Dear Bruce,

I am using FileDropv2.0...

I hope you and all the members of the list can access into this subject.

Thank you for your help in advance,

Rosalia

2017-11-21 18:35 GMT+01:00 Rosalia Dacosta Aguayo rdacostaa@gmail.com:

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/computer/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 > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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