Hi Danny
you need to specify a subject name/id with -s <id>
cheers
Bruce
On Wed, 22 Nov 2017,
Danny Deng wrote:
Dear FS developers,
I have problem as follow when I tried file input/output (original images can
not be identified)
Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i im_0001.dcm
ERROR: must specify a subject id
Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i IM_0001.dcm -s anon
mkdir: /Applications/freesurfer/subjects/anon: Permission denied
mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied
mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied
cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such
file or directory
cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such
file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
/Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or
directory.
Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i IM_0001.dcm -s anon
mkdir: /Applications/freesurfer/subjects/anon: Permission denied
mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied
mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied
cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such
file or directory
cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such
file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
/Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or
directory.
Xues-MacBook-Air:00000001 DannyDeng$
Please help.
Thanks.
Best Regards,Danny Deng
On Nov 22, 2017, at 1:33 AM, Hwee Ling Lee <hweeling....@gmail.com> wrote:
Dear Bruce,
Thanks for your reply.
I checked the folder and did not find the file that was requested.
What I have in the average folder that has 'RB*.gca' are
'RB_all_2016-05-10.vc700.gca' and
'RB_all_withskull_2016-05-10.vc700.gca'.
The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.
Cheers,
Hweeling
On Nov 21, 2017 18:05, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
Hi Hweeling
what is FREESURFER_HOME set to in the environment? Does that file exist?
It is a
standard part of our distribution
cheers
Bruce
On Tue, 21 Nov 2017, Hwee Ling Lee wrote:
Dear all,
I have T1 images collected from the 7T MRI scanner.
I downloaded the most recent freesurfer software, and followed all
instructions to install the software before using it.
I would like to segment the T1 data using its high resolution image,
and
also to segment the hippocampal subfields.
For command, I use this:
recon-all -all -s <subject name> -hires -i <subject dicom T1 image
frame 1
location>
However, I get an error message:
cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca
I'm not sure what I did wrong.
Also, how can I combine high resolution segmentation and hippocampal
subfields segmentation?
Could someone please help?
Thanks.
Best regards,
Hweeling
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