Hi Doug
I did try as you suggested and no matter what I do, I get the following error after about 10 seconds of
make_average_subject. The transforms to the average chimp template are in .xfm format and are in the subject/mri/transforms folder. These subjects were created with --hires, could that be creating a problem?
trisanna@kaplan:/data-01/trisanna/freesurfer/freesurfer_7.1.1$ make_average_subject --out avgApril13 --subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13
setenv SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
/usr/local/freesurfer-7.1.1//bin/make_average_subject --out avgApril13 --subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13
make_average_subject 7.1.1
Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1
output ddir is /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
uid=1001(trisanna) gid=1001(trisanna) groups=1001(trisanna),27(sudo)
make_average_surface --out avgApril13 --subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13
setenv SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
/usr/local/freesurfer-7.1.1//bin/make_average_surface --out avgApril13 --subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13
make_average_surface 7.1.1
Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13
output ddir is /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster
uid=1001(trisanna) gid=1001(trisanna) groups=1001(trisanna),27(sudo)
====================
make_average_surface
====================
Tue Apr 13 15:30:50 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13
/usr/local/freesurfer-7.1.1//bin/make_average_surface
--out avgApril13 --subjects Abby Agatha Amanda Artemus Arthur --xform 2GabrielApril13
input subjects: Abby Agatha Amanda Artemus Arthur
output subject: avgApril13
mri_add_xform_to_header -c auto /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13/mri/mni305.cor.mgz /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13/mri/mni305.cor.mgz
INFO: extension is mgz
#@# Making lh registration template ---------
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13
mris_make_template -norot -annot aparc lh sphere.reg Abby Agatha Amanda Artemus Arthur lh.reg.template.tif
not aligning hemispheres before averaging.
zeroing medial wall in aparc
creating new parameterization...
processing subject Abby (1 of 5)
reading spherical surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Abby/surf/lh.sphere.reg...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Abby/surf/lh.inflated.H...
curvature mean = -0.029, std = 1.033
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Abby/surf/lh.sulc...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Abby/surf/lh.smoothwm...
processing subject Agatha (2 of 5)
reading spherical surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Agatha/surf/lh.sphere.reg...
curvature mean = -0.056, std = 4.266
curvature mean = 0.008, std = 5.997
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Agatha/surf/lh.inflated.H...
curvature mean = -0.045, std = 1.020
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Agatha/surf/lh.sulc...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Agatha/surf/lh.smoothwm...
processing subject Amanda (3 of 5)
reading spherical surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Amanda/surf/lh.sphere.reg...
curvature mean = -0.068, std = 4.037
curvature mean = -0.032, std = 0.313
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Amanda/surf/lh.inflated.H...
curvature mean = -0.046, std = 1.006
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Amanda/surf/lh.sulc...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Amanda/surf/lh.smoothwm...
processing subject Artemus (4 of 5)
reading spherical surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Artemus/surf/lh.sphere.reg...
curvature mean = -0.072, std = 4.167
curvature mean = -0.031, std = 0.297
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Artemus/surf/lh.inflated.H...
curvature mean = -0.035, std = 1.032
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Artemus/surf/lh.sulc...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Artemus/surf/lh.smoothwm...
processing subject Arthur (5 of 5)
reading spherical surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Arthur/surf/lh.sphere.reg...
curvature mean = -0.068, std = 4.276
curvature mean = -0.019, std = 0.305
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Arthur/surf/lh.inflated.H...
curvature mean = 0.055, std = 0.264
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Arthur/surf/lh.sulc...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Arthur/surf/lh.smoothwm...
writing updated template with 5 subjects to lh.reg.template.tif...
curvature mean = -0.023, std = 4.259
curvature mean = -0.034, std = 0.294
#@# Making rh registration template ---------
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13
mris_make_template -norot -annot aparc rh sphere.reg Abby Agatha Amanda Artemus Arthur rh.reg.template.tif
not aligning hemispheres before averaging.
zeroing medial wall in aparc
creating new parameterization...
processing subject Abby (1 of 5)
reading spherical surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Abby/surf/rh.sphere.reg...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Abby/surf/rh.inflated.H...
curvature mean = -0.039, std = 1.014
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Abby/surf/rh.sulc...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Abby/surf/rh.smoothwm...
processing subject Agatha (2 of 5)
reading spherical surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Agatha/surf/rh.sphere.reg...
curvature mean = -0.057, std = 4.264
curvature mean = -0.026, std = 0.315
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Agatha/surf/rh.inflated.H...
curvature mean = -0.066, std = 0.999
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Agatha/surf/rh.sulc...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Agatha/surf/rh.smoothwm...
processing subject Amanda (3 of 5)
reading spherical surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Amanda/surf/rh.sphere.reg...
curvature mean = -0.088, std = 3.995
curvature mean = -0.028, std = 0.314
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Amanda/surf/rh.inflated.H...
curvature mean = -0.046, std = 1.013
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Amanda/surf/rh.sulc...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Amanda/surf/rh.smoothwm...
processing subject Artemus (4 of 5)
reading spherical surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Artemus/surf/rh.sphere.reg...
curvature mean = -0.083, std = 4.140
curvature mean = -0.029, std = 0.297
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Artemus/surf/rh.inflated.H...
curvature mean = -0.042, std = 1.033
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Artemus/surf/rh.sulc...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Artemus/surf/rh.smoothwm...
processing subject Arthur (5 of 5)
reading spherical surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Arthur/surf/rh.sphere.reg...
curvature mean = -0.077, std = 4.286
curvature mean = -0.024, std = 0.300
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
ripping medial wall...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Arthur/surf/rh.inflated.H...
curvature mean = -0.007, std = 0.961
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Arthur/surf/rh.sulc...
computing parameterization for surface /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/Arthur/surf/rh.smoothwm...
writing updated template with 5 subjects to rh.reg.template.tif...
curvature mean = -0.020, std = 4.236
curvature mean = -0.034, std = 0.297
#@# Making average lh.white surface ---------------------
Tue Apr 13 15:31:11 EDT 2021
/data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/avgApril13
mris_make_average_surface -X 2GabrielApril13 -i 7 -o white -sdir-out /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster lh white sphere.reg avgApril13 Abby Agatha Amanda Artemus Arthur
using xform 2GabrielApril13...
reading vertex positions from white...
---------------------------------------------------
hemi = lh
avg_surf_name = white
canon_surf_name = sphere.reg
out_sname = avgApril13
xform = 2GabrielApril13
---------------------------------------------------
Segmentation fault (core dumped)
mris_average_surface failed
ERROR: make_average_surface
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, March 25, 2021 at 11:36 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] make_average_subject without Talairach transform
If you have the transform in the form of an LTA file, I think all you need to do is put it in the subject/mri/transforms folder, then spec --xfrom your.lta when running make_average_subject
On 3/25/2021 11:33 AM, Trisanna Sprung-Much wrote:
External Email - Use Caution
External Email - Use Caution
Hi Doug
The scans were registered (6 parameter) to a common chimp template prior to input to recon-all. The surfaces have reconstructed nicely and match the input volumes.
I would now like to create an average surface from these surfaces that are “in the space of the average chimp volume”.
If you don't have a transform, how will you align the subjects into a common space?
On 3/25/2021 10:19 AM, Trisanna Sprung-Much wrote:
External Email - Use Caution
External Email - Use Caution
Hi there
I’d like to know if it is possible to create an average volume and average surface of several subjects without having to incorporate the Talairach transform and no transform at all.
Thank you,
Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
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