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_fsa
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_fsa
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
and
then apply this
> > same
registration to my
> >
surface overlays? Or am
I
missing something?
> >
> > thanks
very much!
> >
> >
Trisanna
> >
> >
> > --
> > Ph.D.
CandidateMcGill
University
> >
Integrated Program in
Neuroscience
> >
Psychology
> >
> >
> >
> >
> >
_______________________________________________
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
<tel:617-724-2358>
> Fax: 617-726-7422
<tel:617-726-7422>
>
> Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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>
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>
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>
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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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.
_______________________________________________
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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.