On Thu, Nov 10, 2016 at 12:37 PM, Chris Filo Gorgolewski <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> 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>> 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>>> 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
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>

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> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
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> --
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> MGH-NMR Center
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--
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
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