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Dear Eugenio,
thank you for your response. Unfortunately it is not possible to share the whole subject. Would it be helpful to send you more screenshots of all three views (coronal, sagittal, axial) with different mask opacities?
Kind regards, Franziska
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von freesurfer-request@nmr.mgh.harvard.edu Gesendet: Mittwoch, 17. Februar 2021 14:56 An: freesurfer@nmr.mgh.harvard.edu Betreff: Freesurfer Digest, Vol 204, Issue 33
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Today's Topics:
1. Re: overlap/intersection of labels? (Trisanna Sprung-Much) 2. Re: FreeSurfer 7 vs FreeSurfer 6 surface differences (Mike Schmidt) 3. VB password (?????????) 4. Thalamic nuclei segmentation - PuM nucleus mis-segmentation? (Gronow, Franziska) 5. Queries in qdec (Koustav Chatterjee) 6. Re: Thalamic nuclei segmentation - PuM nucleus mis-segmentation? (Iglesias Gonzalez, Juan E.) 7. Re: Thalamic nuclei segmentation - PuM nucleus mis-segmentation? (Iglesias Gonzalez, Juan E.)
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Message: 1 Date: Tue, 16 Feb 2021 21:58:34 +0000 From: Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca Subject: Re: [Freesurfer] overlap/intersection of labels? To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: D5D39FEB-2D09-4051-B15C-49E61BFB8B61@mail.mcgill.ca Content-Type: text/plain; charset="utf-8"
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Hi Cornelius
I found something that computes the overlap of labels across the same vertex when doing some research about this, not sure if this is what you mean:
https://secure-web.cisco.com/116MIwNJShgHoW9J9evPl5bCi0xgcx82bMJ48_l7VTkyo4r...
See specifically: --nhits <nhits_file> This option creates a diagnostic file showing whether the cumulative effect of all the label files happens to assign more than one label to each vertex. The output file is a FreeSurferhttps://secure-web.cisco.com/1QIgJhgEjv5N9NM6Uh6927wVezy6eduY2p7_2aAiUh0J8fE_QRjLZ5IwPbIC4gnKD6g26N7TVbaIwYLg5BdgQSCFY1LmWY1cDfBL-R49zhRDt-6TzW_S84l6Z-4U3QS-SBlj8HR82qBl0HjcfjS2buz3mtuIQomiilbbafLXzRw1wQSaUnmj1OITA84m-fC1C8HrL430p2kCyyotFmJGKKwiiXBgMYlYljQIFiqINhAJFUVeI9kbMvioqTgmQZvjStJ8ARcmqHgrk_981OzG8NQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeSurfer 'overlay' format file, in which each vertex has an associated value, in this case the count of labels assigned to that vertex. This can be displayed in tksurfer as a color. Setting fthresh to 1.5 will distinguish good vertices (count<=1) from bad (count>=2).
I know there is also a command merge_labels that may help?
Best,
Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre --
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Dr. Cornelius Kronlage" Cornelius.Kronlage@med.uni-tuebingen.de Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, February 16, 2021 at 11:19 AM To: "'freesurfer@nmr.mgh.harvard.edu'" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] overlap/intersection of labels?
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Dear freesurfers,
is there an elegant way of computing the intersection or overlap of different labels or - which would be even more useful for my application - annotations?
I only managed to find labels_intersect (which appears to be from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16WQ5tQQPY74lwcUD6e-u4HAYMeACJcAQ4y9i44WDTIAnwC...https://secure-web.cisco.com/12D3ntbm8RDBV366hh41UjEkFWk2mrjQHSMiY8WEom0naUegbdbmI9Bk7UNIwOTDDV40505y4xUMucZzUUWAKig63gNPrAZl0JMYNPDR9rlE4fUcOuQETynMWSKJG67sRNzzZQq8VF7AEsupWpjkrPP17ola-zMVT-3GDtM_dSs0-j76spejYlLevtumd4uKC8BNXwnxiW47uZxy5cBV4IPlI1yL8DP4GKO7QCjCWHuSjiE1xMapPwxOxVnVfHUKM/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg11344.html ) which is awfully slow. In case this is of use for anyone else, I att ached a modified version using 'join' that runs much faster, only has some compatibility issues with Mac.
time labels_intersect precentral.label frontal.label out1.label > /dev/null
real 1m41.862s user 0m31.052s sys 0m30.757s
time bash bash_labels_intersect.sh precentral.label frontal.label out2.label
real 0m0.193s user 0m0.118s sys 0m0.015s
diff -w out1.label out2.label
Thank you and best wishes
Cornelius
-- Cornelius Kronlage Assistenzarzt Klinik f?r Neurologie | Neurologie mit Schwerpunkt Epileptologie Universit?tsklinikum T?bingen Hoppe-Seyler-Str. 3 | 72076 T?bingen
Sure! The more slices the better __ Maybe it would be possible to share norm.mgz (which is skull stripped and thus deidentified) and the segmentation? Or maybe even crop norm.mgz around the thalami with Freeview? Cheers, /E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
On 2/23/21, 11:00, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Gronow, Franziska" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Franziska.Gronow@uniklinikum-dresden.de> wrote:
External Email - Use Caution
Dear Eugenio,
thank you for your response. Unfortunately it is not possible to share the whole subject. Would it be helpful to send you more screenshots of all three views (coronal, sagittal, axial) with different mask opacities?
Kind regards, Franziska
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von freesurfer-request@nmr.mgh.harvard.edu Gesendet: Mittwoch, 17. Februar 2021 14:56 An: freesurfer@nmr.mgh.harvard.edu Betreff: Freesurfer Digest, Vol 204, Issue 33
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1ak9QaJ1_1rhd69MSCjVvSgBkkgvkfHMc4AJu1OKXYs9k4p... or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: overlap/intersection of labels? (Trisanna Sprung-Much) 2. Re: FreeSurfer 7 vs FreeSurfer 6 surface differences (Mike Schmidt) 3. VB password (?????????) 4. Thalamic nuclei segmentation - PuM nucleus mis-segmentation? (Gronow, Franziska) 5. Queries in qdec (Koustav Chatterjee) 6. Re: Thalamic nuclei segmentation - PuM nucleus mis-segmentation? (Iglesias Gonzalez, Juan E.) 7. Re: Thalamic nuclei segmentation - PuM nucleus mis-segmentation? (Iglesias Gonzalez, Juan E.)
----------------------------------------------------------------------
Message: 1 Date: Tue, 16 Feb 2021 21:58:34 +0000 From: Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca Subject: Re: [Freesurfer] overlap/intersection of labels? To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: D5D39FEB-2D09-4051-B15C-49E61BFB8B61@mail.mcgill.ca Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi Cornelius
I found something that computes the overlap of labels across the same vertex when doing some research about this, not sure if this is what you mean:
https://secure-web.cisco.com/116MIwNJShgHoW9J9evPl5bCi0xgcx82bMJ48_l7VTkyo4r...
See specifically: --nhits <nhits_file> This option creates a diagnostic file showing whether the cumulative effect of all the label files happens to assign more than one label to each vertex. The output file is a FreeSurferhttps://secure-web.cisco.com/1QIgJhgEjv5N9NM6Uh6927wVezy6eduY2p7_2aAiUh0J8fE_QRjLZ5IwPbIC4gnKD6g26N7TVbaIwYLg5BdgQSCFY1LmWY1cDfBL-R49zhRDt-6TzW_S84l6Z-4U3QS-SBlj8HR82qBl0HjcfjS2buz3mtuIQomiilbbafLXzRw1wQSaUnmj1OITA84m-fC1C8HrL430p2kCyyotFmJGKKwiiXBgMYlYljQIFiqINhAJFUVeI9kbMvioqTgmQZvjStJ8ARcmqHgrk_981OzG8NQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFreeSurfer 'overlay' format file, in which each vertex has an associated value, in this case the count of labels assigned to that vertex. This can be displayed in tksurfer as a color. Setting fthresh to 1.5 will distinguish good vertices (count<=1) from bad (count>=2).
I know there is also a command merge_labels that may help?
Best,
Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre --
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Dr. Cornelius Kronlage" Cornelius.Kronlage@med.uni-tuebingen.de Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, February 16, 2021 at 11:19 AM To: "'freesurfer@nmr.mgh.harvard.edu'" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] overlap/intersection of labels?
External Email - Use Caution
Dear freesurfers,
is there an elegant way of computing the intersection or overlap of different labels or - which would be even more useful for my application - annotations?
I only managed to find labels_intersect (which appears to be from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16WQ5tQQPY74lwcUD6e-u4HAYMeACJcAQ4y9i44WDTIAnwC...https://secure-web.cisco.com/12D3ntbm8RDBV366hh41UjEkFWk2mrjQHSMiY8WEom0naUegbdbmI9Bk7UNIwOTDDV40505y4xUMucZzUUWAKig63gNPrAZl0JMYNPDR9rlE4fUcOuQETynMWSKJG67sRNzzZQq8VF7AEsupWpjkrPP17ola-zMVT-3GDtM_dSs0-j76spejYlLevtumd4uKC8BNXwnxiW47uZxy5cBV4IPlI1yL8DP4GKO7QCjCWHuSjiE1xMapPwxOxVnVfHUKM/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg11344.html ) which is awfully slow. In case this is of use for anyone else, I att ached a modified version using 'join' that runs much faster, only has some compatibility issues with Mac.
>time labels_intersect precentral.label frontal.label out1.label > >/dev/null
real 1m41.862s user 0m31.052s sys 0m30.757s >time bash bash_labels_intersect.sh precentral.label frontal.label >out2.label
real 0m0.193s user 0m0.118s sys 0m0.015s >diff -w out1.label out2.label >
Thank you and best wishes
Cornelius
-- Cornelius Kronlage Assistenzarzt Klinik f?r Neurologie | Neurologie mit Schwerpunkt Epileptologie Universit?tsklinikum T?bingen Hoppe-Seyler-Str. 3 | 72076 T?bingen
freesurfer@nmr.mgh.harvard.edu
-
Gronow, Franziska -
Iglesias Gonzalez, Juan E.