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 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
- NIFTI files for your subjects are 1.nii, 2.nii, …, 300.nii
- 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/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
freesurfer version: freesurfer-macOS-darwin_x86_64-7.4.1
platform: bash terminal
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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