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Hello FS experts,
I downloaded some anatomical data. I have defaced full images and
pre-skullstripped images for each participant. I tried the defaced images
first, but FS skullstripping looks a little off (possibly because the
defacing hides bits of the cranium in some images and causes problems in
mri_watershed). So I would like to use the pre-skullstripped files as my
initial inputs.
I have placed the pre-skullstripped file for each participant in
$SUBJECTS_DIR/$subjid/mri/orig/. Each participant's skullstripped input
volume is named 001.mgz.
I then submit the following command in a script to my slurm queue (after
setting appropriate FS env vars), where the script input ${1} is the
$subjid mentioned above:
recon-all \
-subject ${1} \
-all \
-openmp 40 \
-noskullstrip
The output log from FS ends with the following error. The
function mri_em_register seems to be looking for brainmask.mgz, and fails
to open it. If the input image is already extracted from the skull, do I
need to manually call it brainmask.mgz rather than 001.mgz? Or am I missing
something else in my function call (like order of flags)? Does
-noskullstrip need to come before -openmp, for example?
Thanks!
Jim H.
End of recon-all output:
writing output to T1.mgz
> 3D bias adjustment took 1 minutes and 20 seconds.
> @#@FSTIME 2023:12:28:16:07:04 mri_normalize N 7 e 80.39 S 0.66 U 102.70 P
> 128% M 581068 F 0 R 24411 W 0 c 32 w 229 I 0 O 0 L 1.00 1.38 9.22
> @#@FSLOADPOST 2023:12:28:16:08:25 mri_normalize N 7 1.99 1.66 8.64
> #-------------------------------------
> #@# EM Registration Thu Dec 28 16:08:25 EST 2023
> /gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri
> mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
> /home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca
> transforms/talairach.lta
> setting unknown_nbr_spacing = 3
> using MR volume brainmask.mgz to mask input volume...
> == Number of threads available to mri_em_register for OpenMP = 40 ==
> reading 1 input volumes...
> logging results to talairach.log
> reading
> '/home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca'...
> GCAread took 0 minutes and 1 seconds.
> average std = 7.2 using min determinant for regularization = 5.2
> 0 singular and 884 ill-conditioned covariance matrices regularized
> reading 'nu.mgz'...
> error:
>
> *mghRead(/gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri/brainmask.mgz,
> -1): could not open file^@error: mri_em_register: could not open mask
> volume brainmask.mgz.^@*
> @#@FSTIME 2023:12:28:16:08:25 mri_em_register N 7 e 1.42 S 0.25 U 1.43 P
> 118% M 446804 F 0 R 108260 W 0 c 2 w 56 I 0 O 0 L 1.99 1.66 8.64
> @#@FSLOADPOST 2023:12:28:16:08:26 mri_em_register N 7 1.99 1.66 8.64
> Linux nia0918.scinet.local 3.10.0-1160.102.1.el7.x86_64 #1 SMP Tue Oct 17
> 15:42:21 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
> recon-all -s 1000108_20252_2_0 exited with ERRORS at Thu Dec 28 16:08:26
> EST 2023
> For more details, see the log file
> /gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/scripts/recon-all.log
> To report a problem, see
> http://secure-web.cisco.com/1ywN1tDbl7MCg8OnWFYEA2Vcf-TaEWXJQlDYsrE7jJo4KqFgIlOWrzhzxDJm5uF11tgXR5fJi2W6vOuAdAAji5cdTjFimLnIGxtWSTB2-y5_HnBRRIRECgA43AhrDctzKRH546l4MaMTjVU30ZQUb5Jk54LqnNfWrh1gB0jsLHkHSgZBFmAXPrV3SIvbWFicYVt_Ebi8mCF-_Gi9xARjm2WPsG0bGNjIIC4gKMbRxQt_nSp83Y3Ik-tj4yEHQqrbfZSKxciUlXvG9xnPomANL8b4bFKfyM3zWmptSyMDvRAsv1F_SGfc8x8zU56LlZL2aPPLp5h3_wxXguFcFo2wxOQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
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