External Email - Use Caution
Hi ,
I have used the following call starting at Freesurfer 5.3
/usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon1 -noskullstrip -no-isrunning -s LAB_S01541_standard_20180307_4541_03072018 -rng-seed 1234
It is still working with Freesurfer 7.1.1 but we now tried updating to 7.3 and it is failing (on the same case). Looking at the recon-all.log it seem that ma_ca_register is not called anymore so that I get the following error message
ERROR: cannot find or read transforms/talairach.m3z
(see attached recon-all .log)
Do I have to add flags ? I need to run with -noskullstrip
Best,
Kilian
Hi Kilian,
I'm wondering what were your initial recon-all commands for FS 5.3 and FS 7.1.1 because I'm not sure '-autorecon1' is making mri_ca_register call by default.
But It looks like you can use '-careg' to turn on mri_ca_register call.
Here is a description of recon-all steps: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
Best,
Yujing
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kilian M Pohl Sent: Wednesday, December 7, 2022 12:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] ma_ca_register is not called anymore in version 7.3.2
External Email - Use Caution
Hi ,
I have used the following call starting at Freesurfer 5.3
/usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon1 -noskullstrip -no-isrunning -s LAB_S01541_standard_20180307_4541_03072018 -rng-seed 1234
It is still working with Freesurfer 7.1.1 but we now tried updating to 7.3 and it is failing (on the same case). Looking at the recon-all.log it seem that ma_ca_register is not called anymore so that I get the following error message
ERROR: cannot find or read transforms/talairach.m3z
(see attached recon-all .log)
Do I have to add flags ? I need to run with -noskullstrip
Best,
Kilian
-- Kilian M. Pohl, Ph.D.
Associate Professor Department of Psychiatry & Behavioral Sciences Stanford University
401 Quarry Road Stanford, CA 94305-5717
https://secure-web.cisco.com/18F69KCiyMWMSCouFYLrT3r9PgA1L7oUNzDa59-gQWUTsSh...
External Email - Use Caution
sorry listed wrong command line - after autrecon1 I run the following command
/usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon2 -autorecon3 -no-isrunning -s LAB_S01541_standard_20180307_4541_03072018 -no-fix-with-ga -rng-seed 1234
which is the one failing bc it cannot find transforms/talairach.m3z
#-------------------------------------- #@# SubCort Seg Tue Dec 6 17:58:54 UTC 2022
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz
sysname Linux hostname 3c46017221f4 machine x86_64
setenv SUBJECTS_DIR /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 cd /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500
== Number of threads available to for OpenMP = 4 == reading 1 input volumes reading classifier array from /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z error: No such file or directory error: transforms/talairach.m3z: could not open transform
Best,
Kilian On 12/7/2022 10:37 AM, Huang, Yujing wrote:
Hi Kilian,
I'm wondering what were your initial recon-all commands for FS 5.3 and FS 7.1.1 because I'm not sure '-autorecon1' is making mri_ca_register call by default.
But It looks like you can use '-careg' to turn on mri_ca_register call.
Here is a description of recon-all steps: https://secure-web.cisco.com/1htG9ZyeR94R_NHNY2O3znkDPMKCM94AkH1H0RTut4TvM_X...
Best,
Yujing
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kilian M Pohl Sent: Wednesday, December 7, 2022 12:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] ma_ca_register is not called anymore in version 7.3.2
External Email - Use CautionHi ,
I have used the following call starting at Freesurfer 5.3
/usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon1 -noskullstrip -no-isrunning -s LAB_S01541_standard_20180307_4541_03072018 -rng-seed 1234
It is still working with Freesurfer 7.1.1 but we now tried updating to 7.3 and it is failing (on the same case). Looking at the recon-all.log it seem that ma_ca_register is not called anymore so that I get the following error message
ERROR: cannot find or read transforms/talairach.m3z
(see attached recon-all .log)
Do I have to add flags ? I need to run with -noskullstrip
Best,
Kilian
-- Kilian M. Pohl, Ph.D.
Associate Professor Department of Psychiatry & Behavioral Sciences Stanford University
401 Quarry Road Stanford, CA 94305-5717
https://secure-web.cisco.com/18F69KCiyMWMSCouFYLrT3r9PgA1L7oUNzDa59-gQWUTsSh...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1qUnFO9DdCSW5zx3g8EStlrjaeIH462pIqGnhyLsCv2gFG4... 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/1lvA-scMVQw1Q4NT1T5Twcwt7R8fNc_A8S3FXA-R449Cuiy... https://secure-web.cisco.com/1lvA-scMVQw1Q4NT1T5Twcwt7R8fNc_A8S3FXA-R449Cuiy3dblzr_mizFqrhRyPVCTMeBa-yxbeDSiTgnJGy22rnK2JsLTJgMisXPTuiX1knhqSIkUocNh8zm-oOgUmaL9vZZ2aMvt_sS4eC743VateUr7l2rC1HLxtvyOAH9JvBNrE3lL3XARBXqMeDQg-d8Ol434Gufw8gji67opykzUDfTU3nak-ajCo7FIakyAJrRkIe6j9to90EABa8X6eA8RNF2RJnz9W6ssOiw4S1PzquEE5pxWz2fWnevU9_9rZXXbrwn5eTJy0oXFZoZH7W/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.
Hi Kilian,
Can you try adding '-careg'? Put it after "-autorecon2 -autorecon3".
Best,
Yujing
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kilian M Pohl Sent: Wednesday, December 7, 2022 10:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ma_ca_register is not called anymore in version 7.3.2
External Email - Use Caution
sorry listed wrong command line - after autrecon1 I run the following command
/usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon2 -autorecon3 -no-isrunning -s LAB_S01541_standard_20180307_4541_03072018 -no-fix-with-ga -rng-seed 1234
which is the one failing bc it cannot find transforms/talairach.m3z
#-------------------------------------- #@# SubCort Seg Tue Dec 6 17:58:54 UTC 2022
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz
sysname Linux hostname 3c46017221f4 machine x86_64
setenv SUBJECTS_DIR /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 cd /data/1541_case/LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7/LAB_S01541_standard_20180307_4541_03072018/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500
== Number of threads available to for OpenMP = 4 == reading 1 input volumes reading classifier array from /usr/local/tools/freesurfer/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z error: No such file or directory error: transforms/talairach.m3z: could not open transform
Best,
Kilian On 12/7/2022 10:37 AM, Huang, Yujing wrote:
Hi Kilian,
I'm wondering what were your initial recon-all commands for FS 5.3 and FS 7.1.1 because I'm not sure '-autorecon1' is making mri_ca_register call by default.
But It looks like you can use '-careg' to turn on mri_ca_register call.
Here is a description of recon-all steps: https://secure-web.cisco.com/1htG9ZyeR94R_NHNY2O3znkDPMKCM94AkH1H0RTut 4TvM_XNOMp0b5IpfWMN7VaDVEGT1aTGDBGyyZvW4Nj5L3Jb4Tp90UiTrCAvyd27dxmIE_X ROTE0gqoE38RdR4TKP6LuV7mtS1Z-CIqEVQbcWi8yu-PKAb0IwpB8IfntCbMCcVlRSbMfJ HKa1FDowaKA1unNg3oUyPiX8AYXRQHKTyuIt5xsfA7-sPU3N4BRDSQSOJ-FH0oNHnApsKU ytFLrwfuhXgCiF_erN1CzrSjUDJxHgWmdO50hq99m225g7BQmmhC7eWJbORDT4zpF-8osy /https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all
Best,
Yujing
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kilian M Pohl Sent: Wednesday, December 7, 2022 12:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] ma_ca_register is not called anymore in version 7.3.2
External Email - Use CautionHi ,
I have used the following call starting at Freesurfer 5.3
/usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon1 -noskullstrip -no-isrunning -s LAB_S01541_standard_20180307_4541_03072018 -rng-seed 1234
It is still working with Freesurfer 7.1.1 but we now tried updating to 7.3 and it is failing (on the same case). Looking at the recon-all.log it seem that ma_ca_register is not called anymore so that I get the following error message
ERROR: cannot find or read transforms/talairach.m3z
(see attached recon-all .log)
Do I have to add flags ? I need to run with -noskullstrip
Best,
Kilian
-- Kilian M. Pohl, Ph.D.
Associate Professor Department of Psychiatry & Behavioral Sciences Stanford University
401 Quarry Road Stanford, CA 94305-5717
https://secure-web.cisco.com/18F69KCiyMWMSCouFYLrT3r9PgA1L7oUNzDa59-gQ WUTsShFpsrS5hQaNO0pEiGsaHKqzn0e7h779L6bRMyMzCb5lAaJ0fwqBPOW8lLemFVir4T X77sLrDhxEwmH-_K67k8Wcj5yqqwssCRe30iCQlZMOzk85FBTQjdmczVPEVeGst3kfkscp PmkXiXo-cwSGKJXv1R11Ewgyiwc5CjQCPFAqtUjQeb7euLkZkt3-C8o6obbJ0vMPi_LRo- acT8JTG3md3jIZp5SKjkGKtcMoXGHrFwNJDMhft67lw3HEeOS622OvlwvJ-uB9Pag7DGyN wYPOk96CddmcVnHow7dIvw/https%3A%2F%2Fweb.stanford.edu%2F%7Ekpohl
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1qUnFO9DdCSW5zx3g8EStlrjaeIH462pIqGnhyLsC v2gFG49_FBGMC6hK6wsYIzKMB6G5XPK2S-Q6PCYyWTIK2AJBwXOAz19gk_RZtwFDBi8Qdr yC1nSNF294ya7EEi_DD_o2Pi6mVr0KXs9cFKi5yAdEnSPwT6jN-FRHQp580WdAHL0G4j3X 5T6xM-L4Xz063X2xdNfSYL6fsa2w0wYbwLo7IElvnkGGlLZ8iRio080k8iMmWKSHEYtNWb iAoz205ho6VyiBtgw90OGWIbixzHMux3FvMZq4xT76y68QuGwk4unOxrCi9gBusFFRZ8ql /https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesur fer 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/1lvA-scMVQw1Q4NT1T5Twcwt7R8fNc_A8S3FXA-R449Cuiy... https://secure-web.cisco.com/1lvA-scMVQw1Q4NT1T5Twcwt7R8fNc_A8S3FXA-R449Cuiy3dblzr_mizFqrhRyPVCTMeBa-yxbeDSiTgnJGy22rnK2JsLTJgMisXPTuiX1knhqSIkUocNh8zm-oOgUmaL9vZZ2aMvt_sS4eC743VateUr7l2rC1HLxtvyOAH9JvBNrE3lL3XARBXqMeDQg-d8Ol434Gufw8gji67opykzUDfTU3nak-ajCo7FIakyAJrRkIe6j9to90EABa8X6eA8RNF2RJnz9W6ssOiw4S1PzquEE5pxWz2fWnevU9_9rZXXbrwn5eTJy0oXFZoZH7W/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.
-- Kilian M. Pohl, Ph.D.
Associate Professor Department of Psychiatry & Behavioral Sciences Stanford University
401 Quarry Road Stanford, CA 94305-5717
https://secure-web.cisco.com/17EKKp7GyuoLKL5W8ZDc6tGhH3rrD3wgATy8X-iPtcUCmZW...
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Huang, Yujing -
Kilian M Pohl