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Hi Douglas,

Previously, after I ran recon-all, I would get multiple labels for the same brain area. For example, for BA3b, I have BA3b.label, BA3b.hmap.label and BA3b.thresh.label for each hemisphere.

However this time I only have BA3b_exvivo.label, I wonder how would I get other labels, which command should I run?

Many Thanks

PL

On Wed, 24 Jun 2020 at 16:09, Douglas N. Greve dgreve@mgh.harvard.edu wrote:

I'm not sure what you mean by "like lh.BA3b.label". Are you just talking about the file name or the actual label?

On 6/24/2020 7:37 AM, Peng Liu wrote:

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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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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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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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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:

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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:

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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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