External Email - Use Caution
Hi Bruce
Sorry about that, I am not a code writer. I fixed that and got this response instead.
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 12:39:54 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$
Thanks again Kevin _______________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: February 1, 2019 12:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]RE: Freesurfer Recon-all error
Hi Kevin,
it looks like your second command line has "-1", which should be "-i"
cheers Bruce
On Fri, 1 Feb 2019, Jones, Kevin wrote:
External Email - Use CautionHi 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
External Email - Use CautionHi 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
External Email - Use CautionDear 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