Hi Dr. FischlI 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 --noconform1 of 51: reading fsaverage_overlay_aalf_icbm-102_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram2 of 51: reading fsaverage_overlay_aalf_icbm-103_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram3 of 51: reading fsaverage_overlay_aalf_icbm-104_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram4 of 51: reading fsaverage_overlay_aalf_icbm-105_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram5 of 51: reading fsaverage_overlay_aalf_icbm-106_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram6 of 51: reading fsaverage_overlay_aalf_icbm-107_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram7 of 51: reading fsaverage_overlay_aalf_icbm-108_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram8 of 51: reading fsaverage_overlay_aalf_icbm-109_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram9 of 51: reading fsaverage_overlay_aalf_icbm-110_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram10 of 51: reading fsaverage_overlay_aalf_icbm-111_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram11 of 51: reading fsaverage_overlay_aalf_icbm-112_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram12 of 51: reading fsaverage_overlay_aalf_icbm-113_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram13 of 51: reading fsaverage_overlay_aalf_icbm-114_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram14 of 51: reading fsaverage_overlay_aalf_icbm-115_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram15 of 51: reading fsaverage_overlay_aalf_icbm-116_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram16 of 51: reading fsaverage_overlay_aalf_icbm-117_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram17 of 51: reading fsaverage_overlay_aalf_icbm-118_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram18 of 51: reading fsaverage_overlay_aalf_icbm-119_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram19 of 51: reading fsaverage_overlay_aalf_icbm-120_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram20 of 51: reading fsaverage_overlay_aalf_icbm-121_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram21 of 51: reading fsaverage_overlay_aalf_icbm-122_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram22 of 51: reading fsaverage_overlay_aalf_icbm-123_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram23 of 51: reading fsaverage_overlay_aalf_icbm-124_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram24 of 51: reading fsaverage_overlay_aalf_icbm-125_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram25 of 51: reading fsaverage_overlay_aalf_icbm-126_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram26 of 51: reading fsaverage_overlay_aalf_icbm-127_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram27 of 51: reading fsaverage_overlay_aalf_icbm-131_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram28 of 51: reading fsaverage_overlay_aalf_icbm-133_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram29 of 51: reading fsaverage_overlay_aalf_icbm-134_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram30 of 51: reading fsaverage_overlay_aalf_icbm-135_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram31 of 51: reading fsaverage_overlay_aalf_icbm-137_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram32 of 51: reading fsaverage_overlay_aalf_icbm-139_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram33 of 51: reading fsaverage_overlay_aalf_icbm-140_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram34 of 51: reading fsaverage_overlay_aalf_icbm-141_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram35 of 51: reading fsaverage_overlay_aalf_icbm-142_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram36 of 51: reading fsaverage_overlay_aalf_icbm-143_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram37 of 51: reading fsaverage_overlay_aalf_icbm-144_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram38 of 51: reading fsaverage_overlay_aalf_icbm-145_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram39 of 51: reading fsaverage_overlay_aalf_icbm-146_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram40 of 51: reading fsaverage_overlay_aalf_icbm-150_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram41 of 51: reading fsaverage_overlay_aalf_icbm-158_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram42 of 51: reading fsaverage_overlay_aalf_icbm-200_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram43 of 51: reading fsaverage_overlay_aalf_icbm-201_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram44 of 51: reading fsaverage_overlay_aalf_icbm-203_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram45 of 51: reading fsaverage_overlay_aalf_icbm-204_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram46 of 51: reading fsaverage_overlay_aalf_icbm-205_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram47 of 51: reading fsaverage_overlay_aalf_icbm-209_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram48 of 51: reading fsaverage_overlay_aalf_icbm-340_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram49 of 51: reading fsaverage_overlay_aalf_icbm-347_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram50 of 51: reading fsaverage_overlay_aalf_icbm-350_left.mgz...embedding and interpolating volumeMRIchangeType: Building histogram51 of 51: reading test.mgz...mghRead(/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsaverage_left/aalf_lh/test.mgz, -1): could not open filemri_average: MRIread(test.mgz) failed--Ph.D. CandidateMcGill UniversityIntegrated Program in NeurosciencePsychologyOn 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
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
> <greve@nmr.mgh.harvard.edu
<mailto:greve@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
> > <fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>
> <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@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
> > <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> > <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@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
> greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
> Bugs:
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>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop:
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>
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
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>
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>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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The information in this e-mail is intended only for the person to whom
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The information in this e-mail is intended only for the person to whom it is
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