External Email - Use Caution
Dear FreeSurfer Developers,
I'm attempting to analyze thickness changes in a longitudinal design using a mass-univariate approach, as described on the Linear Mixed Effects tutorial at https://secure-web.cisco.com/1HwLf5wG3aIAhV84T5KTL4VUiVpoa1DISeYUypdAqYlExO0....
Before starting the tutorial I followed the preprocessing steps described in section 2 at https://secure-web.cisco.com/1DrlLxryQICRHsEOZazZuvsDg0-s9654AX1e3qQgZGXx_GI... I now have a dataset folder that contains 1) for each subject-session pair to include in the analysis a .long folder 2) a subject specific base template folder that used all available sessions from that subject. All recon-all.log files, both in the base template folder and the subject-session specific long folders, seem to have finished without error.
After that, to prepare files for LME, I created a longitudinal qdec file and used it to prepare thickness.mgh files as described in the beginning of the Linear Mixed Effects tutorial for the mass-univariate approach. When advancing in the analysis the function lme_mass_RgGrow gets stuck: in the terminal the output looks like this
``` Starting region growing algorithm Computing seeds ... ``` and stays like this without advancing. I tried to change the thickness file used (lh.thickness.mgh VS lh.thickness_sm5.mgh VS lh.thickness_sm10.mgh etc..) but unfortunately the error persists.
Looking in the mailing list I found an email with a problem that is similar to mine: https://secure-web.cisco.com/166fF5937wdn5yDLqNvdeV6NeSe3cGRWXBnp12bBcQPqvcq... . Upon inspection of my lh.thickness.mgh file I also noticed that some columns are all zeros: do you know what could cause such columns of zeros to appear in the thickness files and how the problem with the function could be solved to continue in the analysis?
Thank you very much for your help, Kind regards
Sara Bonati
1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2) Platform: macOS Catalina version 10.15.7
External Email - Use Caution
Hi Sara,
It is a bit difficult to tell what exactly is the cause of the problem, but as a potential solution, you might try to exclude the vertices from further analysis by excluding them from the analysis mask (e.g., ‚lhcortex' variable).
To further investigate which specific vertices have zeros, it might be helpful to save the analysis mask as an mgh overlay file; see the description for the fs_write_Y() command in the tutorial.
Hope this helps,
Kersten
Am 30.08.2021 um 12:19 schrieb Bonati, Sara <bonati@mpib-berlin.mpg.demailto:bonati@mpib-berlin.mpg.de>:
External Email - Use Caution
Dear FreeSurfer Developers,
I'm attempting to analyze thickness changes in a longitudinal design using a mass-univariate approach, as described on the Linear Mixed Effects tutorial at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#b.29Mass-...https://secure-web.cisco.com/1HwLf5wG3aIAhV84T5KTL4VUiVpoa1DISeYUypdAqYlExO0W460yjt8YeKqyPbuQ85tga-S94ztbdtFWLZWFCAOraPVk3Dn4NQohquNezhXFCvnGtLK7F_uDigP4I8VDKbHpYvxiRievumBuLtT_TDRESWZpnVsy98JWaJ8LlYrEs-6YLtvtSOxA1jidquk1hDkWjbQUbXLCP8VJ6y36vfQ-C_bYANTCRq4TM-r7BDm0N5bxVFpgvJF1_AzE7fPgqKFKxvHpQD4m1byf7XAe8sw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels%23b.29Mass-univariate-1.
Before starting the tutorial I followed the preprocessing steps described in section 2 at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorialhttps://secure-web.cisco.com/1QfbwKIv-I05sWdxiQKgtXEA4KHeHEMrHdRJmxSzRQn3O_OaMfBDCNz34iNmbwk-sTFd2sYg8Rt5cfFd7IHNrsaetKmPYEyVzKopA0iCp7WnTumnd0s3VJR9du9ugA4rTdaQSnnNGH2woy996T21XSeLPOAid8UmnVoJt-6qLdFfdyVDzJ2mrwIrhe1QsFnSCSVXuEjIEJjqD5Lyc2Is6yaXY2-Hi2p-ftLLm_5UwVRQIApOfVq13oq-uYeRJ6HNrW_t0DbMqwzBYNbgJeXocdw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FLongitudinalTutorial: I now have a dataset folder that contains 1) for each subject-session pair to include in the analysis a .long folder 2) a subject specific base template folder that used all available sessions from that subject. All recon-all.log files, both in the base template folder and the subject-session specific long folders, seem to have finished without error.
After that, to prepare files for LME, I created a longitudinal qdec file and used it to prepare thickness.mgh files as described in the beginning of the Linear Mixed Effects tutorial for the mass-univariate approach.When advancing in the analysis the function lme_mass_RgGrow gets stuck: in the terminal the output looks like this
``` Starting region growing algorithm Computing seeds ... ``` and stays like this without advancing. I tried to change the thickness file used (lh.thickness.mgh VS lh.thickness_sm5.mgh VS lh.thickness_sm10.mgh etc..) but unfortunately the error persists.
Looking in the mailing list I found an email with a problem that is similar to mine: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1UCbpuy6fR5lmM1nBKi_YxuEIh1oSkzkBu6ITGgbuUI6hZZ...https://secure-web.cisco.com/166fF5937wdn5yDLqNvdeV6NeSe3cGRWXBnp12bBcQPqvcq8DS7BVWDboI9AU7P8GPw82zqlZHeWk75xXpn4E_oBkZJqAWRAFJBhQyvuQeM6qlAGgwooqpWqwnAJs3DCzBVoleMM-pk5quLMPClADVI9oJHG-n2P0rEh_fx6PypcN76Oc_TI_khCZYWODMnvWhj7dJRNNnTHzajOIaytt7YhW5aZwqGxd3PNh_KvPLoTjBHAiqvg8MigkHCLbIcZVYrmraL4Geoam-NGd97mtvg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg53959.html . Upon inspection of my lh.thickness.mgh file I also noticed that some columns are all zeros: do you know what could cause such columns of zeros to appear in the thickness files and how the problem with the function could be solved to continue in the analysis?
Thank you very much for your help, Kind regards
Sara Bonati
1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 2) Platform: macOS Catalina version 10.15.7
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/19Er7lsOdJjvY4rfOhPbemRDen9pHq7oH__puOyAqamL20Q...
-- Kersten Diers Image Analysis Group (AG Reuter) German Center for Neurodegenerative Diseases (DZNE) B.1.114 | Building 99 | Venusberg-Campus 1 | 53127 Bonn | Germany https://secure-web.cisco.com/1vUOwFn5EZbBch9CnTMbexkk-Ot-R-LrLG1KbUG7jIeeSsX... Phone: +49 / 228 / 43302 - 381
freesurfer@nmr.mgh.harvard.edu
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Bonati, Sara -
Diers, Kersten /DZNE