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
