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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lemley, Rachel
<rlem...@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
External Email - Use Caution
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
To report a problem, see MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<https://secure-web.cisco.com/15SsZG67FPf4GkwwAt31xXc0_geHl5sL5vwj9Hihb4jWriQi4FV0jQ53fKtlBuBhsagDlwGz3kkoFa-XgjkgmV1hYXIqdyHt2AHZj0jkUsT2I2s5WiQkTSow8nIwhjOKWMHzPrtGM28PCGpExJuDjZoARi0etP0aldz5p572mRZZ4LmDShsIFKYJeObSd9Kr1r7nTDjxYFFEP4L5-bzVv6DKJHV-0TPaQHTCkvrn-h1nhOzPk7ZNBf5oPLLWSck-RQ1y2DKeIid8hYRJxz_70YxEzkPwwB2UDkDTy-8vNC-EHTWkL1Ma5Y7UI6VyTccv6Wa2ldGsKJhO4cYovc0ExZg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__secure-2Dweb.cisco.com_1hDoMTcotBNpi6ZDqlu1xK1AeLrzrk-5FQC8e4t7bga0WOa9hSvGd-2D999MOczhyZc22L4ZZzuIbGBJXnhU4QASlwDmJ0PaUFA0XHpiMNM3BgIW-5FE9YtTCOJ-5FHZkpYRCqFw9oY7sYWKgb-5FcD4fQZ62uf49ydN3XcQ8HDaiEUZa536bb5Z9sbGbkfrW-5Fp-5FgQ8-2DshV9-2Dz-2Ds3Xzx-5FQOVnMSUqENJaFxZiCIDJu5L4XzXK4-5F-5FVYIj-5FogBBaw0wD8XXPdGhQ7gujlhyrCFKbYU-2DaFnzfO6ZhDDZr7H-2DAwenNRAfmPKWs3uEy-5FBYngoxlIDDG-2De59EIAb328m7Vv1KTZS3lbKT2A_http-253A-252F-252Fsurfer.nmr.mgh.harvard.edu-252Ffswiki-252FBugReporting%26d%3DDwMFAg%26c%3DWO-RGvefibhHBZq3fL85hQ%26r%3D-e0DvYjg39YIaYmWUrPidZwSId0F4ZBDUASRNj_PoGo%26m%3DnS7EXm-s8-tq_rfjc9Dr767AUnVYonJDPsr6tHbJyKwem_oiAlDHqDRx79KjN6sC%26s%3DTDwSqtVd0VcPqiEvtoENubyQTkOJIiAJTngPlRU37Ls%26e%3D>
_______________________________________________
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 Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
