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Dear Freesurfer experts,
I created .mgh files from a dimensionality reduction analyses (similar to parcels from a known parcellation). These matrices have low values near to 0. When I overlay each of the .mgh file in freeview, it gets automatically thresholded with what seemed to me the median or mean of all the vertices' values (i.e., when looking at the "configure overlay" option)--however, this is not the case. Thus, I wanted to ask how the threshold is precisely set, so that I can automate and incorporate it in other scripts for binarizing my matrices.
Thanks a lot in advance for your help, Rachele
HI Rachele,
You can set overlay threshold from the command-line like this:
freeview -f lh.inflated:overlay=overlay_file:overlay_threshold=low,high
More information about threshold setting can be found by:
freeview -h
Best, Ruopeng
On 3/10/20 11:29 AM, Rachele Sanfelici wrote:
External Email - Use Caution
Dear Freesurfer experts,
I created .mgh files from a dimensionality reduction analyses (similar to parcels from a known parcellation). These matrices have low values near to 0. When I overlay each of the .mgh file in freeview, it gets automatically thresholded with what seemed to me the median or mean of all the vertices' values (i.e., when looking at the "configure overlay" option)--however, this is not the case. Thus, I wanted to ask how the threshold is precisely set, so that I can automate and incorporate it in other scripts for binarizing my matrices.
Thanks a lot in advance for your help, Rachele
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Freesurfer experts,
Sorry for catching up so late, you can imagine the situation here in Europe..
Thank you Ruopeng for your answer! What I’m trying to figure out, though, is how Freeview automatically sets the threshold for overlays, not how to set it myself. I tried several combinations with my data (median, mean, 50th percentile), but none gives me the same result as the freeview automatic threshold. Could you please give me more information or a reference? Are you e.g. excluding the highest values (to avoid outliers) or truncating the values after e.g. 8 numbers after comma?
Thank you again!
Il giorno 10 mar 2020, alle ore 16:44, Ruopeng Wang rpwang@nmr.mgh.harvard.edu ha scritto:
HI Rachele,
You can set overlay threshold from the command-line like this:
freeview -f lh.inflated:overlay=overlay_file:overlay_threshold=low,high file:///overlay_threshold=low,high More information about threshold setting can be found by:
freeview -h
Best, Ruopeng
On 3/10/20 11:29 AM, Rachele Sanfelici wrote:
External Email - Use CautionDear Freesurfer experts,
I created .mgh files from a dimensionality reduction analyses (similar to parcels from a known parcellation). These matrices have low values near to 0. When I overlay each of the .mgh file in freeview, it gets automatically thresholded with what seemed to me the median or mean of all the vertices' values (i.e., when looking at the "configure overlay" option)--however, this is not the case. Thus, I wanted to ask how the threshold is precisely set, so that I can automate and incorporate it in other scripts for binarizing my matrices.
Thanks a lot in advance for your help, Rachele
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Rachele Sanfelici, Psychologin PRONIA Früherkennungsambulanz („Personalized Prognostic Tools for Early Psychosis Management“)
Klinik und Poliklinik für Psychiatrie und Psychotherapie Ludwig-Maximilians-Universität München Nußbaumstr. 7, 80336 München Tel.: +49 (0)89/4400- 52731 Homepage: http://pronia.eu%E2%80%8B%E2%80%8B
Hi Rachele,
The automatic threshold setting of overlay in freeview was meant to just quickly set an initial value for user to see. As I check the code, the high threshold is set as the maximum value, the low is set simply as the mid point between min and max values. It wasn’t meant to be optimal but I think it can definitely be improved. I will update it to 50th percentile in the development version.
Best, Ruopeng
On Mar 17, 2020, at 4:27 AM, Rachele Sanfelici r.sanfelici@gmail.com wrote:
External Email - Use CautionDear Freesurfer experts,
Sorry for catching up so late, you can imagine the situation here in Europe..
Thank you Ruopeng for your answer! What I’m trying to figure out, though, is how Freeview automatically sets the threshold for overlays, not how to set it myself. I tried several combinations with my data (median, mean, 50th percentile), but none gives me the same result as the freeview automatic threshold. Could you please give me more information or a reference? Are you e.g. excluding the highest values (to avoid outliers) or truncating the values after e.g. 8 numbers after comma?
Thank you again!
Il giorno 10 mar 2020, alle ore 16:44, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> ha scritto:
HI Rachele,
You can set overlay threshold from the command-line like this:
freeview -f lh.inflated:overlay=overlay_file:overlay_threshold=low,high file:///overlay_threshold=low,high More information about threshold setting can be found by:
freeview -h
Best, Ruopeng
On 3/10/20 11:29 AM, Rachele Sanfelici wrote:
External Email - Use CautionDear Freesurfer experts,
I created .mgh files from a dimensionality reduction analyses (similar to parcels from a known parcellation). These matrices have low values near to 0. When I overlay each of the .mgh file in freeview, it gets automatically thresholded with what seemed to me the median or mean of all the vertices' values (i.e., when looking at the "configure overlay" option)--however, this is not the case. Thus, I wanted to ask how the threshold is precisely set, so that I can automate and incorporate it in other scripts for binarizing my matrices.
Thanks a lot in advance for your help, Rachele
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Rachele Sanfelici, Psychologin PRONIA Früherkennungsambulanz („Personalized Prognostic Tools for Early Psychosis Management“)
Klinik und Poliklinik für Psychiatrie und Psychotherapie Ludwig-Maximilians-Universität München Nußbaumstr. 7, 80336 München Tel.: +49 (0)89/4400- 52731 Homepage: http://pronia.eu http://pronia.eu/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Rachele Sanfelici -
Ruopeng Wang