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Hi Bronwyn,

the file looks good in a text editor. I just tried in R and it seems to load okay, see the attached screenshot for what it looks like. Is that what you would expect?

Tim

```R library('fsbrain'); lb = freesurferformats::read.fs.label("~/Downloads/rh.area.stack.R3B.fwhm20.lmem.final.200821.s.avg.dx.FDR-0003.label"); vis.labeldata.on.subject(sjd, 'fsaverage', lh_labeldata = lb, rh_labeldata = NULL); ```

On 09/21/2020 3:35 AM Bronwyn Overs b.overs@neura.edu.au wrote:

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Hi Ruopeng,

Thank you for your reply. I have since tried to open these problematic label files using freeview from FS 7.1.1, but I am still not able to see them on my surface. I now attach one of the two label files with this issue (the other was 6.6MB in size so was too large to send by email).

Kind regards,

Bronwyn Overs

Research Assistant

Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725

[ http://neura.edu.au/ | neura.edu.au  ]

[ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

From: "Wang, Ruopeng" RWANG4@MGH.HARVARD.EDU To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 18, 2020 10:28:45 PM Subject: Re: [Freesurfer] Viewing labels in freeview

Hi Bronwyn,

Would it be possible for you to send us the label file? You may also try the latest freeview from FS 7.1.1. A lot of changes and fixes have been made since version 5.3.

Best, Ruopeng

On Sep 18, 2020, at 2:03 AM, Bronwyn Overs < [ mailto:b.overs@neura.edu.au | b.overs@neura.edu.au ] > wrote:

External Email - Use Caution

Dear freesurfer mailing list,

I generated my own label file from a linear mixed effects model and now I want to view this label file on the surface of fsaverage using freeview. I am able to load the surface and label files successfully from the command line using the following:

freeview -f $SUBJECTS_DIR/fsaverage_mod/surf/lh.inflated:label=lh.volume.stack.R3B.fwhm20.lmem.final.200817.gender.FDR-0001.label

However, once freeview is open and the label file is loaded, I cannot see the label displayed on the surface (screenshot attached). I am currently using freesurfer version 5.3.0. Can someone please tell me how to make the label file visible on the surface of fsaverage?

Kind regards,

Bronwyn Overs Research Assistant <neura-logo-email.png>

Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725

[ http://neura.edu.au/ | neura.edu.au  ]

[ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

<Screenshot_Freeview_Label.png> _______________________________________________ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | 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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Hi Ruopeng,

Thank you for looking into this for me, changing the threshold as you suggested has solved my problem.

Kind regards,

Bronwyn Overs

Research Assistant

Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725

[ http://neura.edu.au/ | neura.edu.au  ]

[ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

From: "Wang, Ruopeng" RWANG4@MGH.HARVARD.EDU To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Monday, September 21, 2020 10:44:42 PM Subject: Re: [Freesurfer] Viewing labels in freeview

Hi Bronwyn,

All the values in your label are negative, while in freeview the default threshold is 0. If you change the threshold to a negative value from the GUI, you should see it.

Best, Ruopeng

On Sep 20, 2020, at 9:35 PM, Bronwyn Overs < [ mailto:b.overs@neura.edu.au | b.overs@neura.edu.au ] > wrote:

External Email - Use Caution

Hi Ruopeng,

Thank you for your reply. I have since tried to open these problematic label files using freeview from FS 7.1.1, but I am still not able to see them on my surface. I now attach one of the two label files with this issue (the other was 6.6MB in size so was too large to send by email).

Kind regards,

Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725

[ http://neura.edu.au/ | neura.edu.au  ]

[ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

From: "Wang, Ruopeng" < [ mailto:RWANG4@MGH.HARVARD.EDU | RWANG4@MGH.HARVARD.EDU ] > To: "Freesurfer support list" < [ mailto:freesurfer@nmr.mgh.harvard.edu | freesurfer@nmr.mgh.harvard.edu ] > Sent: Friday, September 18, 2020 10:28:45 PM Subject: Re: [Freesurfer] Viewing labels in freeview

Hi Bronwyn,

Would it be possible for you to send us the label file? You may also try the latest freeview from FS 7.1.1. A lot of changes and fixes have been made since version 5.3.

Best, Ruopeng

BQ_BEGIN

On Sep 18, 2020, at 2:03 AM, Bronwyn Overs < [ mailto:b.overs@neura.edu.au | b.overs@neura.edu.au ] > wrote:

External Email - Use Caution

Dear freesurfer mailing list,

I generated my own label file from a linear mixed effects model and now I want to view this label file on the surface of fsaverage using freeview. I am able to load the surface and label files successfully from the command line using the following:

freeview -f $SUBJECTS_DIR/fsaverage_mod/surf/lh.inflated:label=lh.volume.stack.R3B.fwhm20.lmem.final.200817.gender.FDR-0001.label

However, once freeview is open and the label file is loaded, I cannot see the label displayed on the surface (screenshot attached). I am currently using freesurfer version 5.3.0. Can someone please tell me how to make the label file visible on the surface of fsaverage?

Kind regards,

Bronwyn Overs Research Assistant <neura-logo-email.png>

Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725

[ http://neura.edu.au/ | neura.edu.au  ]

[ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

<Screenshot_Freeview_Label.png> _______________________________________________ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | Freesurfer@nmr.mgh.harvard.edu ] [ https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer | https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ]

_______________________________________________ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | Freesurfer@nmr.mgh.harvard.edu ] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <rh.area.stack.R3B.fwhm20.lmem.final.200821.s.avg.dx.FDR-0003.label> _______________________________________________ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | Freesurfer@nmr.mgh.harvard.edu ] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

BQ_END

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