External Email - Use Caution
Apart from the output about the if statement, it looks like your recon-all command did run and then was killed because mri_synthstrip used too many system resources. That is unless the command took no time to run and immediately exited. If the command exited immediately after you entered it on the terminal, then the output about the if statement could indicate there is something not right with your recon-all arguments. Check you can run mri_synthstrip command directly. A command with actual arguments and processing to do would be a better test, but at least try, $ mri_synthstrip -h You could try reverting recon-all to the old behavior where it will not run the newer mri_* commands as part pf the recon-all pipeline by setting the environment variable FS_V8_XOPTS=0. That should reduce the chances the system will kill the process because of heavy resource usage. $ export FS_V8_XOPTS=0 && recon-all -s NVR-1 -sd /Volumes/INTENSO/Projects/NeuroVR+/MRI/recon/NVR-1_recon -i /Volumes/INTENSO/Projects/NeuroVR+/MRI/Nifti/NVR-1_nii/5_t1_tfl3d_sag_ti1090_fa9_tr2700_09mm_p2.nii.gz -T2 /Volumes/INTENSO/Projects/NeuroVR+/MRI/Nifti/NVR-1_nii/6_t2_space_sag_081x081x09mm_p2.nii.gz -T2pial -all - R. On Sep 9, 2025, at 08:47, Diedrich, Lukas <lukas.diedrich@med.uni-goettingen.de> wrote: External Email - Use Caution Thank you for this suggestion. However, changing the shell from zsh to bash did not help as I get the same error.Any other idea? Best wishes and thanks for your helpLukas
Dr. rer. nat. Lukas DiedrichPostdoctoral researcherNon-invasive Brain Stimulation (NBS) LabDepartment of NeurologyUniversity Medical Center Göttingen, Germany +49 551 39 64838 | lukas.diedrich@med.uni-goettingen.de <NBS_Logo_klein.png> Am 05.09.2025 um 22:35 schrieb fsbuild <fsbuild@contbay.com>: External Email - Use Caution If you have not already done so, please try running your commands in the bash shell as shown in the page referenced via the below link (scroll down to MACOS). So far I've seen no issues running various recon-all tests with 8.0.0 and 8.1.0 on a MacMini running Sequoia 15.5 with an M2 processor and 32GB of RAM using the setups listed on that page.https://secure-web.cisco.com/1rWW9djPvHdA8RjQ5GKcQFsjlPgqBRVuzizVB-1oyQ2oTM_... - R. _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1BLB3A_Aor7vhh4VJU3gnpbq-ikur2FY1421KWRz4gi-ENM... 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/1UwQ7qY2FJsKZtu6W4iR3gRfXytNPCjSCA1LQacPI1mM9V2... <https://secure-web.cisco.com/1FUVZMJbmPHEhJ63RzpfI-Ij12fCKYeL0IS5psFW7yVMJoQ...; . 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.
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External Email - Use Caution
.after finishing installation Iam getting the error pasted below. Can you help me solve this issue? used this command to download wget -c https://secure-web.cisco.com/1ZWUaa1V2V_ZweIEM3PlYtkh5ix2EIRLGNKENTZ81yrkukF...
in ubuntu VERSION_ID="24.04" VERSION="24.04.1 LTS (Noble Numbat)" VERSION_CODENAME=noble
Error displayed ./freesurfer/luts/ReducedLabels4.txt ./freesurfer/luts/FreeSurferColorLUT.txt
gzip: stdin: decompression OK, trailing garbage ignored ./freesurfer/luts/ReducedLabels24.txt ./freesurfer/sessions/ ./freesurfer/sessions/README tar: Child returned status 2 tar: Error is not recoverable: exiting now (base) root@f27029d22b83:/j/freesurfer#
On Sat, Sep 13, 2025 at 4:19 AM fsbuild fsbuild@contbay.com wrote:
External Email - Use CautionApart from the output about the if statement, it looks like your recon-all command did run and then was killed because mri_synthstrip used too many system resources. That is unless the command took no time to run and immediately exited. If the command exited immediately after you entered it on the terminal, then the output about the if statement could indicate there is something not right with your recon-all arguments.
Check you can run mri_synthstrip command directly. A command with actual arguments and processing to do would be a better test, but at least try,
$ mri_synthstrip -h
You could try reverting recon-all to the old behavior where it will not run the newer mri_* commands as part pf the recon-all pipeline by setting the environment variable FS_V8_XOPTS=0. That should reduce the chances the system will kill the process because of heavy resource usage.
$ export FS_V8_XOPTS=0 && recon-all -s NVR-1 -sd /Volumes/INTENSO/Projects/NeuroVR+/MRI/recon/NVR-1_recon -i /Volumes/INTENSO/Projects/NeuroVR+/MRI/Nifti/NVR-1_nii/5_t1_tfl3d_sag_ti1090_fa9_tr2700_09mm_p2.nii.gz -T2 /Volumes/INTENSO/Projects/NeuroVR+/MRI/Nifti/NVR-1_nii/6_t2_space_sag_081x081x09mm_p2.nii.gz -T2pial -all
- R.
On Sep 9, 2025, at 08:47, Diedrich, Lukas lukas.diedrich@med.uni-goettingen.de wrote:
External Email - Use CautionThank you for this suggestion. However, changing the shell from zsh to bash did not help as I get the same error. Any other idea?
Best wishes and thanks for your help Lukas ________________________________
Dr. rer. nat. Lukas Diedrich Postdoctoral researcher Non-invasive Brain Stimulation (NBS) Lab Department of Neurology University Medical Center Göttingen, Germany
+49 551 39 64838 | lukas.diedrich@med.uni-goettingen.de
<NBS_Logo_klein.png>
Am 05.09.2025 um 22:35 schrieb fsbuild fsbuild@contbay.com:
External Email - Use CautionIf you have not already done so, please try running your commands in the bash shell as shown in the page referenced via the below link (scroll down to MACOS). So far I've seen no issues running various recon-all tests with 8.0.0 and 8.1.0 on a MacMini running Sequoia 15.5 with an M2 processor and 32GB of RAM using the setups listed on that page.
https://secure-web.cisco.com/1HIiD1jwXrTjzSq9IOfdeG65rQ5FIIEPXAJYQgR8jN4SvNW...
- R.
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1jP5HzGM5wzdjOdltpGvJ4xJW70NfpW3Hisx5zjqFI0ncD_... 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/1s5mBLKPchPro2UQA1ZKKvnea4czOvdaHNJDPkOisYda7wt... https://secure-web.cisco.com/1s5mBLKPchPro2UQA1ZKKvnea4czOvdaHNJDPkOisYda7wtgM2TcsJsIAF68LnyFiCABfpKV-zkIuuCY4RScr5_aLLwbigyK1aD485ZjNOsVgs2E-k-P9RSF9Vjtx9ofqHHeXEnX_ID9MAf-1tlsSUOWUzg3_h9omj6wJtl9k95tDGA_3Yx--BJil_G4s-i5H7ybjPKt-RdzWjxdFLRZLCZEWFMYbxnplnGpdnA8lfbFQ-VhFaGXf8KbFs7y1wWfhCPDqV1Lrq5RCAMBdUzJ5XuIHz62IfaRxqVPbT2OmO_tdnB2tx18BNUs9aCjcJ3wV-UMxBB520prpf3nagLWHsstTYsJzePW-c7yGZBtjI9M/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.
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Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1jP5HzGM5wzdjOdltpGvJ4xJW70NfpW3Hisx5zjqFI0ncD_... 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/1s5mBLKPchPro2UQA1ZKKvnea4czOvdaHNJDPkOisYda7wt... https://secure-web.cisco.com/1s5mBLKPchPro2UQA1ZKKvnea4czOvdaHNJDPkOisYda7wtgM2TcsJsIAF68LnyFiCABfpKV-zkIuuCY4RScr5_aLLwbigyK1aD485ZjNOsVgs2E-k-P9RSF9Vjtx9ofqHHeXEnX_ID9MAf-1tlsSUOWUzg3_h9omj6wJtl9k95tDGA_3Yx--BJil_G4s-i5H7ybjPKt-RdzWjxdFLRZLCZEWFMYbxnplnGpdnA8lfbFQ-VhFaGXf8KbFs7y1wWfhCPDqV1Lrq5RCAMBdUzJ5XuIHz62IfaRxqVPbT2OmO_tdnB2tx18BNUs9aCjcJ3wV-UMxBB520prpf3nagLWHsstTYsJzePW-c7yGZBtjI9M/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.
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