Hi there
I ran Freesurfer 6.0 on a subject last night and it took about 12 hours (seemed to get to the very end) and then exited with errors. I can open my surfaces so I think it ended roughly with the atlas labelling. I attach the recon-all log file here.
best wishes
Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
hmmm, I've never seen label2label core dump before. Can you tar, gzip and upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
Hi there
I ran Freesurfer 6.0 on a subject last night and it took about 12 hours (seemed to get to the very end) and then exited with errors. I can open my surfaces so I think it ended roughly with the atlas labelling. I attach the recon-all log file here.
best wishes
Trisanna
Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
Hi Bruce
Thanks for the speedy reply. Should I attach it here or is there a place I can upload it to?
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmmm, I've never seen label2label core dump before. Can you tar, gzip and upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
Hi there
I ran Freesurfer 6.0 on a subject last night and it took about 12 hours
(seemed to get to the very end) and then exited with
errors. I can open my surfaces so I think it ended roughly with the
atlas labelling. I attach the recon-all log file here.
best wishes
Trisanna
Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
you can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
Hi Bruce Thanks for the speedy reply. Should I attach it here or is there a place I can upload it to?
best Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: hmmm, I've never seen label2label core dump before. Can you tar, gzip and upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
> Hi there > > I ran Freesurfer 6.0 on a subject last night and it took about 12 hours (seemed to get to the very end) and then exited with > errors. I can open my surfaces so I think it ended roughly with the atlas labelling. I attach the recon-all log file here. > > best wishes > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Thanks Bruce. I have uploaded it but I would like to confirm that you received the ICBM_305.tar. For some reason I was not able to compress it any further.
To clarify, subjects 205 and now subject 202 have both failed after surface extraction.
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
you can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
Hi Bruce Thanks for the speedy reply. Should I attach it here or is there a place
I can upload it to?
best Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
hmmm, I've never seen label2label core dump before. Can you tar,gzip and
upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote: > Hi there > > I ran Freesurfer 6.0 on a subject last night and it took about12 hours (seemed to get
to the very end) and then exited with > errors. I can open my surfaces so I think it ended roughly withthe atlas labelling. I
attach the recon-all log file here. > > best wishes > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person towhom it is
addressed. If you believe this e-mail was sent to you in error andthe e-mail
contains patient information, please contact the PartnersCompliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sentto you in error
but does not contain patient information, please contact thesender and properly
dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Trisanna
there are a bunch of files, but they all look like they are empty:
r--r--r-- 1 ftp ftp 0 Jan 17 14:24 ICBM_305.tar -r--r--r-- 1 ftp ftp 0 Jan 17 14:41 ICBM_305.tar.gz -r--r--r-- 1 ftp ftp 0 Jan 17 15:12 icbm-205.tar.gz
cheers Bruce On Wed, 17 Jan 2018, Trisanna Sprung-Much wrote:
Thanks Bruce. I have uploaded it but I would like to confirm that you received the ICBM_305.tar. For some reason I was not able to compress it any further.
To clarify, subjects 205 and now subject 202 have both failed after surface extraction.
best Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: you can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote: > Hi Bruce > Thanks for the speedy reply. Should I attach it here or is there a place I can upload it to? > > best > Trisanna > > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > hmmm, I've never seen label2label core dump before. Can you tar, gzip and > upload the entire subject dir? > On Tue, 16 Jan 2018, Trisanna Sprung-Much > wrote: > > > Hi there > > > > I ran Freesurfer 6.0 on a subject last night and it took about 12 hours (seemed to get > to the very end) and then exited with > > errors. I can open my surfaces so I think it ended roughly with the atlas labelling. I > attach the recon-all log file here. > > > > best wishes > > > > Trisanna > > -- > > Ph.D. CandidateMcGill University > > Integrated Program in Neuroscience > > Psychology > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, Bruce. ignore my last email. Not sure what happened there.
I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get the following and it happens over and over. Any idea what the problem could be?
trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/ trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls fsaverage icbm-109 icbm-118 icbm-127 icbm-142 icbm-202 icbm-102 icbm-110 icbm-119 icbm-131 icbm-143 icbm-202.tar.gz icbm-103 icbm-111 icbm-120 icbm-133 icbm-144 icbm-203 icbm-104 icbm-112 icbm-121 icbm-135 icbm-146 icbm-204 icbm-105 icbm-113 icbm-122 icbm-137 icbm-150 icbm-205 icbm-106 icbm-114 icbm-123 icbm-139 icbm-158 icbm-205.tar.gz icbm-107 icbm-115 icbm-125 icbm-140 icbm-200 icbm-206 icbm-108 icbm-117 icbm-126 icbm-141 icbm-201 trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ 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:trisanna): 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 icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection.
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
Thanks Bruce. I have uploaded it but I would like to confirm that you received the ICBM_305.tar. For some reason I was not able to compress it any further.
To clarify, subjects 205 and now subject 202 have both failed after surface extraction.
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
you can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
Hi Bruce Thanks for the speedy reply. Should I attach it here or is there a
place I can upload it to?
best Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
hmmm, I've never seen label2label core dump before. Can you tar,gzip and
upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote: > Hi there > > I ran Freesurfer 6.0 on a subject last night and it took about12 hours (seemed to get
to the very end) and then exited with > errors. I can open my surfaces so I think it ended roughly withthe atlas labelling. I
attach the recon-all log file here. > > best wishes > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person towhom it is
addressed. If you believe this e-mail was sent to you in errorand the e-mail
contains patient information, please contact the PartnersCompliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sentto you in error
but does not contain patient information, please contact thesender and properly
dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Trisanna,
Try running 'quote PASV' in ftp before running 'put' - that should hopefully clear up this issue.
best, Andrew
On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca> wrote:
Sorry, Bruce. ignore my last email. Not sure what happened there.
I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get the following and it happens over and over. Any idea what the problem could be?
trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/ trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls fsaverage icbm-109 icbm-118 icbm-127 icbm-142 icbm-202 icbm-102 icbm-110 icbm-119 icbm-131 icbm-143 icbm-202.tar.gz icbm-103 icbm-111 icbm-120 icbm-133 icbm-144 icbm-203 icbm-104 icbm-112 icbm-121 icbm-135 icbm-146 icbm-204 icbm-105 icbm-113 icbm-122 icbm-137 icbm-150 icbm-205 icbm-106 icbm-114 icbm-123 icbm-139 icbm-158 icbm-205.tar.gz icbm-107 icbm-115 icbm-125 icbm-140 icbm-200 icbm-206 icbm-108 icbm-117 icbm-126 icbm-141 icbm-201 trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp [X] surfer.nmr.mgh.harvard.eduhttp://surfer.nmr.mgh.harvard.edu/ Connected to [X] surfer.nmr.mgh.harvard.eduhttp://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-[X]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.eduhttp://surfer.nmr.mgh.harvard.edu:trisanna): 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 icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection.
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca> wrote: Thanks Bruce. I have uploaded it but I would like to confirm that you received the ICBM_305.tar. For some reason I was not able to compress it any further.
To clarify, subjects 205 and now subject 202 have both failed after surface extraction.
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: you can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
Hi Bruce Thanks for the speedy reply. Should I attach it here or is there a place I can upload it to?
best Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: hmmm, I've never seen label2label core dump before. Can you tar, gzip and upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
> Hi there > > I ran Freesurfer 6.0 on a subject last night and it took about 12 hours (seemed to get to the very end) and then exited with > errors. I can open my surfaces so I think it ended roughly with the atlas labelling. I attach the recon-all log file here. > > best wishes > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> [X] [X] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at [X] [X] http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu [X][X]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Andrew
Thank you for your response. I gave it a go and still no luck, unless I am missing something completely obvious here
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ 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:trisanna): 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> quote PASV 227 Entering Passive Mode (132,183,202,158,147,251). ftp> put icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection.
On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
Hi Trisanna,
Try running 'quote PASV' in ftp before running 'put' - that should hopefully clear up this issue.
best, Andrew
On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
Sorry, Bruce. ignore my last email. Not sure what happened there.
I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get the following and it happens over and over. Any idea what the problem could be?
trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/ trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls fsaverage icbm-109 icbm-118 icbm-127 icbm-142 icbm-202 icbm-102 icbm-110 icbm-119 icbm-131 icbm-143 icbm-202.tar.gz icbm-103 icbm-111 icbm-120 icbm-133 icbm-144 icbm-203 icbm-104 icbm-112 icbm-121 icbm-135 icbm-146 icbm-204 icbm-105 icbm-113 icbm-122 icbm-137 icbm-150 icbm-205 icbm-106 icbm-114 icbm-123 icbm-139 icbm-158 icbm-205.tar.gz icbm-107 icbm-115 icbm-125 icbm-140 icbm-200 icbm-206 icbm-108 icbm-117 icbm-126 icbm-141 icbm-201 trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ 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:trisanna): 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 icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection.
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
Thanks Bruce. I have uploaded it but I would like to confirm that you received the ICBM_305.tar. For some reason I was not able to compress it any further.
To clarify, subjects 205 and now subject 202 have both failed after surface extraction.
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
you can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
Hi Bruce Thanks for the speedy reply. Should I attach it here or is there a
place I can upload it to?
best Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
hmmm, I've never seen label2label core dump before. Can you tar,gzip and
upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote: > Hi there > > I ran Freesurfer 6.0 on a subject last night and it took about12 hours (seemed to get
to the very end) and then exited with > errors. I can open my surfaces so I think it ended roughlywith the atlas labelling. I
attach the recon-all log file here. > > best wishes > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the personto whom it is
addressed. If you believe this e-mail was sent to you in errorand the e-mail
contains patient information, please contact the PartnersCompliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sentto you in error
but does not contain patient information, please contact thesender and properly
dispose of the e-mail.
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Trisanna,
Okay - if your file is less than 2GiB, I suggest sending your data via the Martinos file drop (directions at the bottom of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange).
best Andrew
On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca> wrote:
Hi Andrew
Thank you for your response. I gave it a go and still no luck, unless I am missing something completely obvious here
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp surfer.nmr.mgh.harvard.eduhttp://surfer.nmr.mgh.harvard.edu/ Connected to surfer.nmr.mgh.harvard.eduhttp://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.eduhttp://surfer.nmr.mgh.harvard.edu:trisanna): 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> quote PASV 227 Entering Passive Mode (132,183,202,158,147,251). ftp> put icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection.
On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote: Hi Trisanna,
Try running 'quote PASV' in ftp before running 'put' - that should hopefully clear up this issue.
best, Andrew
On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca> wrote:
Sorry, Bruce. ignore my last email. Not sure what happened there.
I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get the following and it happens over and over. Any idea what the problem could be?
trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/ trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls fsaverage icbm-109 icbm-118 icbm-127 icbm-142 icbm-202 icbm-102 icbm-110 icbm-119 icbm-131 icbm-143 icbm-202.tar.gz icbm-103 icbm-111 icbm-120 icbm-133 icbm-144 icbm-203 icbm-104 icbm-112 icbm-121 icbm-135 icbm-146 icbm-204 icbm-105 icbm-113 icbm-122 icbm-137 icbm-150 icbm-205 icbm-106 icbm-114 icbm-123 icbm-139 icbm-158 icbm-205.tar.gz icbm-107 icbm-115 icbm-125 icbm-140 icbm-200 icbm-206 icbm-108 icbm-117 icbm-126 icbm-141 icbm-201 trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp [X] surfer.nmr.mgh.harvard.eduhttp://surfer.nmr.mgh.harvard.edu/ Connected to [X] surfer.nmr.mgh.harvard.eduhttp://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-[X]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.eduhttp://surfer.nmr.mgh.harvard.edu/:trisanna): 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 icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection.
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca> wrote: Thanks Bruce. I have uploaded it but I would like to confirm that you received the ICBM_305.tar. For some reason I was not able to compress it any further.
To clarify, subjects 205 and now subject 202 have both failed after surface extraction.
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: you can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
Hi Bruce Thanks for the speedy reply. Should I attach it here or is there a place I can upload it to?
best Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: hmmm, I've never seen label2label core dump before. Can you tar, gzip and upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
> Hi there > > I ran Freesurfer 6.0 on a subject last night and it took about 12 hours (seemed to get to the very end) and then exited with > errors. I can open my surfaces so I think it ended roughly with the atlas labelling. I attach the recon-all log file here. > > best wishes > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> [X] [X] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at [X] [X] http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu [X][X]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
thanks Andrew. I had seen that and will give it a go - just wanted to make sure that my recipient email would be the FreeSurfer support list.
Trisanna
On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
Hi Trisanna,
Okay - if your file is less than 2GiB, I suggest sending your data via the Martinos file drop (directions at the bottom of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange).
best Andrew
On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
Hi Andrew
Thank you for your response. I gave it a go and still no luck, unless I am missing something completely obvious here
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ 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:trisanna): 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> quote PASV 227 Entering Passive Mode (132,183,202,158,147,251). ftp> put icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection.
On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
Hi Trisanna,
Try running 'quote PASV' in ftp before running 'put' - that should hopefully clear up this issue.
best, Andrew
On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
Sorry, Bruce. ignore my last email. Not sure what happened there.
I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get the following and it happens over and over. Any idea what the problem could be?
trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/ trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls fsaverage icbm-109 icbm-118 icbm-127 icbm-142 icbm-202 icbm-102 icbm-110 icbm-119 icbm-131 icbm-143 icbm-202.tar.gz icbm-103 icbm-111 icbm-120 icbm-133 icbm-144 icbm-203 icbm-104 icbm-112 icbm-121 icbm-135 icbm-146 icbm-204 icbm-105 icbm-113 icbm-122 icbm-137 icbm-150 icbm-205 icbm-106 icbm-114 icbm-123 icbm-139 icbm-158 icbm-205.tar.gz icbm-107 icbm-115 icbm-125 icbm-140 icbm-200 icbm-206 icbm-108 icbm-117 icbm-126 icbm-141 icbm-201 trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ 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:trisanna): 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 icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection.
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
Thanks Bruce. I have uploaded it but I would like to confirm that you received the ICBM_305.tar. For some reason I was not able to compress it any further.
To clarify, subjects 205 and now subject 202 have both failed after surface extraction.
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
you can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
Hi Bruce Thanks for the speedy reply. Should I attach it here or is there a
place I can upload it to?
best Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
hmmm, I've never seen label2label core dump before. Can youtar, gzip and
upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote: > Hi there > > I ran Freesurfer 6.0 on a subject last night and it tookabout 12 hours (seemed to get
to the very end) and then exited with > errors. I can open my surfaces so I think it ended roughlywith the atlas labelling. I
attach the recon-all log file here. > > best wishes > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the personto whom it is
addressed. If you believe this e-mail was sent to you in errorand the e-mail
contains patient information, please contact the PartnersCompliance HelpLine at
http://www.partners.org/complianceline . If the e-mail wassent to you in error
but does not contain patient information, please contact thesender and properly
dispose of the e-mail.
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
You can send it to either my email (ahoopes@mgh.harvard.edumailto:ahoopes@mgh.harvard.edu) or Bruce’s
best, Andrew
On Jan 19, 2018, at 10:12 AM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca> wrote:
thanks Andrew. I had seen that and will give it a go - just wanted to make sure that my recipient email would be the FreeSurfer support list.
Trisanna
On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote: Hi Trisanna,
Okay - if your file is less than 2GiB, I suggest sending your data via the Martinos file drop (directions at the bottom of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange).
best Andrew
On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca> wrote:
Hi Andrew
Thank you for your response. I gave it a go and still no luck, unless I am missing something completely obvious here
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp surfer.nmr.mgh.harvard.eduhttp://surfer.nmr.mgh.harvard.edu/ Connected to surfer.nmr.mgh.harvard.eduhttp://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.eduhttp://surfer.nmr.mgh.harvard.edu/:trisanna): 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> quote PASV 227 Entering Passive Mode (132,183,202,158,147,251). ftp> put icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection.
On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote: Hi Trisanna,
Try running 'quote PASV' in ftp before running 'put' - that should hopefully clear up this issue.
best, Andrew
On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca> wrote:
Sorry, Bruce. ignore my last email. Not sure what happened there.
I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get the following and it happens over and over. Any idea what the problem could be?
trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/ trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls fsaverage icbm-109 icbm-118 icbm-127 icbm-142 icbm-202 icbm-102 icbm-110 icbm-119 icbm-131 icbm-143 icbm-202.tar.gz icbm-103 icbm-111 icbm-120 icbm-133 icbm-144 icbm-203 icbm-104 icbm-112 icbm-121 icbm-135 icbm-146 icbm-204 icbm-105 icbm-113 icbm-122 icbm-137 icbm-150 icbm-205 icbm-106 icbm-114 icbm-123 icbm-139 icbm-158 icbm-205.tar.gz icbm-107 icbm-115 icbm-125 icbm-140 icbm-200 icbm-206 icbm-108 icbm-117 icbm-126 icbm-141 icbm-201 trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp [X] surfer.nmr.mgh.harvard.eduhttp://surfer.nmr.mgh.harvard.edu/ Connected to [X] surfer.nmr.mgh.harvard.eduhttp://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-[X]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.eduhttp://surfer.nmr.mgh.harvard.edu/:trisanna): 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 icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection.
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.camailto:trisanna.sprung-much@mail.mcgill.ca> wrote: Thanks Bruce. I have uploaded it but I would like to confirm that you received the ICBM_305.tar. For some reason I was not able to compress it any further.
To clarify, subjects 205 and now subject 202 have both failed after surface extraction.
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: you can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
Hi Bruce Thanks for the speedy reply. Should I attach it here or is there a place I can upload it to?
best Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: hmmm, I've never seen label2label core dump before. Can you tar, gzip and upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
> Hi there > > I ran Freesurfer 6.0 on a subject last night and it took about 12 hours (seemed to get to the very end) and then exited with > errors. I can open my surfaces so I think it ended roughly with the atlas labelling. I attach the recon-all log file here. > > best wishes > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> [X] [X] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at [X] [X] http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu [X][X]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi there
I uploaded these last week to the file drop and used Bruce's email as it said it requires a ".nmr.mgh.harvard.edu" email type.
Please let me know if you received icbm-202 and icbm-205 as tar.gz files. As I mentioned, I was able to get surfaces for both of these but they seemed to end at the labeling step.
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Fri, Jan 19, 2018 at 10:42 AM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
You can send it to either my email (ahoopes@mgh.harvard.edu) or Bruce’s
best, Andrew
On Jan 19, 2018, at 10:12 AM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
thanks Andrew. I had seen that and will give it a go - just wanted to make sure that my recipient email would be the FreeSurfer support list.
Trisanna
On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
Hi Trisanna,
Okay - if your file is less than 2GiB, I suggest sending your data via the Martinos file drop (directions at the bottom of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange).
best Andrew
On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
Hi Andrew
Thank you for your response. I gave it a go and still no luck, unless I am missing something completely obvious here
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ 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:trisanna): 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> quote PASV 227 Entering Passive Mode (132,183,202,158,147,251). ftp> put icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection.
On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
Hi Trisanna,
Try running 'quote PASV' in ftp before running 'put' - that should hopefully clear up this issue.
best, Andrew
On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
Sorry, Bruce. ignore my last email. Not sure what happened there.
I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get the following and it happens over and over. Any idea what the problem could be?
trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/ trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls fsaverage icbm-109 icbm-118 icbm-127 icbm-142 icbm-202 icbm-102 icbm-110 icbm-119 icbm-131 icbm-143 icbm-202.tar.gz icbm-103 icbm-111 icbm-120 icbm-133 icbm-144 icbm-203 icbm-104 icbm-112 icbm-121 icbm-135 icbm-146 icbm-204 icbm-105 icbm-113 icbm-122 icbm-137 icbm-150 icbm-205 icbm-106 icbm-114 icbm-123 icbm-139 icbm-158 icbm-205.tar.gz icbm-107 icbm-115 icbm-125 icbm-140 icbm-200 icbm-206 icbm-108 icbm-117 icbm-126 icbm-141 icbm-201 trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ 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:trisanna): 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 icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection.
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.ca> wrote:
Thanks Bruce. I have uploaded it but I would like to confirm that you received the ICBM_305.tar. For some reason I was not able to compress it any further.
To clarify, subjects 205 and now subject 202 have both failed after surface extraction.
best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
you can put it on our ftp site:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote:
Hi Bruce Thanks for the speedy reply. Should I attach it here or is there a
place I can upload it to?
best Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
hmmm, I've never seen label2label core dump before. Can youtar, gzip and
upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote: > Hi there > > I ran Freesurfer 6.0 on a subject last night and it tookabout 12 hours (seemed to get
to the very end) and then exited with > errors. I can open my surfaces so I think it ended roughlywith the atlas labelling. I
attach the recon-all log file here. > > best wishes > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the personto whom it is
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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-
Bruce Fischl -
Hoopes, Andrew -
Trisanna Sprung-Much