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Hello Bruce,

As suggested by you, I used tkmeditfv to view the volumetric maps on the surface and it seems like the dACC cluster is lying outside the brain. I checked the registration of the volumetric file using tkregisterfv but surprisingly nothing shows up. I also tried using bbregister and then checked the registration but the same thing happened, the volumetric map doesn't show up in either of those cases.

I am confused, as to why that is happening and how can I fix it such that all the clusters are appropriately aligned.

The files I am using have been exported from neuroelf program. I exported them as analyze format (.img and .hdr) and then converted it to nifti format using mri_convert. However, with both the analyze and nifti format, similar things happened.

Any help is highly appreciated.

Thanks,
Srishti

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
skype: srishti.goel12


On Tue, Jun 26, 2018 at 11:56 PM, Douglas Greve <dgreve@mgh.harvard.edu> wrote:
you can try
tkmeditfv subject orig.mgz -surfs -ov clustermap.nii.gz -fminmax .01 3
you may have to adjust the thresholds (fminmax)


On 6/26/18 10:43 PM, srishti goel wrote:

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Hello Bruce,

You had mentioned about loading the volumetric maps with the surface to check that all my clusters are contained within the surfaces. Since I am very new to freesurfer, could you please guide to where I can find an appropriate command to do that.

Thank you so much for all the help!

Best,
Srishti

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
skype: srishti.goel12


On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Srishti

you should be able to load the volumetric maps with the surfaces and make sure that your clusters are contained within the surface.

cheers
Bruce

On Mon, 25 Jun 2018, srishti goel wrote:


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They are separate clusters not the same clusters but we both of those don't show up when we
project the volume maps on surface. Every other cluster comes up and this has happened in
about 2-3 files. Are you absolutely sure that the surface in freesurfer includes dACC and
insula?

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srishtig@email.unc.edu
skype: srishti.goel12


On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve <dgreve@mgh.harvard.edu> wrote:

      It should be included. But dACC and insula are not close to each other. How can
      there be a cluster that spans both?


      On 6/23/18 7:54 PM, srishti goel wrote:

              External Email - Use Caution        

      Hello,
I am using mri_vol2surf to project my volume maps on to the surface. There is a
dACC/insula cluster visible in my volume maps that doesn't show up when I project
it on the surface.

Is that because dACC/insula is not included in surfaces on Freesurfer?

Thanks!

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srishtig@email.unc.edu
skype: srishti.goel12



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