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Hi there
Still hoping for some help on this.
Trisanna --
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 20, 2021 at 10:50 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] make_average_subject without Talairach transform
External Email - Use Caution Hi there,
Still wondering if we can get some help with this. Our update is the following:
1. When we run make_average_subject with some chimp scans, with default settings, it runs but the average surfaces are inflated compared to the individual subjects, presumably because the Talairach.xfm is being used. 2. When we replace the ?h.sphere.reg of each subject with one that was generated by registering each subject’s surfaces to those of the average chimp template, it runs as well, but the average surfaces are still inflated, again I presume because it is using Talairach.xfm. 3. When we insert an .xfm of each subject to the average chimp template into each subject/mri/transforms and use make_average_subject with –-xform flag, it crashes at the same spot every time. (See below for where it crashes) 4. If I try to start from mris_make_average_surface with –x transform.xfm, I get the output “don’t know what to do with transform.xfm” and it crashes.
#@# Making average lh.white surface --------------------- Tue Apr 20 10:31:38 EDT 2021 /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/average_test_April20/avgtest mris_make_average_surface -X 2GabrielApril15.xfm -i 7 -o white -sdir-out /data-01/trisanna/freesurfer/freesurfer_7.1.1/from_sebas_cluster/average_test_April20/ lh white sphere.reg avgtest Abby Agatha using xform 2GabrielApril15.xfm... reading vertex positions from white... --------------------------------------------------- hemi = lh avg_surf_name = white canon_surf_name = sphere.reg out_sname = avgtest xform = 2GabrielApril15.xfm ---------------------------------------------------
mris_average_surface failed
Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre --
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, April 14, 2021 at 7:32 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] make_average_subject without Talairach transform
External Email - Use Caution Hi there
As a follow-up, we realized that we had to also replace the lh.sphere.reg and rh.sphere.reg in the subject folders with new ones that were created by registering each subject lh and rh.sphere to those of the average chimp template. Once we did this, the script ran. However, as you can see, some serious scaling took place, I presume because it is still incorporating somewhere MNI space. I can see in the log that MNI305 seems to be called.
Any thoughts?
Trisanna --
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 13, 2021 at 3:47 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] make_average_subject without Talairach transform
External Email - Use Caution 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”.
Trisanna --
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Thursday, March 25, 2021 at 11:24 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] make_average_subject without Talairach transform
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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