Sorry Bruce,Here is the problem I wanted to avoid:-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/subjects
MNI_DIR /usr/local/freesurfer/mni
FSL_DIR /usr/share/fsl/5.0
bash: /opt/minc/minc-toolkit-config.sh: No such file or directory
rosalia@rosalia-Lenovo-Y520-15IKBN:~$ $ ftp surfer.nmr.mgh.harvard.edu
$: command not found
rosalia@rosalia-Lenovo-Y520-15IKBN:~$ ftp surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/compute r/nmr-aup.php
220-
220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220- and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220- try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous
331 Please specify the password.
Password:
530 Login incorrect.
Login failed.
ftp>2017-11-21 18:31 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:sorry, I don't understand. I haven't gotten anything, and it is likely way too big to email. If you upload it to the FTP site no one from the outside will have access to it
cheers
Brue
On Tue, 21 Nov 2017, Rosalia Dacosta Aguayo wrote:
Sorry Bruce,
I have sent it to your email directly...in order to avoid the process of
uploading the data...because I am not familiar with it.
Kind regards,
Rosalia
2017-11-21 18:25 GMT+01:00 Rosalia Dacosta Aguayo <rdacostaa@gmail.com>:
Sorry Bruce,
I prefer sending it to your email directly, then if you want to make
it available to the other memebrs, there is not problem at all...
Kind regards,
Rosalia
2017-11-21 18:17 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
tar and gzip the entire subject dir and upload it
following these instructions:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Tue, 21 Nov 2017, Rosalia Dacosta Aguayo wrote:
Hi Bruce,
Thank you for answering.
Not, it is not a bug...in fact
recon-all...-all had not problems. Just I was
looking at the outputs...and as I am running
FreeSurfer for my first time I
wanted to ask about if this was a problem or I
can go on....
Where I should upload the subject and which
files? I mean, in order to do
not overload the mail list...
Kind regards,
Rosalia
2017-11-21 18:09 GMT+01:00 Bruce Fischl
<fischl@nmr.mgh.harvard.edu>:
hmmm, that is odd looking. Can you
upload that subject so we can
see if
it is just a display bug or not?
On Tue, 21 Nov 2017, Rosalia Dacosta
Aguayo
wrote:
> Dear FreeSurfer Developers,
>
> I am checking the OutputData_freeview
after running recon-all
following your
> tutorial:
>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputD ata_freeview
>
> I have loaded T1.mgz, wm.mgz,
brainmask.mgz and aseg.mgz, and
then the
> surfaces: rh.pial, rh.white, lh.pial
and lh.white.
>
> In general, I did not see any
problem...but when I wanted to
see the
> surface&mesh with vertices I saw
something estrange I do not
know if it is a
> problem or it is normal (see the
vertices in the temporal pole
in grey
> scale)...as this is my first run with
FreeSurfer. I attach you
the image.
>
> 1. FreeSurfer version:
>
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> 2. Platform: CentOS release 6.7
> 3. uname -a: Linux
rosalia-PORTEGE-Z930 4.4.0-98-generic
#121-Ubuntu SMP Tue
> Oct 10 14:24:03 UTC 2017 x86_64 x86_64
x86_64 GNU/Linux
> 4. Recon-all.log; see attached
(although it ended without
errors)
>
> I haven't come across this error in my
searches, but I may be
using the
> wrong key terms. Would anyone be able
to point me in the right
direction or
> trouble-shoot fixing this?
>
> Thank you for your time,
> Rosalia
>
>
>
>
>
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