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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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

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