[Freesurfer] mris_expand
Hi, how can I tell mris_expand to expand the surface by a fixed distance rather than by a fraction of the thickness? Thanks, Lars ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] clusterwise correction for multiple comparison
HI! i have a question regarding multiple comparion correction in qdec. can i use a clusterwise correction? i found the following script for glm: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg \ --overwrite but i dont understand how i should apply it in qdec. what shoudl i use as input directory? rosa -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_expand
Hi Lars, that is what it does by default, unless you give it the -thickness flag. cheers, Bruce On Fri, 24 Jul 2009, Lars Tjelta Westlye wrote: > Hi, > > how can I tell mris_expand to expand the surface by a fixed distance > rather than by a fraction of the thickness? > > Thanks, > Lars > > ___ > 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
Re: [Freesurfer] mris_expand
Perfect, thanks. I'm also trying to display a surface at a fixed distance into the WM relative to the white surface. mris_expand lh.white -1 lh.wm1mm does not seem to do what I want. Is what I'm trying to do feasible with mris_expand or would you suggest another tool? > Hi Lars, > > that is what it does by default, unless you give it the -thickness flag. > > cheers, > Bruce > On > Fri, 24 Jul 2009, Lars Tjelta Westlye wrote: > >> Hi, >> >> how can I tell mris_expand to expand the surface by a fixed distance >> rather than by a fraction of the thickness? >> >> Thanks, >> Lars ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_expand
Hi Lars, I recently fixed mris_expand to take negative distances. If you send us your hardware/software platform we'll send you a dev version Bruce On Fri, 24 Jul 2009, Lars Tjelta Westlye wrote: > Perfect, thanks. I'm also trying to display a surface at a fixed distance > into the WM relative to the white surface. > > mris_expand lh.white -1 lh.wm1mm > > does not seem to do what I want. Is what I'm trying to do feasible with > mris_expand or would you suggest another tool? > > >> Hi Lars, >> >> that is what it does by default, unless you give it the -thickness flag. >> >> cheers, >> Bruce >> On >> Fri, 24 Jul 2009, Lars Tjelta Westlye wrote: >> >>> Hi, >>> >>> how can I tell mris_expand to expand the surface by a fixed distance >>> rather than by a fraction of the thickness? >>> >>> Thanks, >>> Lars > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_expand
Here you go: Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0 RedHat release: Red Hat Enterprise Linux Client release 5.3 (Tikanga) Kernel info: Linux 2.6.18-128.1.6.el5 x86_64 Thanks a lot! > Hi Lars, > > I recently fixed mris_expand to take negative distances. If you send us > your hardware/software platform we'll send you a dev version > Bruce > > > On Fri, 24 Jul 2009, Lars Tjelta Westlye wrote: > >> Perfect, thanks. I'm also trying to display a surface at a fixed >> distance >> into the WM relative to the white surface. >> >> mris_expand lh.white -1 lh.wm1mm >> >> does not seem to do what I want. Is what I'm trying to do feasible with >> mris_expand or would you suggest another tool? >> >> >>> Hi Lars, >>> >>> that is what it does by default, unless you give it the -thickness >>> flag. >>> >>> cheers, >>> Bruce >>> On >>> Fri, 24 Jul 2009, Lars Tjelta Westlye wrote: >>> Hi, how can I tell mris_expand to expand the surface by a fixed distance rather than by a fraction of the thickness? Thanks, Lars >> >> >> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] libtiff.so.3 instalaton error ?...
Dear Pedro Paulo: I got the following error when I processing the autorecon2 stage... " 4281 Left-non-WM-hypointensities 0 4382 Right-non-WM-hypointensities 0 4485 Optic-Chiasm 187 187 45 251 CC_Posterior 540 540 46 252 CC_Mid_Posterior 182 182 47 253 CC_Central 131 131 48 254 CC_Mid_Anterior 162 162 49 255 CC_Anterior 219 219 Reporting on 49 segmentations # #...@# Cortical ribbon mask Fri Jul 24 04:47:12 CLT 2009 /home/image/bin/freesurfer/subjects/rezende/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance rezende mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux ubuntu 2.6.27-7-generic #1 SMP Fri Oct 24 06:42:44 UTC 2008 i686 GNU/Linux recon-all exited with ERRORS at Fri Jul 24 04:47:15 CLT 2009" Which is the problem ?... How can install libtiff.so.3 ?.. Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] libtiff.so.3 instalaton error ?...
Hi On Ubuntu, you will need to do the following: cd /usr/lib sudo ln -s libtiff.so.4 libtiff.so.3 ( from http://surfer.nmr.mgh.harvard.edu/fswiki/Download ) The second command only works if you have write access to /usr/lib.. otherwise you could contact your sysadmin. Krish On Jul 24, 2009, at 11:15 AM, Gonzalo Rojas Costa wrote: > Dear Pedro Paulo: > > I got the following error when I processing the autorecon2 stage... > > " 4281 Left-non-WM-hypointensities 0 > 4382 Right-non-WM-hypointensities 0 > 4485 Optic-Chiasm 187 187 > 45 251 CC_Posterior 540 540 > 46 252 CC_Mid_Posterior 182 182 > 47 253 CC_Central 131 131 > 48 254 CC_Mid_Anterior 162 162 > 49 255 CC_Anterior 219 219 > > Reporting on 49 segmentations > # > #...@# Cortical ribbon mask Fri Jul 24 04:47:12 CLT 2009 > /home/image/bin/freesurfer/subjects/rezende/mri > > mris_volmask --label_left_white 2 --label_left_ribbon 3 -- > label_right_white > 41 --label_right_ribbon 42 --save_ribbon --save_distance rezende > > mris_volmask.bin: error while loading shared libraries: libtiff.so. > 3: cannot > open shared object file: No such file or directory > Linux ubuntu 2.6.27-7-generic #1 SMP Fri Oct 24 06:42:44 UTC 2008 > i686 GNU/Linux > > recon-all exited with ERRORS at Fri Jul 24 04:47:15 CLT 2009" > > Which is the problem ?... How can install libtiff.so.3 ?.. > > Sincerely, > > > Gonzalo Rojas Costa > > > ___ > 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
Re: [Freesurfer] libtiff.so.3 instalaton error ?...
Hi: But the sysadmin forgot the password of the superuser... I created the link in the /home/image directory, and in /home/image/freesurfer/bin, but freesurfer didn't find the lib... How can I solve the problem... How can I specify to freesurfer that the lib is in another folder ?... Any idea ?... SIncerely, Gonzalo Rojas Costa Krish Subramaniam escribió: > Hi > > On Ubuntu, you will need to do the following: > cd /usr/lib > sudo ln -s libtiff.so.4 libtiff.so.3 > ( from http://surfer.nmr.mgh.harvard.edu/fswiki/Download ) > > The second command only works if you have write access to /usr/lib.. > otherwise you could contact your sysadmin. > > Krish > > On Jul 24, 2009, at 11:15 AM, Gonzalo Rojas Costa wrote: > >> Dear Pedro Paulo: >> >> I got the following error when I processing the autorecon2 stage... >> >> " 4281 Left-non-WM-hypointensities 0 >> 4382 Right-non-WM-hypointensities 0 >> 4485 Optic-Chiasm 187 187 >> 45 251 CC_Posterior 540 540 >> 46 252 CC_Mid_Posterior 182 182 >> 47 253 CC_Central 131 131 >> 48 254 CC_Mid_Anterior 162 162 >> 49 255 CC_Anterior 219 219 >> >> Reporting on 49 segmentations >> # >> #...@# Cortical ribbon mask Fri Jul 24 04:47:12 CLT 2009 >> /home/image/bin/freesurfer/subjects/rezende/mri >> >> mris_volmask --label_left_white 2 --label_left_ribbon 3 -- >> label_right_white >> 41 --label_right_ribbon 42 --save_ribbon --save_distance rezende >> >> mris_volmask.bin: error while loading shared libraries: libtiff.so. >> 3: cannot >> open shared object file: No such file or directory >> Linux ubuntu 2.6.27-7-generic #1 SMP Fri Oct 24 06:42:44 UTC 2008 >> i686 GNU/Linux >> >> recon-all exited with ERRORS at Fri Jul 24 04:47:15 CLT 2009" >> >> Which is the problem ?... How can install libtiff.so.3 ?.. >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> >> >> ___ >> 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
Re: [Freesurfer] libtiff.so.3 instalaton error ?...
I believe the following might work
- create a symbolic link to libtiff.so.4 in your home directory like
cd /home/image/freesurfer/lib/
ln -s /usr/lib/libtiff.so.4 libtiff.so.3
- add this to your LD_LIBRARY_PATH.. first you need to check your
LD_LIBRARY_PATH is already defined.
echo $LD_LIBRARY_PATH
* if this says undefined variable, do this
setenv LD_LIBRARY_PATH /home/image/freesurfer/lib
* if it's already defined
setenv LD_LIBRARY_PATH /home/image/freesurfer/lib:${LD_LIBRARY_PATH}
and try.
If it works you should take these to your ~/.cshrc where they are
defined everytime
Krish
On Jul 24, 2009, at 11:38 AM, Gonzalo Rojas Costa wrote:
> Hi:
>
> But the sysadmin forgot the password of the superuser... I created
> the link
> in the /home/image directory, and in /home/image/freesurfer/bin, but
> freesurfer didn't find the lib... How can I solve the problem... How
> can I
> specify to freesurfer that the lib is in another folder ?... Any
> idea ?...
>
> SIncerely,
>
>
> Gonzalo Rojas Costa
>
>
> Krish Subramaniam escribió:
>> Hi
>>
>> On Ubuntu, you will need to do the following:
>> cd /usr/lib
>> sudo ln -s libtiff.so.4 libtiff.so.3
>> ( from http://surfer.nmr.mgh.harvard.edu/fswiki/Download )
>>
>> The second command only works if you have write access to /usr/lib..
>> otherwise you could contact your sysadmin.
>>
>> Krish
>>
>> On Jul 24, 2009, at 11:15 AM, Gonzalo Rojas Costa wrote:
>>
>>> Dear Pedro Paulo:
>>>
>>> I got the following error when I processing the autorecon2 stage...
>>>
>>> " 4281 Left-non-WM-hypointensities 0
>>> 4382 Right-non-WM-hypointensities 0
>>> 4485 Optic-Chiasm 187 187
>>> 45 251 CC_Posterior 540 540
>>> 46 252 CC_Mid_Posterior 182 182
>>> 47 253 CC_Central 131 131
>>> 48 254 CC_Mid_Anterior 162 162
>>> 49 255 CC_Anterior 219 219
>>>
>>> Reporting on 49 segmentations
>>> #
>>> #...@# Cortical ribbon mask Fri Jul 24 04:47:12 CLT 2009
>>> /home/image/bin/freesurfer/subjects/rezende/mri
>>>
>>> mris_volmask --label_left_white 2 --label_left_ribbon 3 --
>>> label_right_white
>>> 41 --label_right_ribbon 42 --save_ribbon --save_distance rezende
>>>
>>> mris_volmask.bin: error while loading shared libraries: libtiff.so.
>>> 3: cannot
>>> open shared object file: No such file or directory
>>> Linux ubuntu 2.6.27-7-generic #1 SMP Fri Oct 24 06:42:44 UTC 2008
>>> i686 GNU/Linux
>>>
>>> recon-all exited with ERRORS at Fri Jul 24 04:47:15 CLT 2009"
>>>
>>> Which is the problem ?... How can install libtiff.so.3 ?..
>>>
>>> Sincerely,
>>>
>>>
>>> Gonzalo Rojas Costa
>>>
>>>
>>> ___
>>> 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
Re: [Freesurfer] libtiff.so.3 instalaton error ?...
I think if he forgot the root password there's no way to do this --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business 2009/7/24 Gonzalo Rojas Costa > Hi: > > But the sysadmin forgot the password of the superuser... I created the > link > in the /home/image directory, and in /home/image/freesurfer/bin, but > freesurfer didn't find the lib... How can I solve the problem... How can I > specify to freesurfer that the lib is in another folder ?... Any idea ?... > > SIncerely, > > > Gonzalo Rojas Costa > > > Krish Subramaniam escribió: > > Hi > > > > On Ubuntu, you will need to do the following: > > cd /usr/lib > > sudo ln -s libtiff.so.4 libtiff.so.3 > > ( from http://surfer.nmr.mgh.harvard.edu/fswiki/Download ) > > > > The second command only works if you have write access to /usr/lib.. > > otherwise you could contact your sysadmin. > > > > Krish > > > > On Jul 24, 2009, at 11:15 AM, Gonzalo Rojas Costa wrote: > > > >> Dear Pedro Paulo: > >> > >> I got the following error when I processing the autorecon2 stage... > >> > >> " 4281 Left-non-WM-hypointensities 0 > >> 4382 Right-non-WM-hypointensities 0 > >> 4485 Optic-Chiasm 187 187 > >> 45 251 CC_Posterior 540 540 > >> 46 252 CC_Mid_Posterior 182 182 > >> 47 253 CC_Central 131 131 > >> 48 254 CC_Mid_Anterior 162 162 > >> 49 255 CC_Anterior 219 219 > >> > >> Reporting on 49 segmentations > >> # > >> #...@# Cortical ribbon mask Fri Jul 24 04:47:12 CLT 2009 > >> /home/image/bin/freesurfer/subjects/rezende/mri > >> > >> mris_volmask --label_left_white 2 --label_left_ribbon 3 -- > >> label_right_white > >> 41 --label_right_ribbon 42 --save_ribbon --save_distance rezende > >> > >> mris_volmask.bin: error while loading shared libraries: libtiff.so. > >> 3: cannot > >> open shared object file: No such file or directory > >> Linux ubuntu 2.6.27-7-generic #1 SMP Fri Oct 24 06:42:44 UTC 2008 > >> i686 GNU/Linux > >> > >> recon-all exited with ERRORS at Fri Jul 24 04:47:15 CLT 2009" > >> > >> Which is the problem ?... How can install libtiff.so.3 ?.. > >> > >> Sincerely, > >> > >> > >> Gonzalo Rojas Costa > >> > >> > >> ___ > >> 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
Re: [Freesurfer] freesurfer's template for sphere registration
Hi Jidan,
It sounds to me that what you're asking is whether it is possible to
invert the "mapping" from {lh,rh}.white to {lh,rh}.sphere, but apply
that inversion to {lh,rh}.sphere.reg, thus generating a putative
"{lh,rh}.white.reg" surface. I'm not sure that operation is possible,
or if the resulting surface would even be meaningful.
cheers,
-Mike H.
On Fri, 2009-07-24 at 10:20 +0800, Zhong Jidan wrote:
> Hi Bruce,
>
> For my 2nd point, I mean, after we get the lh.sphere.reg as the
> deformed subject, it should have similar sulco-gyral pattern as the
> template. I want to compute the distance between the deformed subject
> and the template, to see how close they are after the registration. In
> other words, I want to check the distance error. But the distance
> based on the sphere doesn't include the geometry information. I want
> to get the real distance in their white surface, which is between
> lh.reg.white and template.white. Also if I have lh.reg.white, it would
> be interesting to compute the real distance between the subject.white
> and lh.reg.white to see how far it moves.
>
> But from the method you told me, "You can use the mapping to paint the
> geometry of one subject onto another folded surface if you want to
> visualize the geometric mapping (e.g. the curv of one subject on the
> white surface of another)." If "paint" means set a value for
> the vertex for visulization, (just like paint the functional
> information on a surface ) this would not make me get the real
> geometry of the .reg.white, right? When you paint the curvature
> information of the lh.sphere.reg and template.sphere to another white
> surface, you can only see the curvature difference on the
> corresponding point but can not see the real geometry of the two.
> I'm not sure whether I understand your surggestion correctly...This
> what I'm confused.
>
> Thanks,
> Jidan
>
>
> On Thu, Jul 23, 2009 at 8:12 PM, Bruce Fischl
> wrote:
> Hi Jidan,
>
> we construct fsaverage by mapping the icosahedron vertices to
> a set of subjects, then assigning that vertex to the position
> that is the average of the tal coords of those vertices.
> Sorry, I don't understand the 2nd point. Maybe you can
> explain what you are trying to accomplish?
>
> cheers,
> Bruce
>
>
>
>
> On Thu, 23 Jul 2009, Zhong Jidan wrote:
>
> Hi Bruce,
>
> Thanks for your reply. I'm not clear about two points
> you mentioned.
>
> ->To represent a folded surface we either (1) map to
> an individual subject,
> or (2) use a volume transform such as tal and the
> vertex correspondence from
> the sphere.reg to find the average coordinate of a
> vertex. This is how we
> build the fsaverage and average7 surfaces.
>
> For the (2) point, what do you exactly mean? I?m
> confused. I thought your
> fsaverage is derived by averaging 40 subjects' volume
> image and then
> reconstruct the surface based on that. How can I use a
> volume transform such
> as tal and the vertex correspondence from the
> sphere.reg to find the average
> coordinate of a vertex? I'm totally lost with this
> sentence..
>
>
> ->You can use the mapping to paint the geometry of one
> subject onto another
> folded surface if you want to visualize the geometric
> mapping (e.g. the curv
> of one subject on the white surface of another).
>
> For this one, I think you mean that, I can use one
> white surface as a base.
> Then paint the curvature information on the white
> surface to see the
> geometry. But this is not I want... To be specific, if
> I have a lh.sphere,
> lh.sphere.reg, they share the curvature information,
> and the only difference
> is the spherical coordinates. Then it is non sense to
> paint the curvature
> information to another white surface to see the
> geometry because there is
> only one .curv file. Another problem is, this
> lh.sphere may have different
> number of points with the white surface. ... Not sure
> whether I understand
> it correctly, hope for your suggestion.
>
> Thanks,
>
> Jidan
>
>
Re: [Freesurfer] freesurfer's template for sphere registration
Hi Jidan
Lilla Zollei (ccd) has worked on some tools that we just published in IEEE
TMI for applying the surface warp to an entire volume. I guess you could
just warp the surface through forward and inverse transforms, but the
transformed source will be guaranteed to lie within the target surface by
construction, so I'm not sure how interesting it will be.
cheers,
Bruce
On Fri, 24 Jul 2009, Michael Harms wrote:
Hi Jidan,
It sounds to me that what you're asking is whether it is possible to
invert the "mapping" from {lh,rh}.white to {lh,rh}.sphere, but apply
that inversion to {lh,rh}.sphere.reg, thus generating a putative
"{lh,rh}.white.reg" surface. I'm not sure that operation is possible,
or if the resulting surface would even be meaningful.
cheers,
-Mike H.
On Fri, 2009-07-24 at 10:20 +0800, Zhong Jidan wrote:
Hi Bruce,
For my 2nd point, I mean, after we get the lh.sphere.reg as the
deformed subject, it should have similar sulco-gyral pattern as the
template. I want to compute the distance between the deformed subject
and the template, to see how close they are after the registration. In
other words, I want to check the distance error. But the distance
based on the sphere doesn't include the geometry information. I want
to get the real distance in their white surface, which is between
lh.reg.white and template.white. Also if I have lh.reg.white, it would
be interesting to compute the real distance between the subject.white
and lh.reg.white to see how far it moves.
But from the method you told me, "You can use the mapping to paint the
geometry of one subject onto another folded surface if you want to
visualize the geometric mapping (e.g. the curv of one subject on the
white surface of another)." If "paint" means set a value for
the vertex for visulization, (just like paint the functional
information on a surface ) this would not make me get the real
geometry of the .reg.white, right? When you paint the curvature
information of the lh.sphere.reg and template.sphere to another white
surface, you can only see the curvature difference on the
corresponding point but can not see the real geometry of the two.
I'm not sure whether I understand your surggestion correctly...This
what I'm confused.
Thanks,
Jidan
On Thu, Jul 23, 2009 at 8:12 PM, Bruce Fischl
wrote:
Hi Jidan,
we construct fsaverage by mapping the icosahedron vertices to
a set of subjects, then assigning that vertex to the position
that is the average of the tal coords of those vertices.
Sorry, I don't understand the 2nd point. Maybe you can
explain what you are trying to accomplish?
cheers,
Bruce
On Thu, 23 Jul 2009, Zhong Jidan wrote:
Hi Bruce,
Thanks for your reply. I'm not clear about two points
you mentioned.
->To represent a folded surface we either (1) map to
an individual subject,
or (2) use a volume transform such as tal and the
vertex correspondence from
the sphere.reg to find the average coordinate of a
vertex. This is how we
build the fsaverage and average7 surfaces.
For the (2) point, what do you exactly mean? I?m
confused. I thought your
fsaverage is derived by averaging 40 subjects' volume
image and then
reconstruct the surface based on that. How can I use a
volume transform such
as tal and the vertex correspondence from the
sphere.reg to find the average
coordinate of a vertex? I'm totally lost with this
sentence..
->You can use the mapping to paint the geometry of one
subject onto another
folded surface if you want to visualize the geometric
mapping (e.g. the curv
of one subject on the white surface of another).
For this one, I think you mean that, I can use one
white surface as a base.
Then paint the curvature information on the white
surface to see the
geometry. But this is not I want... To be specific, if
I have a lh.sphere,
lh.sphere.reg, they share the curvature information,
and the only difference
is the spherical coordinates. Then it is non sense to
paint the curvature
information to another white surface to see the
geometry because there is
only one .curv file. Another problem is, this
lh.sphere may have different
number of points with the white surface. ... Not sure
whether I understand
it correctly, hope for your suggestion.
Thanks,
Re: [Freesurfer] mris_expand
dev mris_expand found at: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/linux-centos4_x86_64/ On Fri, 2009-07-24 at 14:53 +0200, Lars Tjelta Westlye wrote: > Here you go: > > Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0 > > RedHat release: Red Hat Enterprise Linux Client release 5.3 (Tikanga) > > Kernel info: Linux 2.6.18-128.1.6.el5 x86_64 > > > Thanks a lot! > > > > Hi Lars, > > > > I recently fixed mris_expand to take negative distances. If you send us > > your hardware/software platform we'll send you a dev version > > Bruce > > > > > > On Fri, 24 Jul 2009, Lars Tjelta Westlye wrote: > > > >> Perfect, thanks. I'm also trying to display a surface at a fixed > >> distance > >> into the WM relative to the white surface. > >> > >> mris_expand lh.white -1 lh.wm1mm > >> > >> does not seem to do what I want. Is what I'm trying to do feasible with > >> mris_expand or would you suggest another tool? > >> > >> > >>> Hi Lars, > >>> > >>> that is what it does by default, unless you give it the -thickness > >>> flag. > >>> > >>> cheers, > >>> Bruce > >>> On > >>> Fri, 24 Jul 2009, Lars Tjelta Westlye wrote: > >>> > Hi, > > how can I tell mris_expand to expand the surface by a fixed distance > rather than by a fraction of the thickness? > > Thanks, > Lars > >> > >> > >> > >> > > > > > ___ > 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
Re: [Freesurfer] clusterwise correction for multiple comparison
Rosa, If you have the newest version of qdec, it has a button to generate the mri_glmfit-sim script for you, with the proper directory input and output generated for you. You'll still have to load the results on your own in tksurfer by following these instructions: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons Nick On Fri, 2009-07-24 at 13:48 +0200, Rosa Steimke wrote: > HI! > i have a question regarding multiple comparion correction in qdec. can i use > a clusterwise correction? > > i found the following script for glm: > > mri_glmfit-sim \ > --glmdir lh.gender_age.glmdir \ > --sim mc-z 5 4 mc-z.negative \ > --sim-sign neg \ > --overwrite > > but i dont understand how i should apply it in qdec. what shoudl i use as > input directory? > rosa > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec question
Prapti, To save results in another directory: setenv QDEC_WORKING_DIR some/pathname then run qdec. Nick On Thu, 2009-07-23 at 12:19 -0400, Douglas N Greve wrote: > > Prapti Gautam wrote: > > Dear freesurfers, > > > > I have a few additional questions regarding qdec. > > > > 1. Is it possible to specify in qdec so that the results of the analyses > > run are saved in a separate destination than the SUBJECTS_DIR? > > > I'll leave this for Nick. > > 2. I have read in the qdec tutorial that it is possible to select up to > > 4 variables to regress in analyses, but I can only select 1 discrete and > > 2 continuous variables in my version. I am running Freesurfer v4.3.0. > > Does this mean I have an older version of qdec that only allows > > selection of 2 continuous variables and I need to update to a newer > > version of freesurfer?? > > > The 4 variables are 2 discrete and 2 continuous. This is all it does > right now. If you need more, you'll have to run mri_glmfit manually. > > doug > > Thank you for your help, > > > > Prapti > > > > -Original Message- > > From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu] > > Sent: Friday, 10 July 2009 4:15 AM > > To: Prapti Gautam > > Cc: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] qdec question > > > > The newest version of FreeSurfer does not contain any changes to qdec I > > believe. > > Allison > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] -randomness flag for recon-all
Pernille, My mistake, v4.4.0 still makes use of randomness. The next version, to be released in a couple weeks, with have -norandomness by default. The ReleaseNotes page has been updated. Nick On Thu, 2009-07-23 at 09:52 +0200, Pernille Iversen wrote: > Hi, > In the release notes for version 4.4.0 it says that "The -randomness > flag can be used to allow usage of a random seed", however, running > the following command: > > recon-all -all -nowmsa -randomness -subjid f4168_1r > > gives the following error: > > ERROR: Flag -randomness unrecognized. > > Is there another way to reintroduce the randomness? > > I am using the following version: > v 1.133.2.51 2009/06/11 > > Thanks, > Pernille > ___ > 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
Re: [Freesurfer] clusterwise correction for multiple comparison
The input is already specified as the --glmdir doug Rosa Steimke wrote: > HI! > i have a question regarding multiple comparion correction in qdec. can i use > a clusterwise correction? > > i found the following script for glm: > > mri_glmfit-sim \ > --glmdir lh.gender_age.glmdir \ > --sim mc-z 5 4 mc-z.negative \ > --sim-sign neg \ > --overwrite > > but i dont understand how i should apply it in qdec. what shoudl i use as > input directory? > rosa > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
