I'm glad to hear it worked out Bruce On Tue, 28 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce,
Thanks for your tip. Actually, it didn't work for me. I went to ask one of my
colleagues, Martin
Reuter, for help, and it turns out that the permission of my files in the
$FREESURFER_HOME/bin
folder have been changed to 'read only'. Martin helped me to change the files
in the
$FREESURFER_HOME/bin folder to all executable files by using this command:
'chmod u+w *'.
Hence, I'm replying to this thread so that I hope this will help others in the
future with similar
problems.
Thanks again for your patience!
Cheers,
Hweeling
On 23 November 2017 at 16:24, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
you need to change your path so that
which recon-all
gives you the v6 one. something like:
set path = ($FREESURFER_HOME/bin $path)
rehash
where FREESURFER_HOME points to the v6 version
cheers
Bruce
On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce,
Sorry about the screenshot of text.
You are right that it still uses the older version of recon-all.
How do I
fix this then?
I can't delete the older version because I don't have access to it
at all.
Thanks for your patience.
Cheers,
Hweeling
On 22 November 2017 at 15:52, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
wrote:
Hi Hweeling
please don't send us screenshots of text - either attach the
file or include text in the email.
I'm pretty sure you are using an older recon-all script with a
newer FREESURFER_HOME. Try typing:
which recon-all
I bet it points to somewhere other than your V6
FREESURFER_HOME/bin dir
cheers
Bruce
On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
Dear Bruce,
Thanks for your patience. Attached you will find the
screenshot of my server. In my institute's
server, there is an older version of freesurfer,
which I then change to a newer version before
starting the recon-all.
I look forward to your reply.
Thanks.
Cheers,
Hweeling
On 22 November 2017 at 15:31, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
can you send us the recon-all.log?
On Wed, 22 Nov 2017, Hwee Ling Lee wrote:
Hi Bruce,
I downloaded the latest version of
freesurfer, "CentOS 6 x86_64 (64b)".
Cheers,
Hweeling
On 21 November 2017 at 23:57, Bruce
Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
oh, this may be a version mismatch
then. Which version of FS are you
using?
On Tue, 21 Nov 2017, Hwee Ling Lee
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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