The recon-all ‘WM/GM Contrast’ step is skipped for longitudinal base
processing. So, I’m not sure that ‘-qcache’ option can be used in base
processing.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Dan Levitas
Sent: Thursday, March 21, 2024 11:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all mris_preproc error: Cannot find
surf/lh.w-g.pct.mgh
External Email - Use Caution
Hello,
I have a longitudinal dataset where each participant was scanned twice over the
course of 5 months. I have been following FS's Longitudinal
Tutorial<https://secure-web.cisco.com/1cEj8JFOeCVl553obrTrsTW9AP-8Qv0LHSe3IerGFGTmaPu6kUsXeBfzgONeAa4mmpINzpRDl58mXIB9C_LPuikezWqDYll18nCVVV2NiOodxGk847brmEMiJllZoqGlrXxYObfmT3RIYUazBVpGOsKRSaUkOOWuPjBmsiPt2bcdA0JkjE6sR9OY41j7puo38bGKrY6YGk4ayVwvOT__tRnC2kWDaOZw3mACwbxTa4QBv-5-j5UIFnFKeywba3HIu3mLSTCCJGTxHUyWOPs9UUAZ4NpSsHFT0FnDQhbUfgnSuOquyRIE9WmZGrj_ix-kmTG1hLX-3O8SMYxnTo_dS0kwracWTAgRrXWF_wgalzbk/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FLongitudinalTutorial>.
For the CROSS section, each subjects' session scan successfully completed
recon-all, where I used the following command:
recon-all \
-subjid sub-${sub}_ses-${ses} \
-i $raw_anat_file \
-qcache \
-all
I then used the following recon-all command for the BASE section:
recon-all \
-base sub-${sub}_year-1 \
-tp $subjects_dir/$pre_sub_ses \
-tp $subjects_dir/$post_sub_ses \
-qcache \
-all
This recon-all ran for several hours before failing at the following command:
mris_preproc --s sub-5009_year-1 --hemi lh --meas w-g.pct.mgh --target
fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh
The error message is:
nsubjects = 1
ERROR: cannot find
/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-5009_year-1/surf/lh.w-g.pct.mgh
Command exited with non-zero status 1
@#@FSTIME 2024:03:21:02:30:48 mris_preproc N 10 e 0.09 S 0.05 U 0.02 P 82% M
3568 F 0 R 2201 W 0 c 2 w 45 I 0 O 0 L 60.94 63.09 63.23
@#@FSLOADPOST 2024:03:21:02:30:48 mris_preproc N 10 60.94 63.09 63.23
Linux
c50.quartz.uits.iu.edu<http://secure-web.cisco.com/14Wbu8Wr5_K8JfIcqRcS1Cn5n2xX-aAI3fOWvKkmOStUpOWDMxHIeDQf1JjyGBTOajbFgvBNoQgJrs_ETqhSmG2R2I5-BP-qFM0ASkCdMEM52yhEXthPD2SxkgawnJTEgBlsemYRNuCmj0ELA_8mQ3KS7mhcZ1s5hx4PH1cLZ3dVZID1dFJ4BgdxlYdIR-yE9Szt_NDlw2GgwH78c8aA3aLnF3kzkFKz0yclnpc5C_kg5ONq8BHh7yjqOwPJh26UcKbBc4Xw4YwihTBNPXNSoWXNCk4bqnckKKjWiFgNj0ROdkaEoE_DY-fjtdohepTrnEB_Kgig6OJemyyfrHMp9LEB8j7zKUfGSrv0etcW99pw/http%3A%2F%2Fc50.quartz.uits.iu.edu>
4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64 x86_64
x86_64 GNU/Linux
recon-all -s sub-5009_year-1 exited with ERRORS at Thu Mar 21 02:30:48 EDT 2024
I have checked the archive but can't seem to find a similar question. I'm a bit
new to FreeSurfer, so I am unsure how to resolve this issue. I've attached the
recon-all.log if that might help.
FreeSurfer version: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460
Platform: Red Hat Enterprise Linux 8.9 Ootpa)
uname -a: Linux
i48.red.uits.iu.edu<http://secure-web.cisco.com/15XStCE0IKjVjIAFoiEyXMymmxkHCK5LnWAGzytId4euRRINQRqifyCOAYtM5qwvWWedY6SVMbn3E-7Uvgz6vTc9vqmOvWLbh_OE6LE4FlFlxHRO075UOvskHXCWQ2L2A4OMckWufAAivBMxV3WgBuh4D4_T8cx2fllAaa0nJhodK5RmKJqlokanY_6Hdl1Iqjcsn0Aa_b0Vcjdh8C79HrORXQ_wdfwa-POrIN4qSM4nEUcBnE8Oo3BhNq6OW9tcHmgDPpvrfH8E5Nq7bOI-7DIovKzEHQQ9SIgCr4DYSU12GGtDpn9YsCY42MWh9Uu_Suq35EmZl4sziszMmbkhs2IOSvfS2mSYvLGKYumSKJUw/http%3A%2F%2Fi48.red.uits.iu.edu>
4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64 x86_64
x86_64 GNU/Linux
recon-all log: see attached
Thank you.
Dan
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