They are not in registration. Try running bbregister to create a registration file (lta), then pass the lta to tkregisterfv instead of --regheader

On 4/9/18 11:49 PM, Bruce Fischl wrote:
How did you generate the registration? And give us the details of what you are trying to register
Cheers
Bruce

On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtig...@gmail.com <mailto:23srishtig...@gmail.com>> wrote:

Hi Bruce,

Thanks so much for pointing that out, I totally missed that part.

Also, the registration definitely isn't appropriate.
Could someone please guide me how to correct this problem. I have attached a screenshot of how it looks like currently.


<Screen Shot 2018-04-08 at 2.53.33 PM.png>

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


On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote:

    Hi Srishti

    the directory you are in doesn't matter. YOu either need to set
    SUBJECTS_DIR in the environment, or use --sd <SUBJECTS_DIR> to
    specify the
    directory that contains your subjects. I think you can also give
    it the full path to a target volume if you want, but maybe Doug
    can comment as he knows this stuff better than I do

    cheers
    Bruce



     On Sun, 8 Apr 2018, srishti goel wrote:

        When I type this command:tkregisterfv --mov
        negative_allsocial_proportion.nii --regheader --s
        mni152_subject --surfs --reg reg.deleteme.dat

        It gives me the error: cannot find mni152_subject.
        Although I clearly checked that the directory from which I
        am submitting this command has the
        mni152_subject directory within which there are all the other
        required directories such as: mri,
        stats, surf, scripts, etc.

        I am unsure what is happening here.


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


        On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve
        <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote:
              Those commands look ok. My suspicion goes to the use of
        --regheader. See
              whether the registration is ok with

              tkregisterfv --mov negative_allsocial_proportion.nii
        --regheader --s
              mni152_subject --surfs --reg reg.deleteme.dat


              On 04/05/2018 08:34 AM, srishti goel wrote:
              > Hi,
              >
              > I am trying to compare my volume maps
              > (negative_allsocial_proportion.nii) to someone else's
              > (SN_like_cortical_lh.nii.gz) who have it on a surface
              > (mni152_subject). So I used the steps for
        mri_vol2surf command as
              > follows:
              >
              > Commands:
              > mri_vol2surf --src negative_allsocial_proportion.nii
        --regheader
              > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii
        --projfrac 0.5
              > Then to view it:
              > tksurfer mni152_subject lh inflated -overlay
        ./neg_allsocial_lh.nii
              > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
              >
              > Everything ran fine and we didn't get any error but
        then while viewing
              > the files we could not see our map
        (neg_allsocail_lh.nii) on the
              > surface. This file seemed to work fine as it is not
        an empty file when
              > I checked the file size. However, when we view it
        using tksurfer it
              > does not show up as a highlighted portion on the
        surface. The
              > SN_like_cortical_lh.nii.gz file shows up just fine.
              >
              > Could someone please help me figure out what might
        have gone wrong here.
              >
              > Thanks so much!
              >
              >
              >
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