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 = 1ERROR: cannot find /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-5009_year-1/surf/lh.w-g.pct.mghCommand 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 63.23Linux 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 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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Tutorialhttps://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.eduhttp://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.eduhttp://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
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 YHUANG43@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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-mwvB7BQu... 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-wpjBxxtAUWOgesXqNnCUpgpqY... < https://secure-web.cisco.com/1q7Pmno-rGefDroAX9RTj-wpjBxxtAUWOgesXqNnCUpgpqY... .
freesurfer@nmr.mgh.harvard.edu
-
Dan Levitas -
Huang, Yujing