Re: [Freesurfer] When no control points are needed...
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 < brdiam...@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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta > Aguayo > *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 Caution > > Hi 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 > wrote: > > is that the right directory/path on your end? > > On Mon, 3 Dec 2018, Rosalia Dacosta > Aguayo wrote: > > > > > External Email - Use Caution > > > > Hi 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:
Re: [Freesurfer] When no control points are needed...
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-boun...@nmr.mgh.harvard.edu on behalf of Rosalia Dacosta Aguayo 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 Caution Hi 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 mailto:fis...@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 Caution > > Hi 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<http://surfer.nmr.mgh.harvard.edu> > Connected to surfer.nmr.mgh.harvard.edu<http://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 > mailto:fis...@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<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] When no control points are needed...
External Email - Use Caution Hi 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 wrote: > is that the right directory/path on your end? > > On Mon, 3 Dec 2018, Rosalia Dacosta > Aguayo wrote: > > > > > External Email - Use Caution > > > > Hi 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 > > 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 > > > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] When no control points are needed...
is that the right directory/path on your end? On Mon, 3 Dec 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Hi 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 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] When no control points are needed...
External Email - Use Caution Hi Bruce, Sorry for double posting. I am advancing, but there is still some point I am missing. I would greatly appreciate your help: 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> two_different_problems.txt ?Invalid command ftp> On Mon, Dec 3, 2018 at 4:06 PM Rosalia Dacosta Aguayo wrote: > Hi 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 > 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 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] When no control points are needed...
External Email - Use Caution Hi 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 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] When no control points are needed...
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
[Freesurfer] When no control points are needed...
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
