External Email - Use Caution
Hi Diamond!
I think I did it. Thank you very much!!
-------- 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 rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ cd /home/rosalia/Desktop/transferrosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/transfer $ 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: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd transfer/incoming 250 Directory successfully changed. ftp> put two_different_problems.tar.gz local: two_different_problems.tar.gz remote: two_different_problems.tar.gz 200 PORT command successful. Consider using PASV. 150 Ok to send data.
On Mon, Dec 3, 2018 at 6:46 PM Diamond, Bram Ryder < BRDIAMOND@mgh.harvard.edu> wrote:
Hi Rosalia,
Within the FTP interface, you need to write "put two_different_problems.txt". It seems like you only wrote the file name. Also, the example we provide is "filename.txt", make sure you write your file name - only include ".txt" if your file has that extension.
Let me know if you have any additional questions.
Best,
Bram
*Bram R. Diamond, BSc* Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta Aguayo rdacostaa@gmail.com *Sent:* Monday, December 3, 2018 10:54:53 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] When no control points are needed...
External Email - Use CautionHi Bruce,
This is the directory where I have the data:
/home/rosalia/Desktop/transfer
And I changed the directory before doing FTP...and then asked again for the directory and I wrote the same directory and then when asked me for the name of the file, I provided the name of the file.txt
Thank you, Rosalia
On Mon, Dec 3, 2018 at 4:51 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
is that the right directory/path on your end?
On Mon, 3 Dec 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use CautionHi Bruce,
Thank you for your reply. I am having problems when trying to upload the two files with FTP, it
seems
the problem is with the directory. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ 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: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd home/rosalia/Desktop/transfer 550 Failed to change directory. ftp>
On Mon, Dec 3, 2018 at 3:50 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Rosalia
you always have to run autorecon3 every time autorecon2 is run cheers Bruce On Mon, 3 Dec 2018, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > > Dear Bruce and Bram, > > After improving the pial surface for my participants, I have seen that some of them do not need > control points. My question is: for those ones, should I run -autorecon2 and -autorecon3 or only > -autorecon3. > > Hi Bruce and Bram, I will try to upload two problematic files. When I told you that I have been > editing all my participants I was referring that some of them need more editing than others, and the > ones that needed the less I just tried to improve the pial surface not too much, but now the results > are better than before. > > Thank you in advance for your help.Yours sincerely, > Rosalia > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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