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 --projfrac0.5 > 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! > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.