Thank you for all replies. One more question to bother you. in :
http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsrecon.ppt
In this tutorial, in the page 40 it reads "Flattening not done as part of
standard
reconstruction". Is it possible to get the 2D flat patch too (page 40 and 41)?
I can embed the
graph in 2D space but I am not sure it produces the same results.
Thanks again,
On Tue, Apr 3, 2012 at 8:36 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
read_surf.m will do the trick, but be sure to use 1-based indices! And
note that
the timeCourse.mgz you read is almost certainly a surface overlay with
137654
vertices and 236 time points, so if you read the surface f.vol(1,j,1,:)
would be
the timecourse for the jth index returned by read_surf
cheers,
Bruce
On Tue, 3 Apr 2012, Kaveh Kohan wrote:
I think I figure out the problem with "mri_vol2surf". It seems that
there is
a bug in the executable. I switched to the older version of
freesurfer
(from
5.1 to 5.0) and it just works! I am not sure how to check the
results. In
matlab I used:
>> f = MRIread('timeCourse.mgz');
>> size(f.vol)
1 137654 1 236
it should be OK, right? It seems that there are 137654 voxels. BTW,
how can
I read the graph structure of the vertex, ie x,y,z of each vertex,
which
neighbors of each vertex etc?
In case you want to know the spec. of the sytem:
~$ uname -a
Linux pc71 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC
2012
x86_64 GNU/Linux
maybe the mri_vol2surf is not compatible with this machine?
about the tar file, I just downloaded, it no probelm:
~$ wget http://dl.dropbox.com/u/7895831/tp1.tar.gz .
kayhan kayhan 336958635 2012-04-03 20:09 tp1.tar.gz
~$ tar xvzf tp1.tar.gz
If you still unable to download it let me know I will find another
way
to
upload it.
Thanks,
On Tue, Apr 3, 2012 at 6:06 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu>
wrote:
Can you double check that tar file? I get an error when I try
to
untar it
-rw-r----- 1 greve greve 96469167 Apr 3 18:58 tp1.tar.gz
On 04/03/2012 04:15 PM, Kaveh Kohan wrote:
> Any thought on this? I am wondering there might be something
wrong
> with FSL registration. I don't know what bbregister uses for
> registration but as far as I know "flirt" is unable to
register
> 4d-image (such as fmri ) to 3D; it only accepts 3d as input
and
> output. Is it possible to register freesurfer surface on the
mean
> activation of fmri (therefore both 3d) and then sample from
the
> surface on the fmri space?
>
> Any reply is very appreciated.
>
> On Mon, Apr 2, 2012 at 5:29 PM, Kaveh Kohan
<kaveh.ko...@gmail.com
> <mailto:kaveh.ko...@gmail.com>> wrote:
>
> No it did not work, mri_vol2surf still produces the same error
> (see below). In the link below, I have shared the freesurfer
> results (in the FREESURFER folder) plus fmri image (in the
NITFI
> folder). I am wondering if there is anything wrong with my
> installation of the mri_vol2surf (stable 5). The data is
anonymized.
>
> http://dl.dropbox.com/u/7895831/tp1.tar.gz
>
> --------------------------------- OUTPUT of mri_vol2surf
>
> ~$ mri_vol2surf --mov fMRI.nii.gz --reg
> bbregister/fmri-TO-orig.dat --hemi lh --o ./timeCourse.mgz
> srcvol = fMRI.nii.gz
> srcreg = bbregister/fmri-TO-orig.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> Reading surface
>
/home/kayhan/test/myproject/control001/tp1/FREESURFER/surf/lh.white
> Done reading source surface
> Mapping Source Volume onto Source Subject Surface
> 1 0 0 0
> using old
> Done mapping volume to surface
> Segmentation fault
> -------------------------
>
>
>
>
>
>
>
> On Mon, Apr 2, 2012 at 2:45 PM, Douglas N Greve
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
>
> The new registration looks much better. The value I look
at
is
> the first value in the mincost file. For your data, it's
about
> .6. This value will be between 0 and 1.1. There's no way
to
> determine what a proper cut off is, but in your previous
reg,
> the value as .9 or so, so .6 is probably fine. Did
> mri_vol2surf work with the new registration?
> doug
>
>
> On 04/02/2012 05:05 PM, Kaveh Kohan wrote:
>
> I re-ran the registration with FSL (initfsl option)
and
> the results looks fine to me. I have attached the new
log
> file. If the results look fine and it does not produce
> error, is there any way that I check that my
registration
> failed? Is there any term that I should search for in
the
> log file? Do you think that the whole problem could be
> because of the headers of the files?
>
> The de-identified data are already unloaded here. It
> contains the freesurfer results (in the FREESURFER
foder)
> and the fmri image in the NIFTI folder. I would be
> appreciate if you can tell how to fix the problem with
> mri_vol2surf
>
>
> http://dl.dropbox.com/u/ 7895831/tp1.tar.gz
> <http://dl.dropbox.com/u/7895831/tp1.tar.gz>
>
> Thanks,
>
>
>
>
>
>
>
>
> On Mon, Apr 2, 2012 at 4:12 PM, Douglas Greve
> <gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard. edu
> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
>
> It looks like your registration failed (though it
completed
> without error). Did you check it with tkregister? I
> don't think
> that would explain the segfault, but it is worth
> tracking it down.
> doug
>
>
> On 4/2/12 2:54 PM, Kaveh Kohan wrote:
>
> I have also attached the
"fmri-TO-orig.dat.log"
> maybe that has
> some useful information about the previous step
> (bbregister) .
>
> On Mon, Apr 2, 2012 at 2:48 PM, Kaveh Kohan
> <kaveh.ko...@gmail.com
<mailto:kaveh.ko...@gmail.com>
> <mailto:kaveh.ko...@gmail.com
> <mailto:kaveh.ko...@gmail.com>> > wrote:
>
> No, it does not; sorry for the confusion. I
> have attached a
> clean output below. I don't know what it
means.
> May be there
> is something wrong with the format of the
> files. Do you need
> me to upload the freesurfer results and
fMRI
> somewhere for
> you to inspect it?
>
> ------------ OUTPUT
>
> ~$ mri_vol2surf --mov fMRI.nii.gz --reg
> bbregister/fmri-TO-orig.dat --hemi lh
--o
> ./timeCourse.mgz
> srcvol = fMRI.nii.gz
> srcreg = bbregister/fmri-TO-orig.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> Reading surface
> /home/kayhan/test/myproject/
> control001/tp1/FREESURFER/ surf/lh.white
> Done reading source surface
> Mapping Source Volume onto Source Subject
Surface
> 1 0 0 0
> using old
> Done mapping volume to surface
> Segmentation fault
> ------------
>
>
>
>
>
>
> On Mon, Apr 2, 2012 at 1:44 PM, Douglas N
Greve
> <gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard. edu
> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
>
> Hmmm, I don't know why it is doing
that.
> Does it really
> print "using old" after the seg fault
was
that
> accidentally pasted in? It should not
be
> printing that
> twice, maybe it's a clue.
> doug
>
>
> On 04/02/2012 10:26 AM, Kaveh Kohan
wrote:
>
> I have tried and it did not work
(the
> same seg fault,
> see below). It seems that it
> successfully performs
> the mapping but it fails in final
step
> probably
> saving the results. Is the data
format
> that I used OK?
>
> I am using Ubuntu 10.10, the
version
of
> "mri_vol2surf" is "stable5". Please
let
> me knoe if
> more information is required.
Thanks.
>
> ~$ mri_vol2surf --mov fMRI.nii.gz
--reg
> bbregister/fmri-TO-orig.dat --hemi
lh
> --o
> ./timeCourse.mgz
> srcvol = fMRI.nii.gz
> srcreg =
bbregister/fmri-TO-orig.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> Reading surface
> /home/kayhan/test/myproject/
> control001/tp1/FREESURFER/
surf/lh.white
> Done reading source surface
> Mapping Source Volume onto Source
> Subject Surface
> 1 0 0 0
> using old
> Done mapping volume to surface
> *Segmentation fault*
> using old
>
>
> On Sun, Apr 1, 2012 at 2:34
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>>
> <mailto:fis...@nmr.mgh <mailto:fis...@nmr.mgh>.
> harvard.edu <http://harvard.edu>
>
> <mailto:fis...@nmr.mgh. harvard.edu
> <mailto:fis...@nmr.mgh.harvard.edu>>>>
>
> wrote:
>
> Hi Kaveh
>
> use bbregister to
register
> your functional
> data to the
> surface, then
mri_vol2surf
> to sample it
> from the volume onto
> the surface and you
should
> be all set.
>
> cheers
> Bruce
>
> On Sun, 1 Apr 2012,
Kaveh
> Kohan wrote:
>
> Hi FreeSurfer Users,
>
>
> I am new to the
> Freesurfer, I have a
> question regarding
> mapping of the
> resting state fMRI
time
> courses on the
> cortex area. I
> apologise in case my
> question is naive.
> please bear with me:
>
> Is it possible to
have
> time-courses
> sampled from cortex?
> I mean how can I
> get corresponding
> time-course for each
> vertex on the
> cortex ? I know that
> FreeSurfer can
produce
> mask for cortex
> are but I would
> like to have
> time-courses on the
> flattened (2D)
> map; ie assuming that
> cortex is
> flattened, each
pixel
of
> the 2D
> flattened image which
> resides in the
cortex
> (I guess it
corresponds
> to a vertex on
> the cortex
> manifold?) is
time-series.
>
> I have ran recon-all
on
> the T1. All of
> those operation
> were done using a
> third party packages
> that uses
> freesurfer namely CMTK
> (http://cmtk.org). I
> do not exactly know
how
> to use
> "bbregister" to register
> the parcellation on
> the resting-state
fMRI
> image?
>
> I would be thankful
if
> you can help.
>
>
> Thanks
>
>
>
>
>
>
>
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> The information in this e-mail
is
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> addressed. If you believe this
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> contains patient information,
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard. edu
> <mailto:gr...@nmr.mgh.harvard.edu>>
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> <tel:617-726-7422 <tel:617-726-7422>>
>
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> <http://surfer.nmr.mgh. harvard.edu/fswiki/
> BugReporting
>
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>
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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>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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