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-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@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 Caution
>
> 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-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
> falk.luesebr...@med.ovgu.de [falk.luesebr...@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 Caution
>
> 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-boun...@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 Caution
>
> 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.
>
>
>
&g
