Hi Trisannawe need more information if you want us to help you. What does "very odd mean"? If you do it in .mgz do you get a different answer than in .mnc? If so, why not just compute them in .mgz and convert to .mnc at the end?
cheers Bruce On Mon, 27 Jun 2016, Trisanna Sprung-Much wrote:
any ideas?
Thanks!
Trisanna
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Wed, Jun 22, 2016 at 10:22 PM, Trisanna Sprung-Much
<trisanna.sprung-m...@mail.mcgill.ca> wrote:
thanks Bruce - I had found that option for my fsaverage maps and
it worked.
What about if I am importing probability maps formed as .mnc and
creating overlays from them? The percentages seem to be very odd for
min and max threshold.
Trisanna
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Trisanna
if you are using mri_average you can give it -p as the
first argument and it will compute a percent at the end
Bruce
On Wed, 22 Jun 2016, Trisanna Sprung-Much wrote:
Hi Bruce
Is there is a way to set the probability of an
overlay between 0 and 1?
Would this have to be done when creating the overlay
using mri_vol2surf?
thanks
Trisanna
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Trisanna
the binaries that take mandatory command-line
arguments (i.e.
without a -- or - in front of them) require
all options to be
given before the mandatory arguments
cheers
Bruce
On Mon, 20 Jun 2016, Trisanna Sprung-Much
wrote:
thanks, Bruce. Yes in the end through
trial and
error I tried "mri_average -noconform
input output"
and it worked. I was
surprised that I had to put the
-noconform first as
normally one can put the argument
anywhere in the
command.
Best
Trisanna
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Mon, Jun 20, 2016 at 9:27 AM, Bruce
Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
yes, your last file on the command
line should
be the output file (the average)
cheers
Bruce
On Mon, 20 Jun 2016, Trisanna
Sprung-Much
wrote:
As a follow-up, here is the
mri_info for one
of my overlays in the folder
and the output file that
mri_average seems to
create (if I don't specify an
output and it re-writes my last
file). The
dimensions are off:
Any ideas?
Trisanna
Tgtrisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_
f
sa
vee_left/aalf_lh$ mri_info
fsaverage_overlay_aalf_icbm-102_left.mgz
Volume information for
fsaverage_overlay_aalf_icbm-102_left.mgz
type: MGH
dimensions: 163842 x 1 x 1
voxel sizes: 1.0000, 1.0000,
1.0000
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
ras xform present
xform info: x_r = 1.0000,
y_r =
0.0000, z_r = 0.0000, c_r =
0.5000
: x_a = 0.0000,
y_a =
1.0000, z_a = 0.0000, c_a =
-17.5000
: x_s = 0.0000,
y_s =
0.0000, z_s = 1.0000, c_s =
18.5000
talairach xfm :
Orientation : RAS
Primary Slice Direction: axial
voxel to ras transform:
1.0000 0.0000
0.0000
-81920.5000
0.0000 1.0000
0.0000
-18.0000
0.0000 0.0000
1.0000
18.0000
0.0000 0.0000
0.0000
1.0000
voxel-to-ras determinant 1
ras to voxel transform:
1.0000 -0.0000
-0.0000
81920.5000
-0.0000 1.0000
-0.0000
18.0000
-0.0000 -0.0000
1.0000
-18.0000
0.0000 0.0000
0.0000
1.0000
trisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fs
a
verage_left/aalf_lh$ mri_info
fsaverage_overlay_aalf_icbm-350_left.mgz
Volume information for
fsaverage_overlay_aalf_icbm-350_left.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.0000, 1.0000,
1.0000
type: FLOAT (3)
fov: 256.000
dof: 0
xstart: -128.0, xend:
128.0
ystart: -128.0, yend:
128.0
zstart: -128.0, zend:
128.0
TR: 0.00 msec, TE:
0.00 msec, TI:
0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = -1.0000,
y_r =
0.0000, z_r = 0.0000, c_r =
0.5000
: x_a = 0.0000,
y_a =
0.0000, z_a = 1.0000, c_a =
-17.5000
: x_s = 0.0000,
y_s =
-1.0000, z_s = 0.0000, c_s =
18.5000
talairach xfm :
Orientation : LIA
Primary Slice Direction: coronal
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Mon, Jun 20, 2016 at 12:32 AM,
Trisanna
Sprung-Much
<trisanna.sprung-m...@mail.mcgill.ca>
wrote:
Hi Dr. Fischl
I ran the following mri_average and
consistently get
this message. It
seems to be trying to read my output as
one of the
input volumes. If I
don't specify an output it re-writes my
last file in
the input folder
and when I try to open this it doesn't
work at all.
What exactly does MRIchangeType mean?
(navigated to folder with all .mgz
volumes want to
average)
mri_average *.mgz test.mgz --noconform
1 of 51: reading
fsaverage_overlay_aalf_icbm-102_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
2 of 51: reading
fsaverage_overlay_aalf_icbm-103_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
3 of 51: reading
fsaverage_overlay_aalf_icbm-104_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
4 of 51: reading
fsaverage_overlay_aalf_icbm-105_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
5 of 51: reading
fsaverage_overlay_aalf_icbm-106_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
6 of 51: reading
fsaverage_overlay_aalf_icbm-107_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
7 of 51: reading
fsaverage_overlay_aalf_icbm-108_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
8 of 51: reading
fsaverage_overlay_aalf_icbm-109_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
9 of 51: reading
fsaverage_overlay_aalf_icbm-110_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
10 of 51: reading
fsaverage_overlay_aalf_icbm-111_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
11 of 51: reading
fsaverage_overlay_aalf_icbm-112_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
12 of 51: reading
fsaverage_overlay_aalf_icbm-113_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
13 of 51: reading
fsaverage_overlay_aalf_icbm-114_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
14 of 51: reading
fsaverage_overlay_aalf_icbm-115_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
15 of 51: reading
fsaverage_overlay_aalf_icbm-116_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
16 of 51: reading
fsaverage_overlay_aalf_icbm-117_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
17 of 51: reading
fsaverage_overlay_aalf_icbm-118_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
18 of 51: reading
fsaverage_overlay_aalf_icbm-119_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
19 of 51: reading
fsaverage_overlay_aalf_icbm-120_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
20 of 51: reading
fsaverage_overlay_aalf_icbm-121_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
21 of 51: reading
fsaverage_overlay_aalf_icbm-122_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
22 of 51: reading
fsaverage_overlay_aalf_icbm-123_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
23 of 51: reading
fsaverage_overlay_aalf_icbm-124_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
24 of 51: reading
fsaverage_overlay_aalf_icbm-125_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
25 of 51: reading
fsaverage_overlay_aalf_icbm-126_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
26 of 51: reading
fsaverage_overlay_aalf_icbm-127_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
27 of 51: reading
fsaverage_overlay_aalf_icbm-131_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
28 of 51: reading
fsaverage_overlay_aalf_icbm-133_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
29 of 51: reading
fsaverage_overlay_aalf_icbm-134_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
30 of 51: reading
fsaverage_overlay_aalf_icbm-135_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
31 of 51: reading
fsaverage_overlay_aalf_icbm-137_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
32 of 51: reading
fsaverage_overlay_aalf_icbm-139_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
33 of 51: reading
fsaverage_overlay_aalf_icbm-140_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
34 of 51: reading
fsaverage_overlay_aalf_icbm-141_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
35 of 51: reading
fsaverage_overlay_aalf_icbm-142_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
36 of 51: reading
fsaverage_overlay_aalf_icbm-143_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
37 of 51: reading
fsaverage_overlay_aalf_icbm-144_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
38 of 51: reading
fsaverage_overlay_aalf_icbm-145_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
39 of 51: reading
fsaverage_overlay_aalf_icbm-146_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
40 of 51: reading
fsaverage_overlay_aalf_icbm-150_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
41 of 51: reading
fsaverage_overlay_aalf_icbm-158_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
42 of 51: reading
fsaverage_overlay_aalf_icbm-200_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
43 of 51: reading
fsaverage_overlay_aalf_icbm-201_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
44 of 51: reading
fsaverage_overlay_aalf_icbm-203_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
45 of 51: reading
fsaverage_overlay_aalf_icbm-204_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
46 of 51: reading
fsaverage_overlay_aalf_icbm-205_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
47 of 51: reading
fsaverage_overlay_aalf_icbm-209_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
48 of 51: reading
fsaverage_overlay_aalf_icbm-340_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
49 of 51: reading
fsaverage_overlay_aalf_icbm-347_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
50 of 51: reading
fsaverage_overlay_aalf_icbm-350_left.mgz...
embedding and interpolating volume
MRIchangeType: Building histogram
51 of 51: reading test.mgz...
mghRead(/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsaverage_l
eft/aalf_lh/test.mgz, -1): could not
open file
mri_average: MRIread(test.mgz) failed
--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Sun, Jun 19, 2016 at 12:46 PM, Bruce
Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
no problem.
Bruce
On Sun, 19 Jun 2016, Trisanna
Sprung-Much
wrote:
thanks Dr. Fischl - I think
sometimes my
emails don't get sent out on
the
first try and so I resend -
don't mean
to spam
everyone.
Don't know how I missed the
mri_average
option
- I think I need vacation
too.
thanks and have a lovely
Sunday!
Trisanna
--
Ph.D. CandidateMcGill
University
Integrated Program in
Neuroscience
Psychology
On Sun, Jun 19, 2016 at
11:22 AM, Bruce
Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Trisanna
Doug is on vacation
and his
response
time is likely to be pretty
slow. If any emails go
unanswered
you
should repost them in a
week or two.
As for this, if you
overlays are
mapped
to fsaverage you can
just use mri_average
to average
them.
cheers
Bruce
On Sun, 19 Jun 2016,
Trisanna
Sprung-Much wrote:
Hi Doug
So all of my
overlays for
each
subject have been
registered to
fsaverage
using
mri_surf2surf. I am
now
wondering how I could
create an
average in
"fsaverage
space" using
these
overlays - I
understand that
mris_make_average_surface is
an
option but I cannot
seem to find
whether
this works for
overlays and
not
just surfaces
(white, pial). I
want to
take
each subject
overlay on
fsaverage
and average them
to get a
probability map.
thanks
--
Ph.D.
CandidateMcGill
University
Integrated
Program in
Neuroscience
Psychology
On Fri, Jun 17,
2016 at 5:48
PM,
Trisanna
Sprung-Much
<trisanna.sprung-m...@mail.mcgill.ca>
wrote:
Hi Doug
So all of my
sulci for each
subject have been
registered to
fsaverage
using
mri_surf2surf. I am
now
wondering how I could
create an
average
of a sulcus
using these
overlays -
I understand that
mris_make_average_surface is
an
option but I cannot
seem to find
whether this
works for
overlays
and not just
surfaces (white,
pial). I
want to take
each subject
overlay
on fsaverage and
average them to
get
a probability
map for a
single
sulcus.
thanks
Trisanna
--
Ph.D.
CandidateMcGill
University
Integrated
Program in
Neuroscience
Psychology
On Wed, Jun 15,
2016 at 6:25
PM,
Trisanna
Sprung-Much
<trisanna.sprung-m...@mail.mcgill.ca>
wrote:
worked
beautifully.
Thank
you!
--
Ph.D.
CandidateMcGill
University
Integrated
Program in
Neuroscience
Psychology
On Wed, Jun 15,
2016 at 4:41
PM,
Douglas N Greve
<gr...@nmr.mgh.harvard.edu>
wrote:
Try
surf2surf with
--mapmethod nnf
On
06/15/2016 04:25
PM,
Trisanna Sprung-Much
wrote:
> Hi Doug
- yes they
do
actually, I was quite
pleased. I
did some
trials
> with
other subjects
and
the mri_vol2surf all
looks
good. Very
similar
> to what
I had in our
in-house software.
>
> Would
things be
better if
I were to isolate
each
sulcus as
a .label
> and then
try the
mri_label2label? Someone
suggested
perhaps the
> colours
are
overlapping
with the overlay....
>
> --
> Ph.D.
Candidate
> McGill
University
>
Integrated Program
in
Neuroscience
>
Psychology
>
>
> On Wed,
Jun 15, 2016
at
4:10 PM, Douglas N
Greve
>
<gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
>
> The
problem is
probably that the
vol2surf
command
did not
properly
>
sample the
labels onto
the surface. Do
the
labels on
subject
00350
>
surfaces look
ok?
>
> On
06/15/2016
04:00
PM, Trisanna
Sprung-Much
wrote:
> >
thanks Dr.
Fischl
> >
> > So
the command
seems
to have worked! I
have
copied
what ran in my
> >
terminal. When
I
open the test.mgz
overlay
on the
fsaverage pial
> >
surface,
things look
ok but a bit
funny. I
am
wondering if there
is
> >
anything I can
do to
the mri_surf2surf
command to
improve the
> >
registration
to
fsaverage? *See my
snapshots
attached.*
> >
> >
trisanna@kaplan:~$
mri_surf2surf
--srcsubject 00350
--sval
> >
/data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> >
--trgsubject
fsaverage --tval test.mgz
--hemi lh
> >
srcsubject =
00350
> >
srcval =
>
/data-01/trisanna/freesurfer/00350/surfaceoverlay_left.mgz
> >
srctype =
> >
trgsubject =
fsaverage
> >
trgval =
test.mgz
> >
trgtype =
> >
srcsurfreg =
sphere.reg
> >
trgsurfreg =
sphere.reg
> >
srchemi =
lh
> >
trghemi =
lh
> >
frame = 0
> >
fwhm-in = 0
> >
fwhm-out = 0
> >
label-src =
(null)
> >
label-trg =
(null)
> >
OKToRevFaceOrder =
1
> >
Reading source
surface reg
> >
/data-01/trisanna/freesurfer/00350/surf/lh.sphere.reg
> >
Loading source
data
> >
Reading target
surface reg
> >
/data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg
> >
Done
> >
Mapping Source
Volume onto Source
Subject
Surface
> >
surf2surf_nnfr:
building source hash
(res=16).
> >
Surf2Surf:
Forward
Loop (163842)
> >
> >
surf2surf_nnfr:
building target hash
(res=16).
> >
Surf2Surf:
Reverse
Loop (166912)
> >
Reverse Loop
had
41306 hits
> >
Surf2Surf:
Dividing
by number of hits
(163842)
> >
INFO: nSrcLost
= 0
> >
nTrg121 =
132490,
nTrgMulti = 31352,
MnTrgMultiHits =
2.31749
> >
nSrc121 =
137180,
nSrcLost = 0,
nSrcMulti =
29732,
MnSrcMultiHits
=
> >
2.28602
> >
Saving target
data
> >
Saving to
test.mgz
> >
> >
best
> >
> >
Trisanna
> >
> > --
> >
Ph.D.
Candidate
> >
McGill
University
> >
Integrated
Program
in Neuroscience
> >
Psychology
> >
> >
> > On
Wed, Jun
15, 2016
at 12:13 PM,
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>>>
wrote:
> >
> > Hi
Trisanna
> >
> > you
would only
use
those options of if
you
were
transforming
> a surface
> >
Bruce
> >
> >
> > On
Wed, 15 Jun
2016,
Trisanna
Sprung-Much
wrote:
> >
> >
thanks Dr.
Fischl
> >
> >
I assume
that for
surface overlays
one
cannot specify
> >
--sval-xyz
and
--tval-xyz or the
command
will treat the
> input
> >
as a surface
> >
itself?
> >
> >
best
> >
> >
Trisanna
> >
> >
> >
> >
> >
--
> >
Ph.D.
CandidateMcGill University
> >
Integrated
Program
in Neuroscience
> >
Psychology
> >
> >
> >
On Wed, Jun
15,
2016 at 11:11 AM,
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>>>
wrote:
> >
Hi
Trisanna
> >
> >
you
don't
need to inflate the
overlays. They
can just
> >
use the
existing
surface-based
(sphere.reg)
registration.
> >
> >
cheers
> >
Bruce
> >
On
Wed, 15
Jun 2016, Trisanna
Sprung-Much
wrote:
> >
> >
Hi
there
> >
So I
have sulcal labels
from
another software
> >
(.mnc
format) from
which I am trying
to
generate some
> >
probability maps. I was
able
> >
to
convert the .mnc to
.mgz
surface overlay
> using
> >
mri_vol2surf
for
my MRIs after
running all
MRIs in
> >
recon-all. So, now I
have
> >
all my
painted voxels as
surface
overlays, as I
> >
was
instructed to
do a few months
ago.
> >
> >
I was
told that the next
step
would be to use
> >
mri_surf2surf to
resample the
overlays to
fsaverage.
> >
> >
I am a
bit confused as I
would
think that
> the next
> >
step would
be to
take the surface
overlays
and
> >
inflate them before I
register
> >
them
to fsaverage. I see
that
when recon-all
> runs,
> >
it computes
the
registration of the
MRI
surface to
> >
fsaverage and saves it
as
> >
sphere.reg. Is there a
way I
can inflate my
> >
surface
overlays
in a similar manner
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_______________________________________________ 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.
