On Tue, Apr 3, 2012 at 6:06 PM, Douglas N Greve <greve@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.kohan@gmail.com

> <mailto:kaveh.kohan@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

> <greve@nmr.mgh.harvard.edu <mailto:greve@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
> <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>

> <mailto:greve@nmr.mgh.harvard. edu

> <mailto:greve@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.kohan@gmail.com <mailto:kaveh.kohan@gmail.com>

> <mailto:kaveh.kohan@gmail.com

> <mailto:kaveh.kohan@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
> <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>

> <mailto:greve@nmr.mgh.harvard. edu

> <mailto:greve@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
> <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> <mailto:fischl@nmr.mgh. harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>

> <mailto:fischl@nmr.mgh <mailto:fischl@nmr.mgh>.
> harvard.edu <http://harvard.edu>

>
> <mailto:fischl@nmr.mgh. harvard.edu
> <mailto:fischl@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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> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>

> <mailto:greve@nmr.mgh.harvard. edu

> <mailto:greve@nmr.mgh.harvard.edu>>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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