External Email - Use Caution

Could you please explain more ho to specify all in recon-all command ?

Dunia

On Tue, Nov 21, 2023 at 4:48 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

It looks like you don’t have data processed. Specify ‘-all’ on recon-all on command line.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 10:58 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

Hello Freesurfer Developers

I'm attempting to apply preprocess and segment to my data that consist of 24 subjects by recon-all syntax, as described on the FreeSurfer wiki on macOs software

*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1IEj67qMp5LMgWczVs2eMKPHnJdV8E-s-4d-T35e-YTr1qi... https://secure-web.cisco.com/1sL0UR9IcjyzN-iiFPRBpUbos_zcdbT2W0RQcJ-3jMPXPBbG7t5-6HgMR60s4YWqde4tZa0XWjtkT0aWl3XybyhjThRfDIZmH8oNIZTQHT3KJDNpBj1DUZ6PKEZrrygdbT1DPTNtfO_zUn04IsLpbI6O57RcgvpVsXEx8ujYU-9-eFN0mWsVDj6gaP-ZccrPky_ruv3wCEiKCyGbSpPLpWXig3WAycCHA4_N_rPef9kRpg4gEFbLVjmjTPA3yx66OOHSaNacYpeFWBHZKyZbf4aKwJBcw2IPYCBLyjn1TOfQIc4V1h7skqAUUfgGHtlo3I_FNzpbevSUMMmOhMJUuzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all

ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I83870_MP-RAGE_20071127095752_2/surf/lh.thickness

Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64

1. freesurfer version: freesurfer-macOS-darwin_x86_64-7.4.1

2. platform: bash terminal

3. log file

Tue Nov 21 15:50:35 GMT 2023 cd /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects /Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache

subjid I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects FREESURFER_HOME /Applications/freesurfer/7.4.1 Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 build-stamp.txt: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64 cputime unlimited filesize unlimited datasize unlimited stacksize 8176 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 1333

PhysMem: 7547M used (1397M wired, 2612M compressor), 77M unused.

######################################## program versions used 7.4.1 (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460) 7.4.1

ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk 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http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 mri_motion_correct.fsl 7.4.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 ####################################### GCADIR /Applications/freesurfer/7.4.1/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /Applications/freesurfer/7.4.1/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3 \n mri_convert /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz \n mri_convert /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz

reading from /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii... TR=8.98, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz... #-------------------------------------------- #@# Qdec Cache preproc lh thickness fsaverage Tue Nov 21 15:50:39 GMT 2023 /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/surf \n mris_preproc --s I12250_MP-RAGE_20060321115220_3 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh \n nsubjects = 1 ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/surf/lh.thickness Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64

recon-all -s I12250_MP-RAGE_20060321115220_3 exited with ERRORS at Tue Nov 21 15:50:39 GMT 2023

To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1Y039UnzlOzm5x-kqAx9pzIIy1kkm4Pa_RMFkDSE9rWVdBtr... http://secure-web.cisco.com/1kSmtgzR_pxmyG0Pcf2UmG3i7fQr9HeDya5uym7dX6z6tGZdMuhAr9QAO3NNFaL7EqiWYP3ahWxhaiiv5tbGWQ0AXo2G1smogNP5-5iWwGZQWXQhiA2kHfRzjeDr53nNN6jkHQNUbqwyTgQdhhGsviPdSNnu0IedSruBqCCVVn9tD9qqb-1l_dvLt_VKy-LeuPLheMwTDPkd7Y8D00QuxSFTVFN1eWjVMh4owHpADK6tRvs0RmLF2aXjKlrBm99PPU-qagrrset7G1i0yJVWYxTfUJnFzWssLyDDZQ4YFTCn7qQANuztgiuY8CrrxJWePWp9PbtaLrFxBsRYiJV9G_g/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Thank you

--

*Dunia Ahmad Al-Hamad*

PhD Student

Sheffield Institute of Translational Neuroscience (SiTraN)

The University of Sheffield

385a Glossop Road

Sheffield

S10 2HQ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1NQg2j8HWS3jCm0B8901qkM99ZmZJuC2vU7Q65ZdXTmM8Bm... 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/1jVAH8eFHnAHOHGY9ZAXcOInhwTeJXT0vUl9orYtEPiaRJS... < https://secure-web.cisco.com/1jVAH8eFHnAHOHGY9ZAXcOInhwTeJXT0vUl9orYtEPiaRJS... . 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.

External Email - Use Caution

What if I had 24 subjects. Should I specify the name for each one in the line ?

Dunia

On Tue, Nov 21, 2023 at 4:52 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

This is your recon-all submitted

“/Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache”

Add ‘-all’ to the line.

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 11:50 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

Could you please explain more ho to specify all in recon-all command ?

Dunia

On Tue, Nov 21, 2023 at 4:48 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

It looks like you don’t have data processed. Specify ‘-all’ on recon-all on command line.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 10:58 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

Hello Freesurfer Developers

I'm attempting to apply preprocess and segment to my data that consist of 24 subjects by recon-all syntax, as described on the FreeSurfer wiki on macOs software

*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1UAKgtpVS9B1hORtEOwbUac6j_L7nrAuNWOJVPt5W6xVwVj... https://secure-web.cisco.com/1sL0UR9IcjyzN-iiFPRBpUbos_zcdbT2W0RQcJ-3jMPXPBbG7t5-6HgMR60s4YWqde4tZa0XWjtkT0aWl3XybyhjThRfDIZmH8oNIZTQHT3KJDNpBj1DUZ6PKEZrrygdbT1DPTNtfO_zUn04IsLpbI6O57RcgvpVsXEx8ujYU-9-eFN0mWsVDj6gaP-ZccrPky_ruv3wCEiKCyGbSpPLpWXig3WAycCHA4_N_rPef9kRpg4gEFbLVjmjTPA3yx66OOHSaNacYpeFWBHZKyZbf4aKwJBcw2IPYCBLyjn1TOfQIc4V1h7skqAUUfgGHtlo3I_FNzpbevSUMMmOhMJUuzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all

ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I83870_MP-RAGE_20071127095752_2/surf/lh.thickness

Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64

1. freesurfer version: freesurfer-macOS-darwin_x86_64-7.4.1

2. platform: bash terminal

3. log file

Tue Nov 21 15:50:35 GMT 2023 cd /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects /Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache

subjid I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects FREESURFER_HOME /Applications/freesurfer/7.4.1 Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 build-stamp.txt: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64 cputime unlimited filesize unlimited datasize unlimited stacksize 8176 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 1333

PhysMem: 7547M used (1397M wired, 2612M compressor), 77M unused.

######################################## program versions used 7.4.1 (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460) 7.4.1

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http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 mri_motion_correct.fsl 7.4.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 ####################################### GCADIR /Applications/freesurfer/7.4.1/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /Applications/freesurfer/7.4.1/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3 \n mri_convert /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz \n mri_convert /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz

reading from /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii... TR=8.98, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz... #-------------------------------------------- #@# Qdec Cache preproc lh thickness fsaverage Tue Nov 21 15:50:39 GMT 2023 /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/surf \n mris_preproc --s I12250_MP-RAGE_20060321115220_3 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh \n nsubjects = 1 ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/surf/lh.thickness Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64

recon-all -s I12250_MP-RAGE_20060321115220_3 exited with ERRORS at Tue Nov 21 15:50:39 GMT 2023

To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1RGp03zruzIxxKq6pecaOcRyuumxBQlZ8x4ggUDVH7YP0bWh... http://secure-web.cisco.com/1kSmtgzR_pxmyG0Pcf2UmG3i7fQr9HeDya5uym7dX6z6tGZdMuhAr9QAO3NNFaL7EqiWYP3ahWxhaiiv5tbGWQ0AXo2G1smogNP5-5iWwGZQWXQhiA2kHfRzjeDr53nNN6jkHQNUbqwyTgQdhhGsviPdSNnu0IedSruBqCCVVn9tD9qqb-1l_dvLt_VKy-LeuPLheMwTDPkd7Y8D00QuxSFTVFN1eWjVMh4owHpADK6tRvs0RmLF2aXjKlrBm99PPU-qagrrset7G1i0yJVWYxTfUJnFzWssLyDDZQ4YFTCn7qQANuztgiuY8CrrxJWePWp9PbtaLrFxBsRYiJV9G_g/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Thank you

--

*Dunia Ahmad Al-Hamad*

PhD Student

Sheffield Institute of Translational Neuroscience (SiTraN)

The University of Sheffield

385a Glossop Road

Sheffield

S10 2HQ

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1RXy-weRc76ASiuo4ujg56I-rnILGZrFS91Bje5BsMaCB-1... https://secure-web.cisco.com/1NQg2j8HWS3jCm0B8901qkM99ZmZJuC2vU7Q65ZdXTmM8BmWEBsWge6OK831nzBQsOoAI8dEKP4VOemGu6aH6oEbkjJ6PC6inDcZASwNfdIJ2kHQ5Nzmyvv3AuO9ptJQqLv1HMMRaBm0iLfMhDMMdBIdt9jxxsPX3X-mHS3LlnvZReNKZtiKGlBbdNOCMS0purQpNCImlJBDwLpq8YfeP-dS5VY3w8UAZleG3QOpGQDaayuBuxRcT24kPDSgqW0JCLZc9zbh0NexUuCoiLB-8ehYmyIDXoIzYfZZ70rFGUdwFnnOos8JopkzsAfGBFajtaJ04iy7cQhNf2BveVmotuw/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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/19ADaNFb3mMIYzlIrSh6EbxsmgFbLbSB974evmxQSAVnjd_... https://secure-web.cisco.com/1jVAH8eFHnAHOHGY9ZAXcOInhwTeJXT0vUl9orYtEPiaRJSBebQLUWKDGRy-c5Yk-q3_iBScfIHOoVmwIPzcamocSZPXTCzzhfTVd9iKtPM9L-P67if3_KhGPeHIa7QNIaEYWUa6lWh8AKMNUbDUBjkOb-vB26Mrf_MgrFW4olZMUh0B-33rKv7uJE4v8Umrg45geSY0kr2piZaR80uM9fHTV0TSrY-hs_LQvxB_dfJHFgouW8V3FZXBMQ5KpRfN94cDMol6SHpXepNB0fLX1Sv3QEk655m1scOU6quVOBeJyBYuSpuNhK5x1rxfkRXA0mECgpuO5ZsTAxJeds9_SUQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/19ADaNFb3mMIYzlIrSh6EbxsmgFbLbSB974evmxQSAVnjd_... https://secure-web.cisco.com/1jVAH8eFHnAHOHGY9ZAXcOInhwTeJXT0vUl9orYtEPiaRJSBebQLUWKDGRy-c5Yk-q3_iBScfIHOoVmwIPzcamocSZPXTCzzhfTVd9iKtPM9L-P67if3_KhGPeHIa7QNIaEYWUa6lWh8AKMNUbDUBjkOb-vB26Mrf_MgrFW4olZMUh0B-33rKv7uJE4v8Umrg45geSY0kr2piZaR80uM9fHTV0TSrY-hs_LQvxB_dfJHFgouW8V3FZXBMQ5KpRfN94cDMol6SHpXepNB0fLX1Sv3QEk655m1scOU6quVOBeJyBYuSpuNhK5x1rxfkRXA0mECgpuO5ZsTAxJeds9_SUQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .

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External Email - Use Caution

But this will take long time because I had another group with 300 patients

On Tue, Nov 21, 2023 at 5:03 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

Each subject needs to be processed separately. You will need submit 24 recon-all.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 12:00 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

What if I had 24 subjects. Should I specify the name for each one in the line ?

Dunia

On Tue, Nov 21, 2023 at 4:52 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

This is your recon-all submitted

“/Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache”

Add ‘-all’ to the line.

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 11:50 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

Could you please explain more ho to specify all in recon-all command ?

Dunia

On Tue, Nov 21, 2023 at 4:48 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

It looks like you don’t have data processed. Specify ‘-all’ on recon-all on command line.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 10:58 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

Hello Freesurfer Developers

I'm attempting to apply preprocess and segment to my data that consist of 24 subjects by recon-all syntax, as described on the FreeSurfer wiki on macOs software

*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1-0eWzp1qoP_bfFVOEUqsJvj7MCJEOCEr7vjXlYKiKl4uHM... https://secure-web.cisco.com/1sL0UR9IcjyzN-iiFPRBpUbos_zcdbT2W0RQcJ-3jMPXPBbG7t5-6HgMR60s4YWqde4tZa0XWjtkT0aWl3XybyhjThRfDIZmH8oNIZTQHT3KJDNpBj1DUZ6PKEZrrygdbT1DPTNtfO_zUn04IsLpbI6O57RcgvpVsXEx8ujYU-9-eFN0mWsVDj6gaP-ZccrPky_ruv3wCEiKCyGbSpPLpWXig3WAycCHA4_N_rPef9kRpg4gEFbLVjmjTPA3yx66OOHSaNacYpeFWBHZKyZbf4aKwJBcw2IPYCBLyjn1TOfQIc4V1h7skqAUUfgGHtlo3I_FNzpbevSUMMmOhMJUuzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all

ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I83870_MP-RAGE_20071127095752_2/surf/lh.thickness

Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64

1. freesurfer version: freesurfer-macOS-darwin_x86_64-7.4.1

2. platform: bash terminal

3. log file

Tue Nov 21 15:50:35 GMT 2023 cd /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects /Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache

subjid I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects FREESURFER_HOME /Applications/freesurfer/7.4.1 Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 build-stamp.txt: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64 cputime unlimited filesize unlimited datasize unlimited stacksize 8176 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 1333

PhysMem: 7547M used (1397M wired, 2612M compressor), 77M unused.

######################################## program versions used 7.4.1 (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460) 7.4.1

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http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 mri_motion_correct.fsl 7.4.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:37-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 ####################################### GCADIR /Applications/freesurfer/7.4.1/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /Applications/freesurfer/7.4.1/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3 \n mri_convert /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz \n mri_convert /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz

reading from /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii... TR=8.98, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz... #-------------------------------------------- #@# Qdec Cache preproc lh thickness fsaverage Tue Nov 21 15:50:39 GMT 2023 /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/surf \n mris_preproc --s I12250_MP-RAGE_20060321115220_3 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh \n nsubjects = 1 ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/surf/lh.thickness Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64

recon-all -s I12250_MP-RAGE_20060321115220_3 exited with ERRORS at Tue Nov 21 15:50:39 GMT 2023

To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1AAeuo0bHl-m5rRiEKr1cQvCWDGVPQHhTS2OWWUlsFH_g8OB... http://secure-web.cisco.com/1kSmtgzR_pxmyG0Pcf2UmG3i7fQr9HeDya5uym7dX6z6tGZdMuhAr9QAO3NNFaL7EqiWYP3ahWxhaiiv5tbGWQ0AXo2G1smogNP5-5iWwGZQWXQhiA2kHfRzjeDr53nNN6jkHQNUbqwyTgQdhhGsviPdSNnu0IedSruBqCCVVn9tD9qqb-1l_dvLt_VKy-LeuPLheMwTDPkd7Y8D00QuxSFTVFN1eWjVMh4owHpADK6tRvs0RmLF2aXjKlrBm99PPU-qagrrset7G1i0yJVWYxTfUJnFzWssLyDDZQ4YFTCn7qQANuztgiuY8CrrxJWePWp9PbtaLrFxBsRYiJV9G_g/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Thank you

--

*Dunia Ahmad Al-Hamad*

PhD Student

Sheffield Institute of Translational Neuroscience (SiTraN)

The University of Sheffield

385a Glossop Road

Sheffield

S10 2HQ

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External Email - Use Caution

Could explain more, as I am not very expert in freesurfer For e.g I had 300 subject and their NIFTI files are named by their number (1.nii) How to make a script to launch, do you mean in a txt file ?

Thank you

On Tue, Nov 21, 2023 at 5:29 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

you can write a script to launch them, eg foreach subject (your-list-of-subjects) recon-all -s $subject -all ... end

On 11/21/2023 12:04 PM, Dunia A Alhamad wrote:

    External Email - Use Caution

But this will take long time because I had another group with 300 patients

On Tue, Nov 21, 2023 at 5:03 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

...

Each subject needs to be processed separately. You will need submit 24 recon-all.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 12:00 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

What if I had 24 subjects. Should I specify the name for each one in the line ?

Dunia

On Tue, Nov 21, 2023 at 4:52 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

This is your recon-all submitted

“/Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache”

Add ‘-all’ to the line.

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 11:50 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

Could you please explain more ho to specify all in recon-all command ?

Dunia

On Tue, Nov 21, 2023 at 4:48 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

It looks like you don’t have data processed. Specify ‘-all’ on recon-all on command line.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 10:58 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

Hello Freesurfer Developers

I'm attempting to apply preprocess and segment to my data that consist of 24 subjects by recon-all syntax, as described on the FreeSurfer wiki on macOs software

*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1L8m_zg_RIfZ6_b75_nHg7Tn-fTx3olgLlfK6RW0X2FNFQX... https://secure-web.cisco.com/1sL0UR9IcjyzN-iiFPRBpUbos_zcdbT2W0RQcJ-3jMPXPBbG7t5-6HgMR60s4YWqde4tZa0XWjtkT0aWl3XybyhjThRfDIZmH8oNIZTQHT3KJDNpBj1DUZ6PKEZrrygdbT1DPTNtfO_zUn04IsLpbI6O57RcgvpVsXEx8ujYU-9-eFN0mWsVDj6gaP-ZccrPky_ruv3wCEiKCyGbSpPLpWXig3WAycCHA4_N_rPef9kRpg4gEFbLVjmjTPA3yx66OOHSaNacYpeFWBHZKyZbf4aKwJBcw2IPYCBLyjn1TOfQIc4V1h7skqAUUfgGHtlo3I_FNzpbevSUMMmOhMJUuzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all

ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I83870_MP-RAGE_20071127095752_2/surf/lh.thickness

Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64

1. freesurfer version: freesurfer-macOS-darwin_x86_64-7.4.1

2. platform: bash terminal

3. log file

Tue Nov 21 15:50:35 GMT 2023 cd /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects /Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache

subjid I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects FREESURFER_HOME /Applications/freesurfer/7.4.1 Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 build-stamp.txt: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64 cputime unlimited filesize unlimited datasize unlimited stacksize 8176 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 1333

PhysMem: 7547M used (1397M wired, 2612M compressor), 77M unused.

######################################## program versions used 7.4.1 (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460) 7.4.1

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http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk

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Hi again..

I made the script but I got a problem I would like to mention that I am working on Linux system the message error I got is

duniaa77@TENCC96E5342F26:/usr/local/freesurfer/7.4.1/subjects$ for i in {001..024}; do

echo "Processing subject sub${i} with input ${i}.nii" recon-all -s sub${i} -i ${i}.nii -all done

Processing subject sub001 with input 001.nii ERROR: 001.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub001 exited with ERRORS at Wed Nov 22 10:53:03 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub002 with input 002.nii ERROR: 002.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub002 exited with ERRORS at Wed Nov 22 10:53:06 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub003 with input 003.nii ERROR: 003.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub003 exited with ERRORS at Wed Nov 22 10:53:08 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub004 with input 004.nii ERROR: 004.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub004 exited with ERRORS at Wed Nov 22 10:53:09 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub005 with input 005.nii ERROR: 005.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub005 exited with ERRORS at Wed Nov 22 10:53:11 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub006 with input 006.nii ERROR: 006.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub006 exited with ERRORS at Wed Nov 22 10:53:13 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub007 with input 007.nii ERROR: 007.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub007 exited with ERRORS at Wed Nov 22 10:53:15 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub008 with input 008.nii ERROR: 008.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub008 exited with ERRORS at Wed Nov 22 10:53:16 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub009 with input 009.nii ERROR: 009.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub009 exited with ERRORS at Wed Nov 22 10:53:18 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub010 with input 010.nii ERROR: 010.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub010 exited with ERRORS at Wed Nov 22 10:53:20 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub011 with input 011.nii ERROR: 011.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub011 exited with ERRORS at Wed Nov 22 10:53:21 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub012 with input 012.nii ERROR: 012.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub012 exited with ERRORS at Wed Nov 22 10:53:23 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub013 with input 013.nii ERROR: 013.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub013 exited with ERRORS at Wed Nov 22 10:53:24 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub014 with input 014.nii ERROR: 014.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub014 exited with ERRORS at Wed Nov 22 10:53:26 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub015 with input 015.nii ERROR: 015.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub015 exited with ERRORS at Wed Nov 22 10:53:27 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub016 with input 016.nii ERROR: 016.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub016 exited with ERRORS at Wed Nov 22 10:53:28 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub017 with input 017.nii ERROR: 017.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub017 exited with ERRORS at Wed Nov 22 10:53:29 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub018 with input 018.nii ERROR: 018.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub018 exited with ERRORS at Wed Nov 22 10:53:30 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub019 with input 019.nii ERROR: 019.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub019 exited with ERRORS at Wed Nov 22 10:53:32 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub020 with input 020.nii ERROR: 020.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub020 exited with ERRORS at Wed Nov 22 10:53:33 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub021 with input 021.nii ERROR: 021.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub021 exited with ERRORS at Wed Nov 22 10:53:34 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub022 with input 022.nii ERROR: 022.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub022 exited with ERRORS at Wed Nov 22 10:53:36 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub023 with input 023.nii ERROR: 023.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub023 exited with ERRORS at Wed Nov 22 10:53:37 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

Processing subject sub024 with input 024.nii ERROR: 024.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub024 exited with ERRORS at Wed Nov 22 10:53:39 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9...

On Tue, 21 Nov 2023 at 17:57, Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

Assuming

1. NIFTI files for your subjects are 1.nii, 2.nii, …, 300.nii
2. To name the subjects as sub1, sub2, …, sub300

In bash shell, you can do the batch submission as following at prompt:

for i in {1..300}; \

do \

echo “recon-all -all -s sub${i} -i ${i}.nii” \

recon-all -all -s sub${i} -i ${i}.nii \

done

Adjust recon-all command line options for any additional flags, and change the subject IDs for something more descriptive.

It is a good idea to submit one first to get familiar with Freesurfer recon-all output directory structure before doing the batch submission.

Best,

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 12:35 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors in recon-all command

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Could explain more, as I am not very expert in freesurfer

For e.g I had 300 subject and their NIFTI files are named by their number (1.nii)

How to make a script to launch, do you mean in a txt file ?

Thank you

On Tue, Nov 21, 2023 at 5:29 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

you can write a script to launch them, eg foreach subject (your-list-of-subjects) recon-all -s $subject -all ... end

On 11/21/2023 12:04 PM, Dunia A Alhamad wrote:

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But this will take long time because I had another group with 300 patients

On Tue, Nov 21, 2023 at 5:03 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

Each subject needs to be processed separately. You will need submit 24 recon-all.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 12:00 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

What if I had 24 subjects. Should I specify the name for each one in the line ?

Dunia

On Tue, Nov 21, 2023 at 4:52 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

This is your recon-all submitted

“/Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache”

Add ‘-all’ to the line.

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 11:50 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors in recon-all command

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Could you please explain more ho to specify all in recon-all command ?

Dunia

On Tue, Nov 21, 2023 at 4:48 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

It looks like you don’t have data processed. Specify ‘-all’ on recon-all on command line.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 10:58 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Errors in recon-all command

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Hello Freesurfer Developers

I'm attempting to apply preprocess and segment to my data that consist of 24 subjects by recon-all syntax, as described on the FreeSurfer wiki on macOs software

*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1GYOQxOzQ9UXFpKv_pYoJueFoFEfcX71fOUyLUGlO6CR6NT... https://secure-web.cisco.com/1sL0UR9IcjyzN-iiFPRBpUbos_zcdbT2W0RQcJ-3jMPXPBbG7t5-6HgMR60s4YWqde4tZa0XWjtkT0aWl3XybyhjThRfDIZmH8oNIZTQHT3KJDNpBj1DUZ6PKEZrrygdbT1DPTNtfO_zUn04IsLpbI6O57RcgvpVsXEx8ujYU-9-eFN0mWsVDj6gaP-ZccrPky_ruv3wCEiKCyGbSpPLpWXig3WAycCHA4_N_rPef9kRpg4gEFbLVjmjTPA3yx66OOHSaNacYpeFWBHZKyZbf4aKwJBcw2IPYCBLyjn1TOfQIc4V1h7skqAUUfgGHtlo3I_FNzpbevSUMMmOhMJUuzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all

ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I83870_MP-RAGE_20071127095752_2/surf/lh.thickness

Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64

1. freesurfer version: freesurfer-macOS-darwin_x86_64-7.4.1

2. platform: bash terminal

3. log file

Tue Nov 21 15:50:35 GMT 2023 cd /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects /Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache

subjid I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects FREESURFER_HOME /Applications/freesurfer/7.4.1 Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 build-stamp.txt: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64 cputime unlimited filesize unlimited datasize unlimited stacksize 8176 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 1333

PhysMem: 7547M used (1397M wired, 2612M compressor), 77M unused.

######################################## program versions used 7.4.1 (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460) 7.4.1

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http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine:

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1eb4m59qSo19vdisxCUP-x_9mcPjMCaD-E6B0CfdToVwOfP... 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/1EbAO0pZA8fnqSj2xu9SY8snsfBlp4aV9HCU0-lZ0KlQOIE... < https://secure-web.cisco.com/1EbAO0pZA8fnqSj2xu9SY8snsfBlp4aV9HCU0-lZ0KlQOIE... . 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.

External Email - Use Caution

duniaa77@TENCC96E5342F26:/usr/local/freesurfer/7.4.1/subjects$ for i in {001..024}; do

echo "Processing subject sub${i} with input /subjects${i}.nii" recon-all -s sub${i} -i ${i}.nii -all done

Processing subject sub001 with input /subjects001.nii ERROR: 001.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub001 exited with ERRORS at Wed Nov 22 13:14:23 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub002 with input /subjects002.nii ERROR: 002.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub002 exited with ERRORS at Wed Nov 22 13:14:25 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub003 with input /subjects003.nii ERROR: 003.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub003 exited with ERRORS at Wed Nov 22 13:14:26 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub004 with input /subjects004.nii ERROR: 004.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub004 exited with ERRORS at Wed Nov 22 13:14:28 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub005 with input /subjects005.nii ERROR: 005.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub005 exited with ERRORS at Wed Nov 22 13:14:30 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub006 with input /subjects006.nii ERROR: 006.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub006 exited with ERRORS at Wed Nov 22 13:14:32 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub007 with input /subjects007.nii ERROR: 007.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub007 exited with ERRORS at Wed Nov 22 13:14:33 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub008 with input /subjects008.nii ERROR: 008.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub008 exited with ERRORS at Wed Nov 22 13:14:35 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub009 with input /subjects009.nii ERROR: 009.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub009 exited with ERRORS at Wed Nov 22 13:14:37 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub010 with input /subjects010.nii ERROR: 010.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub010 exited with ERRORS at Wed Nov 22 13:14:39 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub011 with input /subjects011.nii ERROR: 011.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub011 exited with ERRORS at Wed Nov 22 13:14:40 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub012 with input /subjects012.nii ERROR: 012.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub012 exited with ERRORS at Wed Nov 22 13:14:42 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub013 with input /subjects013.nii ERROR: 013.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub013 exited with ERRORS at Wed Nov 22 13:14:44 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub014 with input /subjects014.nii ERROR: 014.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub014 exited with ERRORS at Wed Nov 22 13:14:45 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub015 with input /subjects015.nii ERROR: 015.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub015 exited with ERRORS at Wed Nov 22 13:14:47 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub016 with input /subjects016.nii ERROR: 016.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub016 exited with ERRORS at Wed Nov 22 13:14:49 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub017 with input /subjects017.nii ERROR: 017.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub017 exited with ERRORS at Wed Nov 22 13:14:50 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub018 with input /subjects018.nii ERROR: 018.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub018 exited with ERRORS at Wed Nov 22 13:14:52 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub019 with input /subjects019.nii ERROR: 019.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub019 exited with ERRORS at Wed Nov 22 13:14:53 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub020 with input /subjects020.nii ERROR: 020.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub020 exited with ERRORS at Wed Nov 22 13:14:55 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub021 with input /subjects021.nii ERROR: 021.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub021 exited with ERRORS at Wed Nov 22 13:14:56 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub022 with input /subjects022.nii ERROR: 022.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub022 exited with ERRORS at Wed Nov 22 13:14:58 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub023 with input /subjects023.nii ERROR: 023.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub023 exited with ERRORS at Wed Nov 22 13:14:59 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

Processing subject sub024 with input /subjects024.nii ERROR: 024.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub024 exited with ERRORS at Wed Nov 22 13:15:01 GMT 2023

For more details, see the log file To report a problem, see http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5...

On Wed, 22 Nov 2023 at 13:00, Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

Change your script to specify full path to 001.nii - “</your-filepath>${i}.nii”

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Wednesday, November 22, 2023 5:55 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

Hi again..

I made the script but I got a problem

I would like to mention that I am working on Linux system

the message error I got is

duniaa77@TENCC96E5342F26:/usr/local/freesurfer/7.4.1/subjects$ for i in {001..024}; do

...

echo "Processing subject sub${i} with input ${i}.nii" recon-all -s sub${i} -i ${i}.nii -all done

Processing subject sub001 with input 001.nii ERROR: 001.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub001 exited with ERRORS at Wed Nov 22 10:53:03 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub002 with input 002.nii ERROR: 002.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub002 exited with ERRORS at Wed Nov 22 10:53:06 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub003 with input 003.nii ERROR: 003.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub003 exited with ERRORS at Wed Nov 22 10:53:08 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub004 with input 004.nii ERROR: 004.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub004 exited with ERRORS at Wed Nov 22 10:53:09 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub005 with input 005.nii ERROR: 005.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub005 exited with ERRORS at Wed Nov 22 10:53:11 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub006 with input 006.nii ERROR: 006.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub006 exited with ERRORS at Wed Nov 22 10:53:13 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub007 with input 007.nii ERROR: 007.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub007 exited with ERRORS at Wed Nov 22 10:53:15 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub008 with input 008.nii ERROR: 008.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub008 exited with ERRORS at Wed Nov 22 10:53:16 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub009 with input 009.nii ERROR: 009.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub009 exited with ERRORS at Wed Nov 22 10:53:18 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub010 with input 010.nii ERROR: 010.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub010 exited with ERRORS at Wed Nov 22 10:53:20 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub011 with input 011.nii ERROR: 011.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub011 exited with ERRORS at Wed Nov 22 10:53:21 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub012 with input 012.nii ERROR: 012.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub012 exited with ERRORS at Wed Nov 22 10:53:23 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub013 with input 013.nii ERROR: 013.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub013 exited with ERRORS at Wed Nov 22 10:53:24 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub014 with input 014.nii ERROR: 014.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub014 exited with ERRORS at Wed Nov 22 10:53:26 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub015 with input 015.nii ERROR: 015.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub015 exited with ERRORS at Wed Nov 22 10:53:27 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub016 with input 016.nii ERROR: 016.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub016 exited with ERRORS at Wed Nov 22 10:53:28 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub017 with input 017.nii ERROR: 017.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub017 exited with ERRORS at Wed Nov 22 10:53:29 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub018 with input 018.nii ERROR: 018.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub018 exited with ERRORS at Wed Nov 22 10:53:30 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub019 with input 019.nii ERROR: 019.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub019 exited with ERRORS at Wed Nov 22 10:53:32 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub020 with input 020.nii ERROR: 020.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub020 exited with ERRORS at Wed Nov 22 10:53:33 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub021 with input 021.nii ERROR: 021.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub021 exited with ERRORS at Wed Nov 22 10:53:34 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub022 with input 022.nii ERROR: 022.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub022 exited with ERRORS at Wed Nov 22 10:53:36 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub023 with input 023.nii ERROR: 023.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub023 exited with ERRORS at Wed Nov 22 10:53:37 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub024 with input 024.nii ERROR: 024.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub024 exited with ERRORS at Wed Nov 22 10:53:39 GMT 2023

For more details, see the log file To report a problem, see *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u5... http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

On Tue, 21 Nov 2023 at 17:57, Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

Assuming

1. NIFTI files for your subjects are 1.nii, 2.nii, …, 300.nii
2. To name the subjects as sub1, sub2, …, sub300

In bash shell, you can do the batch submission as following at prompt:

for i in {1..300}; \

do \

echo “recon-all -all -s sub${i} -i ${i}.nii” \

recon-all -all -s sub${i} -i ${i}.nii \

done

Adjust recon-all command line options for any additional flags, and change the subject IDs for something more descriptive.

It is a good idea to submit one first to get familiar with Freesurfer recon-all output directory structure before doing the batch submission.

Best,

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 12:35 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

Could explain more, as I am not very expert in freesurfer

For e.g I had 300 subject and their NIFTI files are named by their number (1.nii)

How to make a script to launch, do you mean in a txt file ?

Thank you

On Tue, Nov 21, 2023 at 5:29 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:

you can write a script to launch them, eg foreach subject (your-list-of-subjects) recon-all -s $subject -all ... end

On 11/21/2023 12:04 PM, Dunia A Alhamad wrote:

•    External Email - Use Caution        *
  
  

But this will take long time because I had another group with 300 patients

On Tue, Nov 21, 2023 at 5:03 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

Each subject needs to be processed separately. You will need submit 24 recon-all.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 12:00 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

What if I had 24 subjects. Should I specify the name for each one in the line ?

Dunia

On Tue, Nov 21, 2023 at 4:52 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

This is your recon-all submitted

“/Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache”

Add ‘-all’ to the line.

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 11:50 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

Could you please explain more ho to specify all in recon-all command ?

Dunia

On Tue, Nov 21, 2023 at 4:48 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

It looks like you don’t have data processed. Specify ‘-all’ on recon-all on command line.

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A Alhamad *Sent:* Tuesday, November 21, 2023 10:58 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Errors in recon-all command

•    External Email - Use Caution        *
  
  

Hello Freesurfer Developers

I'm attempting to apply preprocess and segment to my data that consist of 24 subjects by recon-all syntax, as described on the FreeSurfer wiki on macOs software

*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1KoDa__kt7yD-jyLbuMjbrXAe3y5wrlj7_UCsT0TxO8DtNP... https://secure-web.cisco.com/1sL0UR9IcjyzN-iiFPRBpUbos_zcdbT2W0RQcJ-3jMPXPBbG7t5-6HgMR60s4YWqde4tZa0XWjtkT0aWl3XybyhjThRfDIZmH8oNIZTQHT3KJDNpBj1DUZ6PKEZrrygdbT1DPTNtfO_zUn04IsLpbI6O57RcgvpVsXEx8ujYU-9-eFN0mWsVDj6gaP-ZccrPky_ruv3wCEiKCyGbSpPLpWXig3WAycCHA4_N_rPef9kRpg4gEFbLVjmjTPA3yx66OOHSaNacYpeFWBHZKyZbf4aKwJBcw2IPYCBLyjn1TOfQIc4V1h7skqAUUfgGHtlo3I_FNzpbevSUMMmOhMJUuzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all

ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I83870_MP-RAGE_20071127095752_2/surf/lh.thickness

Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64

1. freesurfer version: freesurfer-macOS-darwin_x86_64-7.4.1

2. platform: bash terminal

3. log file

Tue Nov 21 15:50:35 GMT 2023 cd /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects /Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache

subjid I12250_MP-RAGE_20060321115220_3 setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects FREESURFER_HOME /Applications/freesurfer/7.4.1 Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 build-stamp.txt: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Darwin dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64 cputime unlimited filesize unlimited datasize unlimited stacksize 8176 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 1333

PhysMem: 7547M used (1397M wired, 2612M compressor), 77M unused.

######################################## program versions used 7.4.1 (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460) 7.4.1

ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk 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http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk 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http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine:

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1aeguTmn1vhDYPjm4j30nqvuFDwL5CLfJ1CpG5HE90NN2q5... https://secure-web.cisco.com/1eb4m59qSo19vdisxCUP-x_9mcPjMCaD-E6B0CfdToVwOfPGau-3B-D_ARyuLkBneVELQsaMJgPNuWublgnvk9vJBLqvGnhicvvTkFj5CdoGRFdfbw_EUx_O2vmyZKK9bJBUjFQM--nIynKm4v-Gqcl102OoBmneT9M_Dr9tVt0hDmPHFvedwgjZHUILrAy-U5pX8wydKjey1SrWfDfXcaWT3FSC50OQiikTEc0lerbehuwvizSWarqcEL8RgD0jEFMv5KIDiAA1HkJ5mrDvpJt71E78yIIRokT9H-usL0RwqGIV1Q2WOXNHpUUbn001Jl2DtNgtlt3ks2wqTqKts2g/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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1qZuABWXjAMb8_i6bTTcLgNKx3HsXo473lprZgy_cq3VbJC... https://secure-web.cisco.com/1EbAO0pZA8fnqSj2xu9SY8snsfBlp4aV9HCU0-lZ0KlQOIEi52ANV6SlxPYtewqS-0QABSYZviOb1xV0cKE7G2yhWgjLL6sBoA7wUcG1SbG4zT350QNT8YYa50INVIPTe2PMofOi7YA2ObzZxmoF1LC9DdP34PXKilKN6lF4tVedjeU7IaBelbvFmLvCkLTBGWz2UFNfMC_RJrsUbM_olh5SNVe0LS2W-CsXLzmqdFQr55f_YNd26dMRxFYivJC4jH05XHNbJIiEUV1gsOZRaTHD1PtCk_j11psMvH6mdeiCS2Oh-pUPWHKGB8v3Z1ru_7Wk9-xOB_ftfK4zMZ15YWw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1qZuABWXjAMb8_i6bTTcLgNKx3HsXo473lprZgy_cq3VbJC... https://secure-web.cisco.com/1EbAO0pZA8fnqSj2xu9SY8snsfBlp4aV9HCU0-lZ0KlQOIEi52ANV6SlxPYtewqS-0QABSYZviOb1xV0cKE7G2yhWgjLL6sBoA7wUcG1SbG4zT350QNT8YYa50INVIPTe2PMofOi7YA2ObzZxmoF1LC9DdP34PXKilKN6lF4tVedjeU7IaBelbvFmLvCkLTBGWz2UFNfMC_RJrsUbM_olh5SNVe0LS2W-CsXLzmqdFQr55f_YNd26dMRxFYivJC4jH05XHNbJIiEUV1gsOZRaTHD1PtCk_j11psMvH6mdeiCS2Oh-pUPWHKGB8v3Z1ru_7Wk9-xOB_ftfK4zMZ15YWw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.

--

*Dunia Ahmad Al-Hamad*

PhD Student

Sheffield Institute of Translational Neuroscience (SiTraN)

The University of Sheffield

385a Glossop Road

Sheffield

S10 2HQ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1aeguTmn1vhDYPjm4j30nqvuFDwL5CLfJ1CpG5HE90NN2q5... 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/1qZuABWXjAMb8_i6bTTcLgNKx3HsXo473lprZgy_cq3VbJC... < https://secure-web.cisco.com/1qZuABWXjAMb8_i6bTTcLgNKx3HsXo473lprZgy_cq3VbJC... . 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.

You should talk to someone at your site who knows how to program to do this. It is not hard, but it is not our responsibility to write customized programs for our users. I hope you understand.

On 11/22/2023 8:15 AM, Dunia A Alhamad wrote:

External Email - Use Caution

duniaa77@TENCC96E5342F26:/usr/local/freesurfer/7.4.1/subjects$ for i in {001..024}; do

...

echo "Processing subject sub${i} with input /subjects${i}.nii" recon-all -s sub${i} -i ${i}.nii -all done

Processing subject sub001 with input /subjects001.nii ERROR: 001.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub001 exited with ERRORS at Wed Nov 22 13:14:23 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub002 with input /subjects002.nii ERROR: 002.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub002 exited with ERRORS at Wed Nov 22 13:14:25 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub003 with input /subjects003.nii ERROR: 003.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub003 exited with ERRORS at Wed Nov 22 13:14:26 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub004 with input /subjects004.nii ERROR: 004.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub004 exited with ERRORS at Wed Nov 22 13:14:28 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub005 with input /subjects005.nii ERROR: 005.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub005 exited with ERRORS at Wed Nov 22 13:14:30 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub006 with input /subjects006.nii ERROR: 006.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub006 exited with ERRORS at Wed Nov 22 13:14:32 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub007 with input /subjects007.nii ERROR: 007.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub007 exited with ERRORS at Wed Nov 22 13:14:33 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub008 with input /subjects008.nii ERROR: 008.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub008 exited with ERRORS at Wed Nov 22 13:14:35 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub009 with input /subjects009.nii ERROR: 009.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub009 exited with ERRORS at Wed Nov 22 13:14:37 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub010 with input /subjects010.nii ERROR: 010.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub010 exited with ERRORS at Wed Nov 22 13:14:39 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub011 with input /subjects011.nii ERROR: 011.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub011 exited with ERRORS at Wed Nov 22 13:14:40 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub012 with input /subjects012.nii ERROR: 012.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub012 exited with ERRORS at Wed Nov 22 13:14:42 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub013 with input /subjects013.nii ERROR: 013.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub013 exited with ERRORS at Wed Nov 22 13:14:44 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub014 with input /subjects014.nii ERROR: 014.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub014 exited with ERRORS at Wed Nov 22 13:14:45 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub015 with input /subjects015.nii ERROR: 015.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub015 exited with ERRORS at Wed Nov 22 13:14:47 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub016 with input /subjects016.nii ERROR: 016.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub016 exited with ERRORS at Wed Nov 22 13:14:49 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub017 with input /subjects017.nii ERROR: 017.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub017 exited with ERRORS at Wed Nov 22 13:14:50 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub018 with input /subjects018.nii ERROR: 018.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub018 exited with ERRORS at Wed Nov 22 13:14:52 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub019 with input /subjects019.nii ERROR: 019.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub019 exited with ERRORS at Wed Nov 22 13:14:53 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub020 with input /subjects020.nii ERROR: 020.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub020 exited with ERRORS at Wed Nov 22 13:14:55 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub021 with input /subjects021.nii ERROR: 021.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub021 exited with ERRORS at Wed Nov 22 13:14:56 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub022 with input /subjects022.nii ERROR: 022.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub022 exited with ERRORS at Wed Nov 22 13:14:58 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub023 with input /subjects023.nii ERROR: 023.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub023 exited with ERRORS at Wed Nov 22 13:14:59 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

Processing subject sub024 with input /subjects024.nii ERROR: 024.nii exists but is not readable Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub024 exited with ERRORS at Wed Nov 22 13:15:01 GMT 2023

For more details, see the log file 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 http://secure-web.cisco.com/15Ndad2m6DgYqbtU65OOsUoTpFaAPxPN5aIOfBpJUMf5m2u59lEByQVbofsdQVKE4ojxil741cf0LLBl2S1gW8vmrz5m7TFknNwDVouuAdqiZFzNCuZt3IAgb7MCGBCoQxDhcDI9YUDo7R-Vq_xOSjoFzM1M3Mky3areeTDfWVk6velbNHB0pjecfll5QgCHk-4I0kxA8xxo5FXaTSJmTpqKGYfgopww6Hk2JLiQN9RIBZv7df1YW27C5UIvcTTcuac_X3CxA18T1FCcnHYYpObVtJTFvxJvq42Q1UuGWgqWG2X2UW8CPPoWrJxU1Z0-B/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

On Wed, 22 Nov 2023 at 13:00, Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

Change your script to specify full path to 001.nii -
“</your-filepath>${i}.nii”

*From:* freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia A
Alhamad
*Sent:* Wednesday, November 22, 2023 5:55 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Errors in recon-all command

*        External Email - Use Caution *

Hi again..

I made the script but I got a problem

I would like to mention that I am working on Linux system

the message error I got is

duniaa77@TENCC96E5342F26:/usr/local/freesurfer/7.4.1/subjects$ for
i in {001..024}; do
> echo "Processing subject sub${i} with input ${i}.nii"
> recon-all -s sub${i} -i ${i}.nii -all
> done
Processing subject sub001 with input 001.nii
ERROR: 001.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub001 exited with ERRORS at Wed Nov 22 10:53:03 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub002 with input 002.nii
ERROR: 002.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub002 exited with ERRORS at Wed Nov 22 10:53:06 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub003 with input 003.nii
ERROR: 003.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub003 exited with ERRORS at Wed Nov 22 10:53:08 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub004 with input 004.nii
ERROR: 004.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub004 exited with ERRORS at Wed Nov 22 10:53:09 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub005 with input 005.nii
ERROR: 005.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub005 exited with ERRORS at Wed Nov 22 10:53:11 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub006 with input 006.nii
ERROR: 006.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub006 exited with ERRORS at Wed Nov 22 10:53:13 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub007 with input 007.nii
ERROR: 007.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub007 exited with ERRORS at Wed Nov 22 10:53:15 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub008 with input 008.nii
ERROR: 008.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub008 exited with ERRORS at Wed Nov 22 10:53:16 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub009 with input 009.nii
ERROR: 009.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub009 exited with ERRORS at Wed Nov 22 10:53:18 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub010 with input 010.nii
ERROR: 010.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub010 exited with ERRORS at Wed Nov 22 10:53:20 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub011 with input 011.nii
ERROR: 011.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub011 exited with ERRORS at Wed Nov 22 10:53:21 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub012 with input 012.nii
ERROR: 012.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub012 exited with ERRORS at Wed Nov 22 10:53:23 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub013 with input 013.nii
ERROR: 013.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub013 exited with ERRORS at Wed Nov 22 10:53:24 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub014 with input 014.nii
ERROR: 014.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub014 exited with ERRORS at Wed Nov 22 10:53:26 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub015 with input 015.nii
ERROR: 015.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub015 exited with ERRORS at Wed Nov 22 10:53:27 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub016 with input 016.nii
ERROR: 016.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub016 exited with ERRORS at Wed Nov 22 10:53:28 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub017 with input 017.nii
ERROR: 017.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub017 exited with ERRORS at Wed Nov 22 10:53:29 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub018 with input 018.nii
ERROR: 018.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub018 exited with ERRORS at Wed Nov 22 10:53:30 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub019 with input 019.nii
ERROR: 019.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub019 exited with ERRORS at Wed Nov 22 10:53:32 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub020 with input 020.nii
ERROR: 020.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub020 exited with ERRORS at Wed Nov 22 10:53:33 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub021 with input 021.nii
ERROR: 021.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub021 exited with ERRORS at Wed Nov 22 10:53:34 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub022 with input 022.nii
ERROR: 022.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub022 exited with ERRORS at Wed Nov 22 10:53:36 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub023 with input 023.nii
ERROR: 023.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub023 exited with ERRORS at Wed Nov 22 10:53:37 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

Processing subject sub024 with input 024.nii
ERROR: 024.nii exists but is not readable
Linux TENCC96E5342F26 4.4.0-19041-Microsoft #3636-Microsoft Thu
Oct 19 17:41:00 PST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub024 exited with ERRORS at Wed Nov 22 10:53:39 GMT 2023

For more details, see the log file
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
<http://secure-web.cisco.com/1euA8fMDTY6pbpq_1zy-6W0qLdOLm_sh0IxixBwOj75NXUd9fMgOMyjJ8pBv0qvHwhmGO5Cp_fsEPw8TxoczYVKa4HzSypzqTIyXSsT3HFfkVbbtFHID4gMioSIWhsyeBBYL-ESFB9Ptz0yqNuxeURWRFBUUdSYCm0PnzIEjxi1XHpslAmgM0mXPqcvYB0-jH-sANc2X3gY7sCIsJLNCYvGfRA98RGhvDoJwZGRMzud_PWiBbgx3dO5UDeWSjfQSxnXgo4f85of1CxUggsYVqZXXSuneT9nLlN1DufbOA_e_jcyjMQP6cLvP-RmlaLkhdhg3ZCLzirS8z5uKw2aL9HQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

On Tue, 21 Nov 2023 at 17:57, Huang, Yujing
<YHUANG43@mgh.harvard.edu> wrote:

    Assuming

     1. NIFTI files for your subjects are 1.nii, 2.nii, …, 300.nii
     2. To name the subjects as sub1, sub2, …, sub300

    In bash shell, you can do the batch submission as following at
    prompt:

    for i in {1..300}; \

    do \

    echo “recon-all -all -s sub${i} -i ${i}.nii” \

    recon-all -all -s sub${i} -i ${i}.nii \

    done

    Adjust recon-all command line options for any additional
    flags, and change the subject IDs for something more descriptive.

    It is a good idea to submit one first to get familiar with
    Freesurfer recon-all output directory structure before doing
    the batch submission.

    Best,

    Yujing

    *From:* freesurfer-bounces@nmr.mgh.harvard.edu
    <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Dunia
    A Alhamad
    *Sent:* Tuesday, November 21, 2023 12:35 PM
    *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
    *Subject:* Re: [Freesurfer] Errors in recon-all command

    *        External Email - Use Caution *

    Could explain more, as I am not very expert in freesurfer

    For e.g I had 300 subject and their NIFTI files are named by
    their number (1.nii)

    How to make a script to launch, do you mean in a txt file ?

    Thank you

    On Tue, Nov 21, 2023 at 5:29 PM Douglas N. Greve
    <dgreve@mgh.harvard.edu> wrote:

        you can write a script to launch them, eg
        foreach subject (your-list-of-subjects)
          recon-all -s $subject -all ...
        end

        On 11/21/2023 12:04 PM, Dunia A Alhamad wrote:

            *        External Email - Use Caution *

            But this will take long time because I had another
            group with 300 patients

            On Tue, Nov 21, 2023 at 5:03 PM Huang, Yujing
            <YHUANG43@mgh.harvard.edu> wrote:

                Each subject needs to be processed separately. You
                will need submit 24 recon-all.

                Yujing

                *From:* freesurfer-bounces@nmr.mgh.harvard.edu
                <freesurfer-bounces@nmr.mgh.harvard.edu> *On
                Behalf Of *Dunia A Alhamad
                *Sent:* Tuesday, November 21, 2023 12:00 PM
                *To:* Freesurfer support list
                <freesurfer@nmr.mgh.harvard.edu>
                *Subject:* Re: [Freesurfer] Errors in recon-all
                command

                *        External Email - Use Caution *

                What if I had 24 subjects. Should I specify the
                name for each one in the line ?

                Dunia

                On Tue, Nov 21, 2023 at 4:52 PM Huang, Yujing
                <YHUANG43@mgh.harvard.edu> wrote:

                    This is your recon-all submitted

                    “/Applications/freesurfer/7.4.1/bin/recon-all
                    -s I12250_MP-RAGE_20060321115220_3 -i
                    I12250_MP-RAGE_20060321115220_3.nii -qcache”

                    Add ‘-all’ to the line.

                    *From:* freesurfer-bounces@nmr.mgh.harvard.edu
                    <freesurfer-bounces@nmr.mgh.harvard.edu> *On
                    Behalf Of *Dunia A Alhamad
                    *Sent:* Tuesday, November 21, 2023 11:50 AM
                    *To:* Freesurfer support list
                    <freesurfer@nmr.mgh.harvard.edu>
                    *Subject:* Re: [Freesurfer] Errors in
                    recon-all command

                    *        External Email - Use Caution *

                    Could you please explain more ho to specify
                    all in recon-all command ?

                    Dunia

                    On Tue, Nov 21, 2023 at 4:48 PM Huang, Yujing
                    <YHUANG43@mgh.harvard.edu> wrote:

                        It looks like you don’t have data
                        processed. Specify ‘-all’ on recon-all on
                        command line.

                        Yujing

                        *From:*
                        freesurfer-bounces@nmr.mgh.harvard.edu
                        <freesurfer-bounces@nmr.mgh.harvard.edu>
                        *On Behalf Of *Dunia A Alhamad
                        *Sent:* Tuesday, November 21, 2023 10:58 AM
                        *To:* freesurfer@nmr.mgh.harvard.edu
                        *Subject:* [Freesurfer] Errors in
                        recon-all command

                        *        External Email - Use Caution *

                        Hello Freesurfer Developers

                        I'm attempting to apply preprocess and
                        segment to my data that consist of 24
                        subjects by recon-all syntax, as described
                        on the FreeSurfer wiki on macOs software

                        *MailScanner has detected a possible fraud
                        attempt from "secure-web.cisco.com"
                        claiming to be*
                        https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
                        <https://secure-web.cisco.com/1sL0UR9IcjyzN-iiFPRBpUbos_zcdbT2W0RQcJ-3jMPXPBbG7t5-6HgMR60s4YWqde4tZa0XWjtkT0aWl3XybyhjThRfDIZmH8oNIZTQHT3KJDNpBj1DUZ6PKEZrrygdbT1DPTNtfO_zUn04IsLpbI6O57RcgvpVsXEx8ujYU-9-eFN0mWsVDj6gaP-ZccrPky_ruv3wCEiKCyGbSpPLpWXig3WAycCHA4_N_rPef9kRpg4gEFbLVjmjTPA3yx66OOHSaNacYpeFWBHZKyZbf4aKwJBcw2IPYCBLyjn1TOfQIc4V1h7skqAUUfgGHtlo3I_FNzpbevSUMMmOhMJUuzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all>

                        ERROR: cannot find
                        /Users/duniaalhamad/Desktop/subjects/I83870_MP-RAGE_20071127095752_2/surf/lh.thickness

                        Darwin dyn145223.shef.ac.uk
                        <http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk>
                        23.1.0 Darwin Kernel Version 23.1.0: Mon
                        Oct  9 21:28:31 PDT 2023;
                        root:xnu-10002.41.9~6/RELEASE_ARM64_T8112
                        arm64

                        1) freesurfer version:
                        freesurfer-macOS-darwin_x86_64-7.4.1

                        2) platform: bash terminal

                        3) log file


                        Tue Nov 21 15:50:35 GMT 2023
                        cd
                        /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3
                        setenv SUBJECTS_DIR
                        /Users/duniaalhamad/Desktop/subjects
                        /Applications/freesurfer/7.4.1/bin/recon-all
                        -s I12250_MP-RAGE_20060321115220_3 -i
                        I12250_MP-RAGE_20060321115220_3.nii -qcache

                        subjid I12250_MP-RAGE_20060321115220_3
                        setenv SUBJECTS_DIR
                        /Users/duniaalhamad/Desktop/subjects
                        FREESURFER_HOME /Applications/freesurfer/7.4.1
                        Actual FREESURFER_HOME
                        /Applications/freesurfer/7.4.1
                        build-stamp.txt:
                        freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
                        Darwin dyn145223.shef.ac.uk
                        <http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk>
                        23.1.0 Darwin Kernel Version 23.1.0: Mon
                        Oct  9 21:28:31 PDT 2023;
                        root:xnu-10002.41.9~6/RELEASE_ARM64_T8112
                        arm64
                        cputime  unlimited
                        filesize unlimited
                        datasize unlimited
                        stacksize  8176 kbytes
                        coredumpsize 0 kbytes
                        memoryuse  unlimited
                        descriptors  256
                        memorylocked unlimited
                        maxproc  1333

                        PhysMem: 7547M used (1397M wired, 2612M
                        compressor), 77M unused.

                        ########################################
                        program versions used
                        7.4.1
                        (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460)
                        7.4.1

                        ProgramName: lta_convert
                         ProgramArguments: lta_convert -all-info
                         ProgramVersion: 7.4.1  TimeStamp:
                        2023/11/21-15:50:36-GMT  BuildTime: Jun 14
                        2023 00:15:19  BuildStamp:
                        freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
                         User: duniaalhamad  Machine:
                        dyn145223.shef.ac.uk
                        <http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk>
                         Platform: Darwin  PlatformVersion: 23.1.0
                         CompilerName: Clang  CompilerVersion: 12.0.0
                        ProgramName: mri_and  ProgramArguments:
                        mri_and -all-info  ProgramVersion: 7.4.1
                         TimeStamp: 2023/11/21-15:50:36-GMT
                         BuildTime: Jun 14 2023 00:15:19
                         BuildStamp:
                        freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
                         User: duniaalhamad  Machine:
                        dyn145223.shef.ac.uk
                        <http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk>
                         Platform: Darwin  PlatformVersion: 23.1.0
                         CompilerName: Clang  CompilerVersion: 12.0.0
                        ProgramName: mri_annotation2label
                         ProgramArguments: mri_annotation2label
                        -all-info  ProgramVersion: 7.4.1
                         TimeStamp: 2023/11/21-15:50:36-GMT
                         BuildTime: Jun 14 2023 00:15:19
                         BuildStamp:
                        freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
                         User: duniaalhamad  Machine:
                        dyn145223.shef.ac.uk
                        <http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk>
                         Platform: Darwin  PlatformVersion: 23.1.0
                         CompilerName: Clang  CompilerVersion: 12.0.0
                        ProgramName: mri_aparc2aseg
                         ProgramArguments: mri_aparc2aseg
                        -all-info  ProgramVersion: 7.4.1
                         TimeStamp: 2023/11/21-15:50:36-GMT
                         BuildTime: Jun 14 2023 00:15:19
                         BuildStamp:
                        freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
                         User: duniaalhamad  Machine:
                        dyn145223.shef.ac.uk
                        <http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk>
                         Platform: Darwin  PlatformVersion: 23.1.0
                         CompilerName: Clang  CompilerVersion: 12.0.0
                        ProgramName: mri_surf2volseg
                         ProgramArguments: mri_surf2volseg
                        -all-info  ProgramVersion: 7.4.1
                         TimeStamp: 2023/11/21-15:50:36-GMT
                         BuildTime: Jun 14 2023 00:15:19
                         BuildStamp:
                        freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
                         User: duniaalhamad  Machine:
                        dyn145223.shef.ac.uk
                        <http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk>
                         Platform: Darwin  PlatformVersion: 23.1.0
                         CompilerName: Clang  CompilerVersion: 12.0.0
                        ProgramName: mri_binarize
                         ProgramArguments: mri_binarize -all-info
                         ProgramVersion: 7.4.1  TimeStamp:
                        2023/11/21-15:50:36-GMT  BuildTime: Jun 14
                        2023 00:15:19  BuildStamp:
                        freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
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-- 

*Dunia Ahmad Al-Hamad*

PhD Student

Sheffield Institute of Translational Neuroscience (SiTraN)

The University of Sheffield

385a Glossop Road

Sheffield

S10 2HQ

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-- *Dunia Ahmad Al-Hamad* PhD Student Sheffield Institute of Translational Neuroscience (SiTraN) The University of Sheffield 385a Glossop Road Sheffield S10 2HQ

---

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