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): [email protected]
skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve <[email protected]>
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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