Re: [Freesurfer] Surface Area in Toddlers/Children

[Raffington, Laurel]

External Email - Use Caution

Hi Derek,


you could try creating a study-specific template to replace fsaverage with 
make_average_subject and then re-run your reconall.


Best,


Laurel


Laurel Raffington

Postdoctoral Researcher

Center for Lifespan Psychology

Max Planck Institute for Human Development

Lentzeallee 94, 14195 Berlin, Germany

https://www.mpib-berlin.mpg.de/en/staff/laurel-raffington


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Derek Sayre Andrews 

Sent: Thursday, August 9, 2018 9:49:09 PM
To: Freesurfer support list
Subject: [Freesurfer] Surface Area in Toddlers/Children


External Email - Use Caution
Dear Freesurfer Developers and Experts,

I have been exploring various vertex wise (mass univariate) effects using 
freesurfer measures of cortical thickness and surface area in a cohort of 
toddlers/children aged 25-70 months.

When looking at the effect of age on surface area using individuals’ measures 
mapped to fsaverage and smoothed at 15mm fwhm (area.pial. fwhm15.fsaverage.mgh) 
I observed a widespread negative effect of age (i.e. decreased surface area 
with age). Given the age group of the cohort this seems implausible. Plotting 
the sum of each individuals lh+rh.area.pialfsaverage.fwhm15.mgh against age 
shows the relationship:
[cid:image001.png@01D42FCE.C197B360]

However, plotting the lh+rh total surface area returned by 
mris_anatomical_stats reveals a much more plausible relationship between 
surface area and age:
[cid:image002.png@01D42FCE.C197B360]


My working hypothesis is that the significantly smaller brain sizes of our 
cohort compared to fsaverage, and the fact(?) that -qcache does not preserve 
global surface area, is causing an “over adjustment” in our cohorts smallest 
brains when mapped to fsaverage.

Thus, my questions are three fold


  1.  Is the mapping of our significantly smaller brains to fsaverage a 
potential explanation for the results we are seeing in our mass univariate 
analyses of surface area?


  1.  If this is the case, would this effect be limited to surface area or also 
extend to other freesurfer measures including cortical thickness, lGI, sulcal 
depth etc.


  1.  How would you recommend approaching vertex wise analyses in a cohort of 
this age? Create a study specific average subject using make_average_subject to 
map onto?

Thank you for your insight and guidance!

Best, Derek


PS: All processing was performed using freesurfer v5.1



Derek Sayre Andrews, PhD
Postdoctoral Scholar
Department of Psychiatry and Behavioral Sciences
The M.I.N.D Institute
University of California Davis

Telephone: +1 916 703 0360
Email: dandr...@ucdavis.edu


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Bug in make_average_subject

[Raffington, Laurel]

External Email - Use Caution

Dear Freesurfer Developers,


My goal is to build a study-specific pediatric template brain to rerun the 
recon-all-all. I am encountering the same error while running 
make_average_subject Freesurfer version 6.0.0 on MacOS High Sierra 10.13.6 as 
described here and implemented the suggested changes replacing mri_glmfit-sim, 
make_average_subject, make_average_surface, and mri_aparc2aseg: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054933.html

Yet, another error persists.


Any help would be appreciated.


Thanks,


Laurel



Laurel Raffington

Postdoctoral Researcher

Center for Lifespan Psychology

Max Planck Institute for Human Development

Lentzeallee 94, 14195 Berlin, Germany

https://www.mpib-berlin.mpg.de/en/staff/laurel-raffington





recon-all.error
Description: recon-all.error


recon-all.log
Description: recon-all.log
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Bug in make_average_subject

[Raffington, Laurel]

External Email - Use Caution

Dear Freesurfer Developers,


My goal is to build a study-specific pediatric template brain to rerun the 
recon-all-all. I am encountering the same error while running 
make_average_subject Freesurfer version 6.0.0 on MacOS High Sierra 10.13.6 as 
described here and implemented the suggested changes replacing mri_glmfit-sim, 
make_average_subject, make_average_surface, and mri_aparc2aseg: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054933.html

Yet, the the mri/norm.mgz file is still missing (see attached logs).


Exits on:

#@# AParc-to-ASeg aparc Mon Jul 16 17:45:19 CEST 2018
/Volumes/FB-LIP/MRI/Jacobs/Freesurfer2/Jacobs/avgsubjectT1
\n mri_aparc2aseg --s avgsubjectT1 --volmask --aseg aseg.presurf.hypos 
--relabel mri/norm.mgz mri/transforms/talairach.m3z 
/Volumes/Mac/Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca 
mri/aseg.auto_noCCseg.label_intensities.txt --no-relabel \n
/Volumes/Mac/Applications/freesurfer/bin/mri_aparc2aseg: Exec format error. 
Binary file not executable.
Darwin lip-osx-004040 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 
PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64

recon-all -s avgsubjectT1 exited with ERRORS at Mon Jul 16 17:45:19 CEST 2018


Any help would be appreciated.


Thanks,


Laurel



Laurel Raffington

Postdoctoral Researcher

Center for Lifespan Psychology

Max Planck Institute for Human Development

Lentzeallee 94, 14195 Berlin, Germany

https://www.mpib-berlin.mpg.de/en/staff/laurel-raffington





recon-all.log
Description: recon-all.log


recon-all.error
Description: recon-all.error
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.