Hi Jasmin
if this is the first time you have run this subject (that is, the subject
dir doesn't exist within $SUBJECTS_DIR), you still need to specify the
input volume with -i T1_original_joya.nii
cheers
Bruce
On Tue, 26 Jan 2016, Jasmin Alves wrote:
Bruce,
Sorry to be a pain, but for some reason, I cannot still get recon-all to
work.
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya -all &
[1] 14655
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: SUBJECTS_DIR
/Desktop/Brain_Child_subs does not exist.
Thanks,
Jasmin
On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Jasmin
you need a '-' sign first. It should be:
recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii
-subject \
joya -all &
cheers
Bruce
On Mon, 25 Jan 2016, Jasmin Alves wrote:
Hi Bruce,
Thanks for the reply, I attempted to direct
Subjects_dir to the folder with
my data but I received the following error.
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
export
SUBJECTS_DIR=/Desktop/Brain_Child_subs
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii
-subject joya all &
[1] 13867
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$
ERROR: Flag all
unrecognized.
-sd /Desktop/Brain_Child_subs -i
T1_original_joya.nii -subject joya all
Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin
Kernel Version 14.5.0: Tue
Sep 1 21:23:09 PDT 2015;
root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
recon-all -s joya exited with ERRORS at Mon Jan 25
21:12:58 PST 2016
Thanks so much,
Jasmin
On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Jasmin
you need to create a directory where you have
write permission
and room for the subject reconstruction to be
written to, then
set the SUBJECTS_DIR environment variable to
point to it. At the
moment you are trying to use the subject
directory we
distribute, which is in some system (and
read-only) location.
You can do this on the command line of
recon-all via:
recon-all -sd <path to directory> ...
cheers
Bruce
On Sun, 24 Jan 2016, Jasmin Alves wrote:
Hello Freesurfer,
I am trying to learn freesurfer and ran into
the following
issues below
running the recon -all command.
FREESURFER_HOME: /Applications/freesurfer
Build stamp:
freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.5.0 x86_64
1)
joya
2)
Jasmins-MacBook-Pro:subjects jasminalves$
recon-all -i
T1_original_joya.nii
-subject joya -all &
3)
[1] 12300
Jasmins-MacBook-Pro:subjects jasminalves$
mkdir:
/Applications/freesurfer/subjects/joya:
Permission denied
mkdir:
/Applications/freesurfer/subjects/joya/scripts:
Permission denied
mkdir:
/Applications/freesurfer/subjects/joya/scripts:
Permission denied
cp:
/Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
No such
file or directory
cat:
/Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
No such
file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp:
freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is
/Applications/freesurfer/subjects
Actual FREESURFER_HOME
/Applications/freesurfer
/Applications/freesurfer/subjects/joya: No
such file or
directory.
[1]+ Exit 1 recon-all -i
T1_original_joya.nii -subject
joya -a
Thank you,Jasmin
Jasmin AlvesPredoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Jasmin AlvesPredoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
_______________________________________________
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The information in this e-mail is intended only for the person to whom
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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.
--
Jasmin AlvesPredoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
_______________________________________________
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.
