From: Jürgen Hänggi <j.haenggi@psychologie.uzh.ch>
To: aini ismafairus <aini_ismafairus@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.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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.