I think you can still do what Bruce suggested and keep things separate.
What's the problem?
On 11/10/2020 1:11 PM, Kelli Ann Nini wrote:
External Email - Use Caution
Dr. Fischl,
Thank you so much for your reply. The brains I'm using have been
processed and analyzed numerous times for a variety of projects in our
department and are in several directories on the same computer.
However, I copied only the .nii files over to a new directory and set
the environment before attempting to run recon-1. I'm tasked with
teaching FreeSurfer to our incoming lab students, so I'd like to keep
the copies separate if possible. Any advice is sincerely appreciated.
-Kelli
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce
<bfis...@mgh.harvard.edu>
*Sent:* Sunday, November 8, 2020 10:07 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Recon1 command
*WARNING: This email originated outside of the University of New
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HI Kelli
It sounds like you started running at some point but didn’t get very
far? Try something like:
mv /home/blah/blah/blah/1234 /home/blah/blah/blah/saved.1234
recon-all -subjid 1234 -i 1234.nii -autorecon1
and see if that works (then you can probably delete the saved.1234 dir
if you want)
cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Kelli Ann Nini
*Sent:* Saturday, November 7, 2020 5:28 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] Recon1 command
* External Email - Use Caution *
Greetings, esteemed Surfers! I have a .nii file that I am trying to
run through recon1 and I'm not sure I have my commands correct. At
first I typed this command line and received this error: recon-all
-subjid 1234 -i 1234.nii -autorecon1
ERROR: You are trying to re-run an existing subject with (possibly)
new input data (-i). If this is truly new input data, you should delete
the subject folder and re-run, or specify a different subject name.
If you are just continuing an analysis of an existing subject, then
omit all -i flags.
However, if I omit the -i flag, I receive this message: recon-all
-subjid 1234 -autorecon1
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /home/scanlab1/Desktop/FSTraining_2020
Actual FREESURFER_HOME /usr/local/freesurfer
Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb
12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
'/usr/local/freesurfer/bin/recon-all' ->
'/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.local-copy'
#--------------------------------------------
#@# MotionCor Tue Nov 3 17:46:26 CST 2020
ERROR: no run data found in /home/blah/blah/blah/1234/mri. Make sure to
have a volume called 001.mgz in /home/blah/blah/blah/1234/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: *MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
<https://secure-web.cisco.com/1XmF2hq0ynrYUSHhpakdzBns7IF7IAQizGno9mghzMczNeIIHshC_H2E9ghuwePacEyXUPjSIDCqJeKI5h7dTblTen4_6tORF8-xEm7nyRkrXvnCILp2-rPmJ-H4i25tbK55V9c-e6k-VC3pnDKEUbzofOBKXCjoIyfIgBPuTnNi86i5ZJKsf6EkadfMhsiSHOvVEVyjHIcNJI3C8tc6kgwKPz_jqGomQDlgoSerE9Vuaqr5qCgDmkyGoIfL9Gwq3-wkq1PoKlbvcLc1mo93kHQ/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FFsTutorial%252FConversion%26data%3D04%257C01%257Cknallen1%2540my.uno.edu%257Cd1166d295e5a4f9129fd08d884007305%257C31d4dbf540044469bfeedf294a9de150%257C0%257C0%257C637404484769176619%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D%252FSDW2NLc8qibs29r7v8cZFJg8Bdb0TLWKJGuyQMqTeU%253D%26reserved%3D0>
Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb
12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 2556 exited with ERRORS at Tue Nov 3 17:46:26 CST 2020
For more details, see the log file
/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.log
To report a problem, see MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to be *MailScanner has
detected a possible fraud attempt from "secure-web.cisco.com" claiming
to be* http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
<https://secure-web.cisco.com/1ebwEFFSRf2fkEyuaf2K-ZGR7Xq7HS0ujZadhGo9BnVcvk-a5XAkM2za5S5fxd5BnmyREotljsiPlqez672NxGMazjjddTQiP4fYptIlZ1mjU-rfWuZhONWopAzWAfkZxG_pkX9-5BoLMuWOMbemqyAnmyovC_D20xl2EEFAGBX31WWQdv5UcLoC9bU83Dmvh_5fSDiCxfaB_U7oZjXa4ugvVkdexRpKVM_k8kFgQxuSe8y1Igvd2KjAvEzY0rQChdCzvUd1R-BhLUaJ4EahZJQ/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FBugReportin%26data%3D04%257C01%257Cknallen1%2540my.uno.edu%257Cd1166d295e5a4f9129fd08d884007305%257C31d4dbf540044469bfeedf294a9de150%257C0%257C0%257C637404484769176619%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DOeRGPqn1Kub%252BM4S6RyUcBXgku0dQDBHs206eg%252FnWhT4%253D%26reserved%3D0>
It's also been approx 1 year since FS was run on our machines. Perhaps
an update is needed? Thank you so much!
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