Ph.D. Candidate

McGill University

Integrated Program in Neuroscience

Psychology

On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Trisanna

what commands did you use to generate the volumetric probability map?

Bruce

On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:

Hi Bruce
So, when I take a probability map formed using linear volumetric
registration with minc tools and saved as .mnc and convert it to an
overlay.mgz and open it in Freeview, the probability seems to be out of 255
(See the image attached). This is different from my Freesurfer generated
probability maps where I use -p in the mri_average command.

Is there a way to change these probability values that are displaying from
1-255?

many thanks

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology

On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
Hi Trisanna

we 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-much@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
<fischl@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
<fischl@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
<fischl@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_f
s
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-much@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
<fischl@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

<fischl@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-much@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-much@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

<greve@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

...

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