Hi Akila
You haven't told it to do anything, so all it does is create the directory
structure and import the data. You need to add a directive like "- all" to the
recon-all command line
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of A.R. Sekar
Sent: Tuesday, March 16, 2021 8:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all Ending Fast
External Email - Use Caution
External Email - Use Caution
Hello,
I am trying to run the recon-all function and the whole process is completing
within a minute or so. I was told that the whole process would take between
6-24 hours. This is the output I am getting after entering the command:
Akilas-MacBook-Air:Sub01 akilasekar$ recon-all -s sub_01 -i sub1.fspgr.nii
Subject Stamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
Current Stamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
INFO: SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects
Actual FREESURFER_HOME /Applications/freesurfer/7.1.1
Darwin Akilas-MacBook-Air.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21
00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64
/Applications/freesurfer/7.1.1/subjects/sub_01
\n mri_convert /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii
/Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz \n
mri_convert /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii
/Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz
reading from /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
writing to /Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz...
/Applications/freesurfer/7.1.1/subjects/sub_01/mri/transforms
/Applications/freesurfer/7.1.1/subjects/sub_01
/Applications/freesurfer/7.1.1/subjects/sub_01
Started at Tue Mar 16 14:41:43 EAT 2021
Ended at Tue Mar 16 14:41:49 EAT 2021
#@#%# recon-all-run-time-hours 0.002
recon-all -s sub_01 finished without error at Tue Mar 16 14:41:49 EAT 2021
done
It would great if you can help me out! Thank you!
Akila
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