External Email - Use Caution Not exactly. I can successfully create a nifti mask with this exvivo label, and the brain area it highlighted is correct from observation. But when I try to employ this mask to ROI analysis. The results I got are exactly the same, with and without this mask.
That is why I said it seems not working. If exvivo label is the same label as I used before, I will further look into the script and parameter setups. Thank you for all your help PL On Thu, 25 Jun 2020 at 19:20, Tim Schäfer <ts...@rcmd.org> wrote: > External Email - Use Caution > > What do you mean with 'not working'? Is an incorrect area highlighted on > the brain? Does some command you are using respond with an error message? > > Tim > > > On June 25, 2020 at 5:33 PM Peng Liu <claudialiu1...@gmail.com> wrote: > > > > > > External Email - Use Caution > > > > I usually convert BA3b.label to a nifti mask with SPM to perform ROI > > analysis. But with exvivo label, the mask seems not working. > > > > Many Thanks > > > > PL > > > > On Thu, 25 Jun 2020 at 16:24, Fischl, Bruce <bfis...@mgh.harvard.edu> > wrote: > > > > > Can you elaborate? What do you mean it is not working as it should be? > > > > > > > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > > > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu > > > *Sent:* Thursday, June 25, 2020 7:23 AM > > > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > > *Subject:* Re: [Freesurfer] Brodmann area labels > > > > > > > > > > > > * External Email - Use Caution * > > > > > > Hi Bruce, > > > > > > > > > > > > I have tried this label, but it seems not working as it should be. > That is > > > why I wanted to create labels like before. > > > > > > > > > > > > Thank you so much! > > > > > > > > > > > > PL > > > > > > > > > > > > On Wed, 24 Jun 2020 at 16:58, Fischl, Bruce <bfis...@mgh.harvard.edu> > > > wrote: > > > > > > Hi Peng > > > > > > > > > > > > I think 'lh.BA3b*_exvivo*.label' is the label you want. The _exvivo > just > > > means that the data that went into the prediction was acquired on ex > vivo > > > brains. > > > > > > Cheers > > > > > > Bruce > > > > > > > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > > > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu > > > *Sent:* Wednesday, June 24, 2020 7:38 AM > > > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > > *Subject:* [Freesurfer] Brodmann area labels > > > > > > > > > > > > * External Email - Use Caution * > > > > > > Dear Freesurfer experts, > > > > > > > > > > > > I was trying to perform some ROI analysis with results obtained from > > > recon-all. However I noticed that after recon-all, the labels created > were > > > like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to > create > > > are like 'lh.BA3b.label'. > > > > > > > > > > > > I have tried mri_annotation2label command, but the results I got were > not > > > as wanted either. > > > > > > > > > > > > Does anyone know how to create labels like 'lh.BA3b.label'? > > > > > > > > > > > > Any help would be appreciated a lot! > > > > > > > > > > > > Many Thanks > > > > > > > > > > > > PL > > > > > > -------------------------------------------- > > > > > > [image: Otto-von-Guericke University Magdeburg] > > > > > > > > > > > > Peng Liu, PhD Candidate > > > > > > > > > > > > Institut für Kognitive Neurologie und Demenzforschung (IKND) > > > > > > Otto-von-Guericke Universität Magdeburg > > > > > > Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) > > > > > > > > > > > > Leipziger Str. 44| Haus 64| Raum 217 > > > > > > 39120 Magdeburg, Deutschland > > > > > > > > > > > > Email: peng....@med.ovgu.de/peng....@dzne.de > > > > > > Phone: +49 391 67 25074 > > > > > > _______________________________________________ > > > 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 > > _______________________________________________ > > 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
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