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Hi Falk 

Thanks for your suggestion. I tried that again without success. 

Last login: Fri Feb  1 07:00:13 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$ recon-all -all -i 758251.dcm -s Subj14

ERROR: cannot find 758251.dcm

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 11:34:00 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$ recon-all -all -1 758251.dcm -s Subj14

ERROR: Flag -1 unrecognized.

-all -1 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 11:35:10 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$ 


I have attached a T1 MRI file with and without the .dcm added. Could this be a file issue or just code writing mistakes. 


Thanks so  much for advice, Kevin  

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of falk.luesebrink@med.ovgu.de [falk.luesebrink@med.ovgu.de]
Sent: February 1, 2019 10:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Recon-all error

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Hi Kevin,

 

just an educated guess, but did you copy the line “recon-all –all –i 758251.dcm –s Subj14” from somewhere (e.g. word)? Because it seems the dash in front of each flag is an emphasized dash, probably resulting in the error. Try the following: “recon-all -all -i 758251.dcm -s Subj14”

 

Best,

Falk

 

Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Jones, Kevin
Gesendet: Freitag, 1. Februar 2019 13:00
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Freesurfer Recon-all error

 

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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