Hi Doug,
Still no luck getting the script- the site does not load for some reason.
Any chance you might be able to paste it into the message body?
Thanks,
- Arkadiy
On Sun, Jun 19, 2016 at 12:00 PM, <freesurfer-requ...@nmr.mgh.harvard.edu>
wrote:
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more
specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: GLM_Fit Question (Douglas Greve)
2. Using Freesurfer commands in matlab (HARI GURAGAIN)
3. change the algorithm (N Saf)
4. Re: change the algorithm (Bruce Fischl)
5. Re: registering to fsaverage (Trisanna Sprung-Much)
6. Re: registering to fsaverage (Bruce Fischl)
----------------------------------------------------------------------
Message: 1
Date: Sat, 18 Jun 2016 23:54:18 +0200
From: Douglas Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] GLM_Fit Question
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5765c30a.5080...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
try now
On 6/16/16 11:50 PM, Arkadiy Maksimovskiy wrote:
> Hi Freesurfers,
>
> I am having a similar problem with the FSGD file as the user
indicated
> at this thread:
>
>
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html
>
> I am trying to access the script that Doug wrote in order to
fix it,
> however, the link to download the script does not seem to be
working.
> I was wondering if someone might be able to upload it again.
>
> Thank you in advance for your help,
>
> Arkadiy
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 2
Date: Sat, 18 Jun 2016 18:02:26 -0500
From: HARI GURAGAIN <nuclear.h...@gmail.com>
Subject: [Freesurfer] Using Freesurfer commands in matlab
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<cadp7hjx6qhmjov1gzmckdmg7vhma439wkqg81unyjgkzfjz...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Freesurfer,
I am using the new development version of freesurfer (
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev).
I am trying to call some of the freesurfer commands like:
mri_coreg or some
other. When I use the something like the following in Matlab:
command='/Applications/freesurfer/bin/mri_coreg'
and the below:
[status,cmdout]=system(command)
It is showing a weird error message like below:
###########################################
dyld: lazy symbol binding failed: Symbol not found:
___emutls_get_address
Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address
Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
###########################################
I really don't understand why this error is coming. I have seen
people have
used the mri_*** commands a lot of times in matlab but
unfortunately, it
shows the above error in my case.
Is it the error from Matlab, freesurfer, mac or something else?
Any help in solving this issue will be greatly appreciated.
Thank you.
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Message: 3
Date: Sun, 19 Jun 2016 12:06:56 +0430
From: N Saf <nali...@gmail.com>
Subject: [Freesurfer] change the algorithm
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<capmqmelhyw65v+yhsbxseksx-esbvw1t6mqa5dp9sps5n4l...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Freesurfer,
I wonder if it is possible to segment just one sub-cortical
structures like
hippocampus by changing the algorithm (e.g. according to spatial
prior
knowledge divided the image to some sub-images and do analysis
just on that
sub-image which we sure the hippocampus located)and by that
reducing the
processing time ? and another general question I have is that in
sub-cortical segmentation commands 1to12 commands of -all flag
which
parameters can I change to affect the outputs?
Sincerely,
Nazanin
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Message: 4
Date: Sun, 19 Jun 2016 10:51:58 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] change the algorithm
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1606191050540.7...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Nazanin
no, sorry, that isn't possible. Our accuracy is improved by the
fact that
we model all subcortical structures simultaneously.
As for your second question you need to be more specific. Are
you finding
some inaccuracies that you want to correct?
cheers
Bruce
On Sun, 19 Jun 2016, N Saf wrote:
> Dear Freesurfer,
>
> I wonder if it is possible to segment just one sub-cortical
structures like
> hippocampus by changing the algorithm (e.g. according to
spatial prior
> knowledge divided the image to some sub-images and do analysis
just on that
> sub-image which we sure the hippocampus located)and by that
reducing the
> processing time ? and another general question I have is that
in
> sub-cortical segmentation commands 1to12 commands of -all
flag? which
> parameters can I change to affect the outputs?
>
> Sincerely,
> Nazanin
>
> ?
>
>
------------------------------
Message: 5
Date: Sun, 19 Jun 2016 11:17:54 -0400
From: Trisanna Sprung-Much <trisanna.sprung-m...@mail.mcgill.ca>
Subject: Re: [Freesurfer] registering to fsaverage
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<cag+torurx1_5wjpo0qh4ebabi1wwqr-na0d8i76awb_fquw...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
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. Candidate
McGill 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. Candidate
> McGill 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. Candidate
>> McGill 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
>>>
>>
>>
>
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Message: 6
Date: Sun, 19 Jun 2016 11:22:41 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] registering to fsaverage
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1606191121510.7...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
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>
> >? ? ?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/
> >
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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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End of Freesurfer Digest, Vol 148, Issue 28
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