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Dear Freesurfer team 

Thanks for you help. I am new to freesurfer, using a mac and getting an error with recon all when using my MRI data. 

I ran your tutorial recon all and the tutorial data worked fine. My burned CD T1 MRI files did not have the .dcm added so after renaming all the files with .dcm,  the recon function still gives an error message as below.

Last login: Fri Feb  1 06:51:44 on ttys000

Kevins-MacBook-Pro:~ kevin$ export FREESURFER_HOME=/Applications/freesurfer

Kevins-MacBook-Pro:~ kevin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

-------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c --------

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME       /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR      /Applications/freesurfer/subjects

MNI_DIR           /Applications/freesurfer/mni

Kevins-MacBook-Pro:~ kevin$ export Case14=Applications/freesurfer/Case14

Kevins-MacBook-Pro:~ kevin$ export SUBJECTS_DIR=$Case14/7581/7583

Kevins-MacBook-Pro:~ kevin$ cd $Subjects_DIR

Kevins-MacBook-Pro:~ kevin$ echo $SUBJECTS_DIR

Applications/freesurfer/Case14/7581/7583

Kevins-MacBook-Pro:~ kevin$ 

Kevins-MacBook-Pro:~ kevin$ recon-all –all –i 758251.dcm –s Subj14

ERROR: Flag all unrecognized.

all i 758251.dcm s Subj14

Darwin Kevins-MacBook-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Mon Nov 12 20:24:46 PST 2018; root:xnu-4903.231.4~2/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Fri Feb  1 06:55:38 EST 2019


For more details, see the log file 

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Kevins-MacBook-Pro:~ kevin$


Your suggestions are most appreciated. 

Thanks Kevin