many thanks - will give this a go! -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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 >
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