Hi Peng

In general you need to give us a lot more information. What ROI analysis are you doing? What command  did you type? What was the screen output of it? That kind of thing

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Peng Liu
Sent: Friday, June 26, 2020 4:51 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Brodmann area labels

        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+ml@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 <claudialiu1120@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 <BFISCHL@mgh.harvard.edu> wrote:
>
> > Can you elaborate? What do you mean it is not working as it should be?
> >
> >
> >
> > *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> > freesurfer-bounces@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 <BFISCHL@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-bounces@nmr.mgh.harvard.edu <
> > freesurfer-bounces@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.liu@med.ovgu.de/Peng.Liu@dzne.de
> >
> > Phone: +49 391 67 25074
> >
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