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
> intended only
> for the person to
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> 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
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> MGH-NMR Center
> 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/>
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> <http://surfer.nmr.mgh. harvard.edu/fswiki/
> BugReporting
>
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>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
>
>
>
>
>
> --
> 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>
>
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>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>
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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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