don't use --init-rr ( you don't need to spec an init in version 6)

On 4/10/18 9:48 PM, srishti goel wrote:

When I run bbregister, it gives me an error. Attached is the register.dat.log file for it.
Error:

reading source './tmp.bbregister.91068/template.nii'...

mri_robust_register.bin: only pass single frame MRI source ./tmp.bbregister.91068/template.nii.

No such file or directory

Any help is greatly appreciated!
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 Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve <dgreve@mgh.harvard.edu> wrote:
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 <23srishtigoel@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): srishtig@email.unc.edu

skype: srishti.goel12

On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl <fischl@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): srishtig@email.unc.edu
skype: srishti.goel12

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