Re: [Freesurfer] Tksurfer + Histogram

Thanks for reply bruce.

I got my mistake.Actually i am learning Cortical thickness using freesurfer.In which ROI5.nii n *TT_avg152T1.nii*. image is required which i took from our own data set,but didnt have thickness file for surface to surface mapping.Now i will do recon all on my data set to get complete information.Thanks again for your advice.

cheers Saurabh Thakur,

On Wed, Mar 26, 2014 at 5:59 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

Hi Saurabh

I'm not sure I understand. This is the purpose of recon-all - to generate morphomological models, including the thickness estimates in lh.thickness. Is that would you mean? BTW: I wouldn't look at thickness in the hippocampus, the results will be unreliable due to all the internal structure in the hippocampus that is not well-resolved at current resolutions.

cheers Bruce

On Wed, 26 Mar 2014, Saurabh Thakur wrote:

Hello Bruce,

...

I am referring to link

http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

to calculate the cortical thickness of particular area such as Left hippocampus for our own data set.

But i am looking for forward to generate lh.thickness file in freesurfer for own data set which can be used as overlay. (Used for surface to surface overlay)

Can u suggest how to generate lh.thickness file for my own data using freesurfer...?

Thanks in advanced.

cheers Saurabh Thakur,

On Tue, Mar 11, 2014 at 10:28 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: try configure->functional overlay or something like that after loading the thickness into a functional overlay On Tue, 11 Mar 2014, Saurabh Thakur wrote:

        I am referring one paper.
        It mentioned about the freesurfer and cortical
        thickness they hv got in
        tksurfer.

        I m just want to know how to get that done in
        tksurfer.

        I hv attached that paper for the reference.

        cheers
        Saurabh Thakur,






        On Tue, Mar 11, 2014 at 7:14 AM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              what is it that you want to histogram? If the
        thickness,
              tksurfer will do
              this for you if you load it as an overlay. Or
        you can read it
              into matlab
              and show it there

              On Tue, 11 Mar 2014, Saurabh Thakur
              wrote:

              > Hello Freesurfer Expert,
              >
              > Can anyone help me with histogram plotting
        of different
              surfaces in
              > tksurfer.
              >
              > I looking to calculate the thickness of
        cortex.
              >
              > Thanks in advance,
              >
              >
              > Saurabh Thakur,
              >
              >
              >
              >
              >
              >
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