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): srish...@email.unc.edu skype: srishti.goel12 On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve <dgr...@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 <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 > skype: srishti.goel12 > > > On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl <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 >>> 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! >>> > >>> > >>> > >>> > _______________________________________________ >>> > 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 > listfreesur...@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. > >
register.dat.log
Description: Binary data
_______________________________________________ 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.
