yes, but the surface overlay is in mgz (or nii.gz) format On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: > Hi Doug > > below is the email I had written last Friday. I thought it got lost in > the mix. I was told by Bruce to use identity.nofile as the > transformation since my labels and T1s are already in the same space > and I just want to resample my labels to the surfaces. > > *I will try, as you suggest, --regheader * > > When I do "mri_cor2label --help" it says it uses surface overlays or > volumes. *I am not sure why I want to generate a volume with > mri_vol2surf* - shouldn't I generate a surface overlay that I can then > create as a label using mri_cor2label? > > many thanks > > Trisanna > > > > thanks Bruce > > I could not find identity.nofile anywhere, when I ran mri_vol2surf I > got the following error > > trisanna@kaplan:~$ mri_vol2surf --mov > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o > /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh > srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz > srcreg = identity.nofile > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > regio_read_register(): No such file or directory > Could not open identity.nofile > > > > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > Hi Trisanna > > you can give the transformation "file" named identity.nofile and it > will assume that the transform is the identity. You can then use > mri_vol2label to sample the label onto the surface and visualize it with: > > freeview -f lh.inflated:label=lh.labels.label > > or some such > > cheers > Bruce > > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: > > Hi there > > Just to reiterate my point above, when I open a surface created in > Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no > transformations have been performed) I get the following snapshot > #1. Clearly, my original labels are aligned with the surface, as they > should > be since Freesurfer did not alter the space. So, how can I use mrivol2surf > to resample the surface such that the vertices carry the label info? What > output format should I use in mrivol2surf? How can I open this output in > Freeview? > > For instance, when I try a .dat that creates no transformation and > save the > output as .mgz and use Overlay in Freeview, I get snapshot #2. So, > something > is going wrong in my mrivol2surf command. > > My apologies for the questions > Trisanna > > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > I'm not sure what identity.nofile is or what you are trying to do (no > previous info in the email). If whatever you are trying to map to the > surface is already in anatomical space (so no registration necessary), > then you can use --regheader with mri_vol2surf. mri_cor2label will > take > a volume format as input (ie, mgz, nii.gz ,etc) > > On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: > > > > Hi All! > > > > Could someone please tell me how to run mri_vol2surf using > > identity.nofile as the transformation? I cannot find any > documentation > > on identity.nofile > > > > Additionally, if my next step is to use the output of > mri_vol2surf in > > mri_cor2label, which takes surface overlays OR volumes, what format > > should my output be for mri_vol2surf? > > > > many thanks! > > > > Trisanna > > > > -- > > Ph.D. Candidate > > McGill University > > Integrated Program in Neuroscience > > Psychology > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
