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
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