    > surf2surf_nnfr: building target hash (res=16).
    > Surf2Surf: Reverse Loop (163842)
    > Reverse Loop had 117731 hits
    > Surf2Surf: Dividing by number of hits (157000)
    > INFO: nSrcLost = 0
    > nTrg121 = 152424, nTrgMulti =  4576, MnTrgMultiHits = 26.7279
    > nSrc121 = 133857, nSrcLost =     0, nSrcMulti = 29985,
    MnSrcMultiHits
    > = 4.69815
    > Saving target data
    > Saving to /tmp/out.mgh
    >
    > real    16m25.129s
    > user    16m24.160s
    > sys     0m0.260s
    >
    > On Thu, Nov 10, 2016 at 11:40 AM, Douglas N Greve
    > <greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
    >
    >     Years ago I used to have code that would cache this
    transform, but we
    >     abandoned it because it would get out of synch whenever
    someone
    >     updated
    >     their recon, and, for ordinary apps, it does not take
    that much time.
    >
    >
    >     On 11/10/2016 02:13 PM, Chris Filo Gorgolewski wrote:
    >     > Thanks for a quick reply. I'm actually in a situation
    where I do not
    >     > have all of the overlays at the same time so I cannot
    >     concatenate them.
    >     >
    >     > To put more contexts: I am building surface support
    into neurovault.
    >     > When someone uploads a surface statistical map I want to
    >     automatically
    >     > calculate a projection of this map into MNI volume. To
    improve
    >     the MNI
    >     > volume surface mapping I have reconstructed the
    surface of the
    >     > 2009c_asym_nlin template. For every incoming map I am
    doing
    >     > fsaverage -> MNI2009c mri_surf2surf followed by
    mri_surf2vol.
    >     However,
    >     > the mri_surf2surf takes quite a bit of time to run and
    most of it is
    >     > spend on coregistration - which is always the same. If
    only I could
    >     > calculate the coregistration once and apply it to
    every incoming map
    >     > it would speed things up tremendously.
    >     >
    >     > Let me know if you have any ideas.
    >     >
    >     > Best,
    >     > Chris
    >     >
    >     > On Thu, Nov 10, 2016 at 10:26 AM, Douglas N Greve
    >     > <greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
    >     <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
    >  <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
    >     >
    >     >     You can use mri_concat to create a stack of
    overlays, then
    >     >     mri_surf2surf
    >     >     the entire stack, then split the stack.
    >     >
    >     >
    >     >     On 11/10/2016 12:28 AM, Chris Filo Gorgolewski wrote:
    >     >     > Hi,
    >     >     > I need to convert a big number of scalar surface
    maps from
    >     fsaverage
    >     >     > to one particular subject space. This means running
    >     mri_surf2surf
    >     >     > command many times. For each execution the same
    >     transformation is
    >     >     > calculated and then applied. Since estimating the
    >     transformation
    >     >     take
    >     >     > a substantial amount of time I was wondering if
    I could
    >     >     calculate the
    >     >     > transformation once and just apply it (which is
    a common
    >     thing in
    >     >     > volumetric registration). I perused the website
    and the
    >     command line
    >     >     > options, but I could not find anything. Is it
    possible to
    >     save and
    >     >     > reuse surface transformations?
    >     >     >
    >     >     > Best,
    >     >     > Chris
    >     >     >
    >     >     >
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