try it with the noconform as the first argument. I think it will ignore it
at the end
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
> >
> >
> >
> >
> >
_______________________________________________
> > Freesurfer mailing
list
> > Freesurfer@nmr.mgh.harvard.edu
>
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> >
<mailto:Freesurfer@nmr.mgh.harvard.edu
>
<mailto: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.
> >
> >
> >
> >
> >
_______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
>
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>
<mailto:Freesurfer@nmr.mgh.harvard.edu
>
<mailto: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.
> >
> >
> >
> >
> >
_______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
>
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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>
> FileDrop:
https://gate.nmr.mgh.harvard.edu/filedrop2
>
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing:
>
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
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
FileDrop:
https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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.
_______________________________________________
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.
_______________________________________________
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.
