Hi Kevin you need to specify the full path to the file 758251.dcm
cheers Bruce On Fri, 1 Feb 2019, Jones, Kevin wrote:
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 <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. 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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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