External Email - Use Caution Thanks Yujing,
I realized that was likely the issue after sending my message. Indeed, removing the -qcache option for this longitudinal processing step resolved my issue. Thanks for the clarification. Dan On Mon, Mar 25, 2024 at 9:37 AM Huang, Yujing <yhuan...@mgh.harvard.edu> wrote: > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/15JVDGWH0muukYX3WQqEohbfht0lDnSyO7hM-u-mwvB7BQuKYRCPkAbFe7GxIilghz8jSsynneTr0vkxX8IRZ00SJOIkeaXz8hkuR2Bc_ffsz0BX6NJLhSmWtiuqcd9luBHo2GSGRS3QNEcmLhD_vpFEZQMLfyCGNHgRiQ8l5gRqb0uca7QuUGivU_RBI41MzI0g_AH8Il8F4DtO149zG8pCy0hThlUiv8JtocO1MRR-v4jdPdZuODkZi25if4nYia-2nqVvYd2FwibSgstvD9ZjtO9KcnkbUtMim1wYXWwcTrjWa48gIh_5RLEc_k3Vw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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://secure-web.cisco.com/1q7Pmno-rGefDroAX9RTj-wpjBxxtAUWOgesXqNnCUpgpqYmr21Yc8KFJlF4Y6MySF8ggTmFQ_mMD6lmUmRJNCjidMXLQIwgfbWyXL7BGtMdkxSpjsjNYZ6s22aQS90NVj9Fo5WK47wO76HLIoUskSg1rdFmk3q_K1Cq4KwVVdxTrbufuGF8BTSDbMk-H4A1G0J3YNDEzKbnmXMWasXwC81hxd0jEZdFjchyW1qCCUmvGerkgNZBUsTc8rvBUx8Ek37rHJ4LpoFGikOp-rWRWFCAYHOJfh8atN61ptN-tyV5DVGg_3D-F_wrspFFkHDpl/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1q7Pmno-rGefDroAX9RTj-wpjBxxtAUWOgesXqNnCUpgpqYmr21Yc8KFJlF4Y6MySF8ggTmFQ_mMD6lmUmRJNCjidMXLQIwgfbWyXL7BGtMdkxSpjsjNYZ6s22aQS90NVj9Fo5WK47wO76HLIoUskSg1rdFmk3q_K1Cq4KwVVdxTrbufuGF8BTSDbMk-H4A1G0J3YNDEzKbnmXMWasXwC81hxd0jEZdFjchyW1qCCUmvGerkgNZBUsTc8rvBUx8Ek37rHJ4LpoFGikOp-rWRWFCAYHOJfh8atN61ptN-tyV5DVGg_3D-F_wrspFFkHDpl/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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