External Email - Use Caution 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" <[email protected]> To: "Freesurfer support list" <[email protected]> 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:[email protected] | [email protected] ] > 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:[email protected] | [email protected] ] > To: "Freesurfer support list" < [ mailto:[email protected] | [email protected] ] > 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:[email protected] | [email protected] ] > 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:[email protected] | [email protected] ] [ https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer | https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ] _______________________________________________ Freesurfer mailing list [ mailto:[email protected] | [email protected] ] 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:[email protected] | [email protected] ] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer BQ_END _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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