External Email - Use Caution
Dear Freesurfer mailing list,
I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p -value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file?
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 ]
External Email - Use Caution
Hi,
I suppose what we are seeing in the top row of your figure are Freesurfer labels, right? I.e. you probably used the '--olab' argument with the 'mri_surfcluster' command, and are loading each cluster from a different label file?
If my speculation is correct, then what you observe could be due to the 'threshold' setting in freeview, i.e. this little box just below the label box in the left part of the GUI.
This threshold is by default set to zero, but lowering it to some sufficiently negative value (i.e. the minimum value in the 'sig' map) should also display those regions that seem to be missing at the moment.
At least this is what I observed when I tried to reproduce your observation, i.e. I could create (and reverse by setting another threshold) similar 'cut-outs' in the cluster maps.
In addition, you could also load the ouput files that are produced by the '--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I would guess that they don't show this pattern of missing areas.
Hope this helps,
Kersten
On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote:
External Email - Use Caution
Dear Freesurfer mailing list,
I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p-value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1567613630.3700.24.camel@dzne.de]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
neura.edu.au http://neura.edu.au/
Twitterhttps://twitter.com/neuraustralia | Facebookhttps://www.facebook.com/NeuroscienceResearchAustralia | Subscribehttp://www.neura.edu.au/help-research/subscribe
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Kersten,
Thank you for your detailed reply and sorry for this delayed response.
Yes the top row in my figure (attached again) was produced by using the '--olab' argument with the 'mri_surfcluster' command and then loading each cluster from a different label file. I attempted to follow your suggestion and adjust the label 'threshold' in Freeview to minimum value in my significance map (-5), but this did not display the missing regions - the surface remained the same as row 1 of the attached figure.
To provide you with a little more detail about my method - am using 'mri_surfcluster' with the '--olab' argument to derive all of my significant clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each label files (from the 'mri_surfcluster' command) back onto the images for each of my individual subjects, and then generate subject level stats for each cluster using 'mris_anatomical_stats'. At the moment I am concerned that the subject level stats I have derived from my label files do not accurately represent each significant cluster in totality as regions appear to be missing even when i adjust the minimum threshold. As an alternative, when using 'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments for '--olab', and still perform my 'mri_label2label' and 'mris_anatomical_stats' steps?
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: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 5, 2019 2:13:50 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi,
I suppose what we are seeing in the top row of your figure are Freesurfer labels, right? I.e. you probably used the '--olab' argument with the 'mri_surfcluster' command, and are loading each cluster from a different label file?
If my speculation is correct, then what you observe could be due to the 'threshold' setting in freeview, i.e. this little box just below the label box in the left part of the GUI.
This threshold is by default set to zero, but lowering it to some sufficiently negative value (i.e. the minimum value in the 'sig' map) should also display those regions that seem to be missing at the moment.
At least this is what I observed when I tried to reproduce your observation, i.e. I could create (and reverse by setting another threshold) similar 'cut-outs' in the cluster maps.
In addition, you could also load the ouput files that are produced by the '--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I would guess that they don't show this pattern of missing areas.
Hope this helps,
Kersten
On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote:
External Email - Use Caution
Dear Freesurfer mailing list,
I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p -value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file?
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 ]
_______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bronwyn,
thanks for the update and additional info.
I have to say that I have no very good clue at the moment.
Could you maybe upload an examplary file to the Freesurfer FileDrop at https://gate.nmr.mgh.harvard.edu/filedrop2/ so that we can take a closer look?
Best regards,
Kersten
On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote:
External Email - Use Caution
Hi Kersten,
Thank you for your detailed reply and sorry for this delayed response.
Yes the top row in my figure (attached again) was produced by using the '--olab' argument with the 'mri_surfcluster' command and then loading each cluster from a different label file. I attempted to follow your suggestion and adjust the label 'threshold' in Freeview to minimum value in my significance map (-5), but this did not display the missing regions - the surface remained the same as row 1 of the attached figure.
To provide you with a little more detail about my method - am using 'mri_surfcluster' with the '--olab' argument to derive all of my significant clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each label files (from the 'mri_surfcluster' command) back onto the images for each of my individual subjects, and then generate subject level stats for each cluster using 'mris_anatomical_stats'. At the moment I am concerned that the subject level stats I have derived from my label files do not accurately represent each significant cluster in totality as regions appear to be missing even when i adjust the minimum threshold. As an alternative, when using 'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments for '--olab', and still perform my 'mri_label2label' and 'mris_anatomical_stats' steps?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1569997292.6432.28.camel@dzne.de]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
neura.edu.au http://neura.edu.au/
Twitterhttps://twitter.com/neuraustralia | Facebookhttps://www.facebook.com/NeuroscienceResearchAustralia | Subscribehttp://www.neura.edu.au/help-research/subscribe
________________________________ From: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 5, 2019 2:13:50 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi,
I suppose what we are seeing in the top row of your figure are Freesurfer labels, right? I.e. you probably used the '--olab' argument with the 'mri_surfcluster' command, and are loading each cluster from a different label file?
If my speculation is correct, then what you observe could be due to the 'threshold' setting in freeview, i.e. this little box just below the label box in the left part of the GUI.
This threshold is by default set to zero, but lowering it to some sufficiently negative value (i.e. the minimum value in the 'sig' map) should also display those regions that seem to be missing at the moment.
At least this is what I observed when I tried to reproduce your observation, i.e. I could create (and reverse by setting another threshold) similar 'cut-outs' in the cluster maps.
In addition, you could also load the ouput files that are produced by the '--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I would guess that they don't show this pattern of missing areas.
Hope this helps,
Kersten
On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote:
External Email - Use Caution
Dear Freesurfer mailing list,
I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p-value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1569997292.6432.28.camel@dzne.de]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
neura.edu.au http://neura.edu.au/
Twitterhttps://twitter.com/neuraustralia | Facebookhttps://www.facebook.com/NeuroscienceResearchAustralia | Subscribehttp://www.neura.edu.au/help-research/subscribe
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Kersten,
That would be very helpful thank you. What email address should I designate as the recipient when using Freesurfer FileDrop?
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: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, October 2, 2019 4:21:32 PM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi Bronwyn,
thanks for the update and additional info.
I have to say that I have no very good clue at the moment.
Could you maybe upload an examplary file to the Freesurfer FileDrop at [ https://gate.nmr.mgh.harvard.edu/filedrop2/ | https://gate.nmr.mgh.harvard.edu/filedrop2/ ] so that we can take a closer look?
Best regards,
Kersten
On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote:
External Email - Use Caution
Hi Kersten,
Thank you for your detailed reply and sorry for this delayed response.
Yes the top row in my figure (attached again) was produced by using the '--olab' argument with the 'mri_surfcluster' command and then loading each cluster from a different label file. I attempted to follow your suggestion and adjust the label 'threshold' in Freeview to minimum value in my significance map (-5), but this did not display the missing regions - the surface remained the same as row 1 of the attached figure.
To provide you with a little more detail about my method - am using 'mri_surfcluster' with the '--olab' argument to derive all of my significant clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each label files (from the 'mri_surfcluster' command) back onto the images for each of my individual subjects, and then generate subject level stats for each cluster using 'mris_anatomical_stats'. At the moment I am concerned that the subject level stats I have derived from my label files do not accurately represent each significant cluster in totality as regions appear to be missing even when i adjust the minimum threshold. As an alternative, when using 'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments for '--olab', and still perform my 'mri_label2label' and 'mris_anatomical_stats' steps?
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: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 5, 2019 2:13:50 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi,
I suppose what we are seeing in the top row of your figure are Freesurfer labels, right? I.e. you probably used the '--olab' argument with the 'mri_surfcluster' command, and are loading each cluster from a different label file?
If my speculation is correct, then what you observe could be due to the 'threshold' setting in freeview, i.e. this little box just below the label box in the left part of the GUI.
This threshold is by default set to zero, but lowering it to some sufficiently negative value (i.e. the minimum value in the 'sig' map) should also display those regions that seem to be missing at the moment.
At least this is what I observed when I tried to reproduce your observation, i.e. I could create (and reverse by setting another threshold) similar 'cut-outs' in the cluster maps.
In addition, you could also load the ouput files that are produced by the '--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I would guess that they don't show this pattern of missing areas.
Hope this helps,
Kersten
On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote:
BQ_BEGIN
External Email - Use Caution
Dear Freesurfer mailing list,
I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p -value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file?
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 ]
_______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu 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 | https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ]
BQ_END
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi,
please use mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu, he'll forward it to me.
Thanks,
Kersten
On Di, 2019-10-15 at 11:03 +1100, Bronwyn Overs wrote:
External Email - Use Caution
Hi Kersten,
That would be very helpful thank you. What email address should I designate as the recipient when using Freesurfer FileDrop?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1571152553.22849.38.camel@dzne.de]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
neura.edu.au http://neura.edu.au/
Twitterhttps://twitter.com/neuraustralia | Facebookhttps://www.facebook.com/NeuroscienceResearchAustralia | Subscribehttp://www.neura.edu.au/help-research/subscribe
________________________________ From: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, October 2, 2019 4:21:32 PM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi Bronwyn,
thanks for the update and additional info.
I have to say that I have no very good clue at the moment.
Could you maybe upload an examplary file to the Freesurfer FileDrop at https://gate.nmr.mgh.harvard.edu/filedrop2/ so that we can take a closer look?
Best regards,
Kersten
On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote:
External Email - Use Caution
Hi Kersten,
Thank you for your detailed reply and sorry for this delayed response.
Yes the top row in my figure (attached again) was produced by using the '--olab' argument with the 'mri_surfcluster' command and then loading each cluster from a different label file. I attempted to follow your suggestion and adjust the label 'threshold' in Freeview to minimum value in my significance map (-5), but this did not display the missing regions - the surface remained the same as row 1 of the attached figure.
To provide you with a little more detail about my method - am using 'mri_surfcluster' with the '--olab' argument to derive all of my significant clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each label files (from the 'mri_surfcluster' command) back onto the images for each of my individual subjects, and then generate subject level stats for each cluster using 'mris_anatomical_stats'. At the moment I am concerned that the subject level stats I have derived from my label files do not accurately represent each significant cluster in totality as regions appear to be missing even when i adjust the minimum threshold. As an alternative, when using 'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments for '--olab', and still perform my 'mri_label2label' and 'mris_anatomical_stats' steps?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1571152553.22849.38.camel@dzne.de]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
neura.edu.au http://neura.edu.au/
Twitterhttps://twitter.com/neuraustralia | Facebookhttps://www.facebook.com/NeuroscienceResearchAustralia | Subscribehttp://www.neura.edu.au/help-research/subscribe
________________________________ From: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 5, 2019 2:13:50 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi,
I suppose what we are seeing in the top row of your figure are Freesurfer labels, right? I.e. you probably used the '--olab' argument with the 'mri_surfcluster' command, and are loading each cluster from a different label file?
If my speculation is correct, then what you observe could be due to the 'threshold' setting in freeview, i.e. this little box just below the label box in the left part of the GUI.
This threshold is by default set to zero, but lowering it to some sufficiently negative value (i.e. the minimum value in the 'sig' map) should also display those regions that seem to be missing at the moment.
At least this is what I observed when I tried to reproduce your observation, i.e. I could create (and reverse by setting another threshold) similar 'cut-outs' in the cluster maps.
In addition, you could also load the ouput files that are produced by the '--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I would guess that they don't show this pattern of missing areas.
Hope this helps,
Kersten
On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote:
External Email - Use Caution
Dear Freesurfer mailing list,
I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p-value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1571152553.22849.38.camel@dzne.de]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
neura.edu.au http://neura.edu.au/
Twitterhttps://twitter.com/neuraustralia | Facebookhttps://www.facebook.com/NeuroscienceResearchAustralia | Subscribehttp://www.neura.edu.au/help-research/subscribe
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Kersten,
Did you recieve the files I dropped to [ mailto:mreuter@nmr.mgh.harvard.edu | mreuter@nmr.mgh.harvard.edu ] on the 16th of October (titled 'BAR_Sydney_FSIssues_SurfThreshLabels.zip')?
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: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, October 16, 2019 2:15:53 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi,
please use [ mailto:mreuter@nmr.mgh.harvard.edu | mreuter@nmr.mgh.harvard.edu ] , he'll forward it to me.
Thanks,
Kersten
On Di, 2019-10-15 at 11:03 +1100, Bronwyn Overs wrote:
External Email - Use Caution
Hi Kersten,
That would be very helpful thank you. What email address should I designate as the recipient when using Freesurfer FileDrop?
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: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, October 2, 2019 4:21:32 PM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi Bronwyn,
thanks for the update and additional info.
I have to say that I have no very good clue at the moment.
Could you maybe upload an examplary file to the Freesurfer FileDrop at [ https://gate.nmr.mgh.harvard.edu/filedrop2/ | https://gate.nmr.mgh.harvard.edu/filedrop2/ ] so that we can take a closer look?
Best regards,
Kersten
On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote:
BQ_BEGIN
External Email - Use Caution
Hi Kersten,
Thank you for your detailed reply and sorry for this delayed response.
Yes the top row in my figure (attached again) was produced by using the '--olab' argument with the 'mri_surfcluster' command and then loading each cluster from a different label file. I attempted to follow your suggestion and adjust the label 'threshold' in Freeview to minimum value in my significance map (-5), but this did not display the missing regions - the surface remained the same as row 1 of the attached figure.
To provide you with a little more detail about my method - am using 'mri_surfcluster' with the '--olab' argument to derive all of my significant clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each label files (from the 'mri_surfcluster' command) back onto the images for each of my individual subjects, and then generate subject level stats for each cluster using 'mris_anatomical_stats'. At the moment I am concerned that the subject level stats I have derived from my label files do not accurately represent each significant cluster in totality as regions appear to be missing even when i adjust the minimum threshold. As an alternative, when using 'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments for '--olab', and still perform my 'mri_label2label' and 'mris_anatomical_stats' steps?
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: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 5, 2019 2:13:50 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi,
I suppose what we are seeing in the top row of your figure are Freesurfer labels, right? I.e. you probably used the '--olab' argument with the 'mri_surfcluster' command, and are loading each cluster from a different label file?
If my speculation is correct, then what you observe could be due to the 'threshold' setting in freeview, i.e. this little box just below the label box in the left part of the GUI.
This threshold is by default set to zero, but lowering it to some sufficiently negative value (i.e. the minimum value in the 'sig' map) should also display those regions that seem to be missing at the moment.
At least this is what I observed when I tried to reproduce your observation, i.e. I could create (and reverse by setting another threshold) similar 'cut-outs' in the cluster maps.
In addition, you could also load the ouput files that are produced by the '--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I would guess that they don't show this pattern of missing areas.
Hope this helps,
Kersten
On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote:
BQ_BEGIN
External Email - Use Caution
Dear Freesurfer mailing list,
I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p -value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file?
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 ]
_______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu 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 | https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ]
BQ_END
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 | https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ]
BQ_END
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hm,
I think I replied last Wednesday; anyway, below is the message again.
Best regards,
Kersten
-------- Forwarded Message -------- From: "Diers, Kersten /DZNE" <Kersten.Diers@dzne.demailto:%22Diers,%20Kersten%20/DZNE%22%20%3cKersten.Diers@dzne.de%3e> Reply-to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:%22freesurfer@nmr.mgh.harvard.edu%22%20%3cfreesurfer@nmr.mgh.harvard.edu%3e> Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels Date: Wed, 23 Oct 2019 07:39:54 +0000
External Email - Use Caution
Hi Bronwyn,
thanks for sending the files.
I've taken a look, and suggest that you leave out the '--thmax 5' argument from your mri_surfcluster command. Then, it may still be necessary to set the label threshold value in Freeview to a value below zero.
When I run the modified mri_surfcluster command with the example data you provided, the created label resembled the mgh file, i.e. no cut-outs in regions of high significance were present.
Best regards,
Kersten
On Di, 2019-10-29 at 16:46 +1100, Bronwyn Overs wrote:
External Email - Use Caution
Hi Kersten,
Did you recieve the files I dropped to mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu on the 16th of October (titled 'BAR_Sydney_FSIssues_SurfThreshLabels.zip')?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1572344519.5609.7.camel@dzne.de]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
neura.edu.au http://neura.edu.au/
Twitterhttps://twitter.com/neuraustralia | Facebookhttps://www.facebook.com/NeuroscienceResearchAustralia | Subscribehttp://www.neura.edu.au/help-research/subscribe
________________________________ From: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, October 16, 2019 2:15:53 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi,
please use mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu, he'll forward it to me.
Thanks,
Kersten
On Di, 2019-10-15 at 11:03 +1100, Bronwyn Overs wrote:
External Email - Use Caution
Hi Kersten,
That would be very helpful thank you. What email address should I designate as the recipient when using Freesurfer FileDrop?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1572344519.5609.7.camel@dzne.de]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
neura.edu.au http://neura.edu.au/
Twitterhttps://twitter.com/neuraustralia | Facebookhttps://www.facebook.com/NeuroscienceResearchAustralia | Subscribehttp://www.neura.edu.au/help-research/subscribe
________________________________ From: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, October 2, 2019 4:21:32 PM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi Bronwyn,
thanks for the update and additional info.
I have to say that I have no very good clue at the moment.
Could you maybe upload an examplary file to the Freesurfer FileDrop at https://gate.nmr.mgh.harvard.edu/filedrop2/ so that we can take a closer look?
Best regards,
Kersten
On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote:
External Email - Use Caution
Hi Kersten,
Thank you for your detailed reply and sorry for this delayed response.
Yes the top row in my figure (attached again) was produced by using the '--olab' argument with the 'mri_surfcluster' command and then loading each cluster from a different label file. I attempted to follow your suggestion and adjust the label 'threshold' in Freeview to minimum value in my significance map (-5), but this did not display the missing regions - the surface remained the same as row 1 of the attached figure.
To provide you with a little more detail about my method - am using 'mri_surfcluster' with the '--olab' argument to derive all of my significant clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each label files (from the 'mri_surfcluster' command) back onto the images for each of my individual subjects, and then generate subject level stats for each cluster using 'mris_anatomical_stats'. At the moment I am concerned that the subject level stats I have derived from my label files do not accurately represent each significant cluster in totality as regions appear to be missing even when i adjust the minimum threshold. As an alternative, when using 'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments for '--olab', and still perform my 'mri_label2label' and 'mris_anatomical_stats' steps?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1572344519.5609.7.camel@dzne.de]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
neura.edu.au http://neura.edu.au/
Twitterhttps://twitter.com/neuraustralia | Facebookhttps://www.facebook.com/NeuroscienceResearchAustralia | Subscribehttp://www.neura.edu.au/help-research/subscribe
________________________________ From: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 5, 2019 2:13:50 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi,
I suppose what we are seeing in the top row of your figure are Freesurfer labels, right? I.e. you probably used the '--olab' argument with the 'mri_surfcluster' command, and are loading each cluster from a different label file?
If my speculation is correct, then what you observe could be due to the 'threshold' setting in freeview, i.e. this little box just below the label box in the left part of the GUI.
This threshold is by default set to zero, but lowering it to some sufficiently negative value (i.e. the minimum value in the 'sig' map) should also display those regions that seem to be missing at the moment.
At least this is what I observed when I tried to reproduce your observation, i.e. I could create (and reverse by setting another threshold) similar 'cut-outs' in the cluster maps.
In addition, you could also load the ouput files that are produced by the '--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I would guess that they don't show this pattern of missing areas.
Hope this helps,
Kersten
On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote:
External Email - Use Caution
Dear Freesurfer mailing list,
I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p-value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1572344519.5609.7.camel@dzne.de]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
neura.edu.au http://neura.edu.au/
Twitterhttps://twitter.com/neuraustralia | Facebookhttps://www.facebook.com/NeuroscienceResearchAustralia | Subscribehttp://www.neura.edu.au/help-research/subscribe
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Kersten,
Thanks you so much for your reply and sorry I missed your earlier message. I'll implement the suggestions you've suggested. Thanks again.
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: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 29, 2019 9:21:59 PM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hm,
I think I replied last Wednesday; anyway, below is the message again.
Best regards,
Kersten
-------- Forwarded Message -------- From : "Diers, Kersten /DZNE" < [ mailto:%22Diers,%20Kersten%20/DZNE%22%20%3cKersten.Diers@dzne.de%3e | Kersten.Diers@dzne.de ] > Reply-to: Freesurfer support list freesurfer@nmr.mgh.harvard.edu To : freesurfer@nmr.mgh.harvard.edu < [ mailto:%22freesurfer@nmr.mgh.harvard.edu%22%20%3cfreesurfer@nmr.mgh.harvard.edu%3e | freesurfer@nmr.mgh.harvard.edu ] > Subject : Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels Date : Wed, 23 Oct 2019 07:39:54 +0000
External Email - Use Caution
Hi Bronwyn,
thanks for sending the files.
I've taken a look, and suggest that you leave out the '--thmax 5' argument from your mri_surfcluster command. Then, it may still be necessary to set the label threshold value in Freeview to a value below zero.
When I run the modified mri_surfcluster command with the example data you provided, the created label resembled the mgh file, i.e. no cut-outs in regions of high significance were present.
Best regards,
Kersten
On Di, 2019-10-29 at 16:46 +1100, Bronwyn Overs wrote:
External Email - Use Caution
Hi Kersten,
Did you recieve the files I dropped to [ mailto:mreuter@nmr.mgh.harvard.edu | mreuter@nmr.mgh.harvard.edu ] on the 16th of October (titled 'BAR_Sydney_FSIssues_SurfThreshLabels.zip')?
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: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, October 16, 2019 2:15:53 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi,
please use [ mailto:mreuter@nmr.mgh.harvard.edu | mreuter@nmr.mgh.harvard.edu ] , he'll forward it to me.
Thanks,
Kersten
On Di, 2019-10-15 at 11:03 +1100, Bronwyn Overs wrote:
BQ_BEGIN
External Email - Use Caution
Hi Kersten,
That would be very helpful thank you. What email address should I designate as the recipient when using Freesurfer FileDrop?
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: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, October 2, 2019 4:21:32 PM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi Bronwyn,
thanks for the update and additional info.
I have to say that I have no very good clue at the moment.
Could you maybe upload an examplary file to the Freesurfer FileDrop at [ https://gate.nmr.mgh.harvard.edu/filedrop2/ | https://gate.nmr.mgh.harvard.edu/filedrop2/ ] so that we can take a closer look?
Best regards,
Kersten
On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote:
BQ_BEGIN
External Email - Use Caution
Hi Kersten,
Thank you for your detailed reply and sorry for this delayed response.
Yes the top row in my figure (attached again) was produced by using the '--olab' argument with the 'mri_surfcluster' command and then loading each cluster from a different label file. I attempted to follow your suggestion and adjust the label 'threshold' in Freeview to minimum value in my significance map (-5), but this did not display the missing regions - the surface remained the same as row 1 of the attached figure.
To provide you with a little more detail about my method - am using 'mri_surfcluster' with the '--olab' argument to derive all of my significant clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each label files (from the 'mri_surfcluster' command) back onto the images for each of my individual subjects, and then generate subject level stats for each cluster using 'mris_anatomical_stats'. At the moment I am concerned that the subject level stats I have derived from my label files do not accurately represent each significant cluster in totality as regions appear to be missing even when i adjust the minimum threshold. As an alternative, when using 'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments for '--olab', and still perform my 'mri_label2label' and 'mris_anatomical_stats' steps?
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: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 5, 2019 2:13:50 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution
Hi,
I suppose what we are seeing in the top row of your figure are Freesurfer labels, right? I.e. you probably used the '--olab' argument with the 'mri_surfcluster' command, and are loading each cluster from a different label file?
If my speculation is correct, then what you observe could be due to the 'threshold' setting in freeview, i.e. this little box just below the label box in the left part of the GUI.
This threshold is by default set to zero, but lowering it to some sufficiently negative value (i.e. the minimum value in the 'sig' map) should also display those regions that seem to be missing at the moment.
At least this is what I observed when I tried to reproduce your observation, i.e. I could create (and reverse by setting another threshold) similar 'cut-outs' in the cluster maps.
In addition, you could also load the ouput files that are produced by the '--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I would guess that they don't show this pattern of missing areas.
Hope this helps,
Kersten
On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote:
BQ_BEGIN
External Email - Use Caution
Dear Freesurfer mailing list,
I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p -value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file?
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 ]
_______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu 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 | https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ]
BQ_END
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 | https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ]
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 | https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ]
BQ_END
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bronwyn,
thanks for sending the files.
I've taken a look, and suggest that you leave out the '--thmax 5' argument from your mri_surfcluster command. Then, it may still be necessary to set the label threshold value in Freeview to a value below zero.
When I run the modified mri_surfcluster command with the example data you provided, the created label resembled the mgh file, i.e. no cut-outs in regions of high significance were present.
Best regards,
Kersten
On Di, 2019-10-15 at 11:03 +1100, Bronwyn Overs wrote:
External Email - Use Caution
Hi Kersten,
That would be very helpful thank you. What email address should I designate as the recipient when using Freesurfer FileDrop?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1571816394.29396.7.camel@dzne.de]
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________________________________ From: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, October 2, 2019 4:21:32 PM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
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Hi Bronwyn,
thanks for the update and additional info.
I have to say that I have no very good clue at the moment.
Could you maybe upload an examplary file to the Freesurfer FileDrop at https://gate.nmr.mgh.harvard.edu/filedrop2/ so that we can take a closer look?
Best regards,
Kersten
On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote:
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Hi Kersten,
Thank you for your detailed reply and sorry for this delayed response.
Yes the top row in my figure (attached again) was produced by using the '--olab' argument with the 'mri_surfcluster' command and then loading each cluster from a different label file. I attempted to follow your suggestion and adjust the label 'threshold' in Freeview to minimum value in my significance map (-5), but this did not display the missing regions - the surface remained the same as row 1 of the attached figure.
To provide you with a little more detail about my method - am using 'mri_surfcluster' with the '--olab' argument to derive all of my significant clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each label files (from the 'mri_surfcluster' command) back onto the images for each of my individual subjects, and then generate subject level stats for each cluster using 'mris_anatomical_stats'. At the moment I am concerned that the subject level stats I have derived from my label files do not accurately represent each significant cluster in totality as regions appear to be missing even when i adjust the minimum threshold. As an alternative, when using 'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments for '--olab', and still perform my 'mri_label2label' and 'mris_anatomical_stats' steps?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1571816394.29396.7.camel@dzne.de]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
neura.edu.au http://neura.edu.au/
Twitterhttps://twitter.com/neuraustralia | Facebookhttps://www.facebook.com/NeuroscienceResearchAustralia | Subscribehttp://www.neura.edu.au/help-research/subscribe
________________________________ From: "Kersten Diers, DZNE" Kersten.Diers@dzne.de To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, September 5, 2019 2:13:50 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
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Hi,
I suppose what we are seeing in the top row of your figure are Freesurfer labels, right? I.e. you probably used the '--olab' argument with the 'mri_surfcluster' command, and are loading each cluster from a different label file?
If my speculation is correct, then what you observe could be due to the 'threshold' setting in freeview, i.e. this little box just below the label box in the left part of the GUI.
This threshold is by default set to zero, but lowering it to some sufficiently negative value (i.e. the minimum value in the 'sig' map) should also display those regions that seem to be missing at the moment.
At least this is what I observed when I tried to reproduce your observation, i.e. I could create (and reverse by setting another threshold) similar 'cut-outs' in the cluster maps.
In addition, you could also load the ouput files that are produced by the '--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I would guess that they don't show this pattern of missing areas.
Hope this helps,
Kersten
On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote:
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Dear Freesurfer mailing list,
I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p-value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1571816394.29396.7.camel@dzne.de]
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725
neura.edu.au http://neura.edu.au/
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Diers, Kersten /DZNE