Hi Rachel,
The autorecon-pial option is not yet implemented in infant freesurfer that is why you see the below error.
Best, Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lemley, Rachel rlemley@fas.harvard.edu Sent: Monday, April 22, 2024 3:21 PM To: Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FW: Infant Freesufer auto-recon failure
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Good afternoon,
We are attempting to run freesurfer on infant data, but are running into an issue with the autorecon-pial code. We corrected the pial surface on the brainmask.mgz in freeview, saved the brainmask.mgz edits, and are trying to run autorecon-pial, but we get the following error that I have attached below. It is looking for a file in surf labeled lh.orig.premesh, but it does not exist. Any suggestions on how to fix this? Am I missing a step?
Respectfully,
Rachel Lemley
The error log is attached below:
Subject Stamp: freesurfer-linux-centos7_x86_64-infant-dev-4a14499-20210109-4a14499
Current Stamp: freesurfer-linux-centos7_x86_64-infant-dev-4a14499-20210109-4a14499
INFO: SUBJECTS_DIR is /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects
Actual FREESURFER_HOME /n/sw/ncf/apps/infant-freesurfer/4a14499/centos7_x64
Linux holy7c090602.rc.fas.harvard.edu 4.18.0-425.10.1.el8_7.x86_64 #1 SMP Thu Jan 12 16:32:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
'/n/sw/ncf/apps/infant-freesurfer/4a14499/centos7_x64/bin/recon-all' -> '/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/scripts/recon-all.local-copy'
/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri/transforms /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02
/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02
#--------------------------------------------
#@# Mask BFS Mon Apr 22 14:06:18 EDT 2024
/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5
DoAbs = 0
Found 401939 voxels in mask (pct= 2.40)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME 2024:04:22:14:06:19 mri_mask N 5 e 2.09 S 0.01 U 0.76 P 37% M 77200 F 0 R 3233 W 0 c 64 w 51 I 768 O 768 L 2.29 1.57 1.12
@#@FSLOADPOST 2024:04:22:14:06:21 mri_mask N 5 2.29 1.57 1.12
#--------------------------------------------
#@# AutoDetGWStats lh Mon Apr 22 14:06:21 EDT 2024
cd /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh
infant-dev-4a14499
cd /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri
setenv SUBJECTS_DIR /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh
Reading in intensity volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
Reading in surf ../surf/lh.orig.premesh
error: No such file or directory
error: MRISread(../surf/lh.orig.premesh): could not open file
Command exited with non-zero status 1
@#@FSTIME 2024:04:22:14:06:21 mris_autodet_gwstats N 8 e 0.73 S 0.00 U 0.28 P 39% M 43208 F 0 R 1873 W 0 c 23 w 20 I 120 O 0 L 2.29 1.57 1.12
@#@FSLOADPOST 2024:04:22:14:06:22 mris_autodet_gwstats N 8 2.29 1.57 1.12
Linux holy7c090602.rc.fas.harvard.edu 4.18.0-425.10.1.el8_7.x86_64 #1 SMP Thu Jan 12 16:32:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s KAN1_02 exited with ERRORS at Mon Apr 22 14:06:23 EDT 2024
For more details, see the log file /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/scripts/recon-all.log
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