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
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve <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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