you must change the subject directory outside the application Azeez Adebimpe
Date: Sun, 2 Dec 2012 00:40:28 +0800 From: aini_ismafai...@yahoo.com.my To: j.haen...@psychologie.uzh.ch; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error Hi, Have been tried that but still exited with errors.is it because of iMac doesn't enable freesurfer to create the subject files without security password?do anybody know how to settle this problems? Thank you. Best,Isma From: Jürgen Hänggi <j.haen...@psychologie.uzh.ch> To: aini ismafairus <aini_ismafai...@yahoo.com.my>; Freesurfer Mailinglist <freesurfer@nmr.mgh.harvard.edu> Sent: Saturday, 1 December 2012 12:42 PM Subject: Re: [Freesurfer] recon-all error Re: [Freesurfer] recon-all error Dear Aina Unzip us03.nii.gz and try it again Cheers Jürgen On [DATE], "aini ismafairus" <[ADDRESS]> wrote: Hello, I still new in using freesurfer. the freesurfer was successfully installed. but when i tried to run recon-all it give an error. [Ainis-iMac:~] ismafairus% setenv FREESURFER_HOME Applications/freesurfer [Ainis-iMac:~] ismafairus% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- 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 FSL_DIR FSL/fsl Ainis-iMac:~] ismafairus% recon-all -i $SUBJECTS_DIR/us03.nii.gz -o us03 -all ERROR: cannot find Applications/freesurfer/subjects/us03.nii.gz Darwin Ainis-iMac.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Sat Dec 1 11:42:54 CET 2012 Advice on how to troubleshoot this would be appreciate. Thank you. Regards, Isma _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ---------------------------------------------------------------------------- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
