External Email - Use Caution
when i run recon all it creates all the subfolders but they're empty. the only thing that is actually generated is orig.mgz and rawavg.mgz in the mri subfolder. i didn't get any errors when running recon all so was hoping someone could shed some light on this.
Many thanks
External Email - Use Caution
Dear Alison,
Could you copy&paste the full command line that you are using to run recon-all?
Best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
On 11/10/2021 4:48 PM Alison McDonnell amcdonn8@tcd.ie wrote:
External Email - Use Caution
when i run recon all it creates all the subfolders but they're empty. the only thing that is actually generated is orig.mgz and rawavg.mgz in the mri subfolder. i didn't get any errors when running recon all so was hoping someone could shed some light on this.
Many thanks _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1pv0QRKxHHm3bK95pbGMtqIVB26pP3kYoNfmyodrdaZ5YBK...
External Email - Use Caution
the full line after setting up the environment is recon-all -i /Users/ali?Arch_Raim/IM-0001-0001.dcm -s IM-0001 -all
On Wed, 10 Nov 2021 at 15:53, Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionDear Alison,
Could you copy&paste the full command line that you are using to run recon-all?
Best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
On 11/10/2021 4:48 PM Alison McDonnell amcdonn8@tcd.ie wrote:
External Email - Use Caution
when i run recon all it creates all the subfolders but they're empty. the only thing that is actually generated is orig.mgz and rawavg.mgz in the
mri
subfolder. i didn't get any errors when running recon all so was hoping someone could shed some light on this.
Many thanks _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1pv0QRKxHHm3bK95pbGMtqIVB26pP3kYoNfmyodrdaZ5YBK...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ac1v8vDVEStKdGxbXhRU86UENFU1Wy0erfYeMr0ZrBu_k0...
And send the recon-all.log file
On 11/10/2021 10:57 AM, Alison McDonnell wrote:
External Email - Use Caution
the full line after setting up the environment is recon-all -i /Users/ali?Arch_Raim/IM-0001-0001.dcm -s IM-0001 -all
On Wed, 10 Nov 2021 at 15:53, Tim Schäfer <ts+ml@rcmd.org mailto:ts%2Bml@rcmd.org> wrote:
External Email - Use Caution Dear Alison, Could you copy&paste the full command line that you are using to run recon-all? Best, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > On 11/10/2021 4:48 PM Alison McDonnell <amcdonn8@tcd.ie> wrote: > > > External Email - Use Caution > > when i run recon all it creates all the subfolders but they're empty. the > only thing that is actually generated is orig.mgz and rawavg.mgz in the mri > subfolder. i didn't get any errors when running recon all so was hoping > someone could shed some light on this. > > Many thanks > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1pv0QRKxHHm3bK95pbGMtqIVB26pP3kYoNfmyodrdaZ5YBK5DqXeXuJWOM6OcK_ljpNhflF8kTem02uOZuJ4HwhzFzAy80ffLKB3JTufvAYmtGJwy8lrzvlVbiehfYYjBcD6cyqPa5QaoIoIJ2-L-EZFGNLElJby5pcSXF-luj3ZOWYJnGfrjtR5v9sYGxjaTphwgIH8Tsv1bkGIa2Vp6snWZBYE2uDFNFP0y6mYkGnJrSHy-mLciEcyXAMEgtuagLKOdcN3oM_3Ymv1zhhROBcgqSCr-U6tJOkm5kKEDwHZzg_zlf_U-nyQaEDqhKE0z2i285YvnxVTdIl6r95_4FQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1ac1v8vDVEStKdGxbXhRU86UENFU1Wy0erfYeMr0ZrBu_k0Q2azo3leEbEiSkvEBauht-pFSITeqSyQiwPvDLyh4psjX52C0WMCBtUEmi9WPkn5GwHdh825HUpF08NPcDxCO3uS1y60RMv6efR0TrdbiMpQ-xplURRKKtz7oMNTLq1SvE8VXGn6nSpNHGxcNAjUFEBgQPf5x2jMuELdhka7FmqGjdKxscav9-CryBuhIHwusas25LiMlnbP7-zrNQxSeoND3HCSwpZRHSfcfBbAiLnoYbPoK-mM6YP1V4EVdnIo4uOfqDpAAnPLTdwree/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
recon-all.log is attached. have tried to run again with different data and had the same problem
On Wed, 10 Nov 2021 at 22:39, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
And send the recon-all.log file
On 11/10/2021 10:57 AM, Alison McDonnell wrote:
External Email - Use Cautionthe full line after setting up the environment is recon-all -i /Users/ali?Arch_Raim/IM-0001-0001.dcm -s IM-0001 -all
On Wed, 10 Nov 2021 at 15:53, Tim Schäfer ts+ml@rcmd.org wrote:
External Email - Use CautionDear Alison,
Could you copy&paste the full command line that you are using to run recon-all?
Best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
On 11/10/2021 4:48 PM Alison McDonnell amcdonn8@tcd.ie wrote:
External Email - Use Caution
when i run recon all it creates all the subfolders but they're empty.
the
only thing that is actually generated is orig.mgz and rawavg.mgz in the
mri
subfolder. i didn't get any errors when running recon all so was hoping someone could shed some light on this.
Many thanks _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1pv0QRKxHHm3bK95pbGMtqIVB26pP3kYoNfmyodrdaZ5YBK...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Na-myl1E0RJGh5pxYM0ADIGQlH_fv8739vZUlYPjl79JJt... https://secure-web.cisco.com/1ac1v8vDVEStKdGxbXhRU86UENFU1Wy0erfYeMr0ZrBu_k0Q2azo3leEbEiSkvEBauht-pFSITeqSyQiwPvDLyh4psjX52C0WMCBtUEmi9WPkn5GwHdh825HUpF08NPcDxCO3uS1y60RMv6efR0TrdbiMpQ-xplURRKKtz7oMNTLq1SvE8VXGn6nSpNHGxcNAjUFEBgQPf5x2jMuELdhka7FmqGjdKxscav9-CryBuhIHwusas25LiMlnbP7-zrNQxSeoND3HCSwpZRHSfcfBbAiLnoYbPoK-mM6YP1V4EVdnIo4uOfqDpAAnPLTdwree/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Na-myl1E0RJGh5pxYM0ADIGQlH_fv8739vZUlYPjl79JJt... 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 Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/13t0Q-qbL5YzBZXNd-QS28f33Llh1ydbxT_yRq0mm01Vp6mf... . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
You need to tell it what to do, eg, -all to do everything.
On 11/15/2021 8:49 AM, Alison McDonnell wrote:
External Email - Use Caution
recon-all.log is attached. have tried to run again with different data and had the same problem
On Wed, 10 Nov 2021 at 22:39, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
And send the recon-all.log file On 11/10/2021 10:57 AM, Alison McDonnell wrote:External Email - Use Caution the full line after setting up the environment is recon-all -i /Users/ali?Arch_Raim/IM-0001-0001.dcm -s IM-0001 -all On Wed, 10 Nov 2021 at 15:53, Tim Schäfer <ts+ml@rcmd.org <mailto:ts%2Bml@rcmd.org>> wrote: External Email - Use Caution Dear Alison, Could you copy&paste the full command line that you are using to run recon-all? Best, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > On 11/10/2021 4:48 PM Alison McDonnell <amcdonn8@tcd.ie> wrote: > > > External Email - Use Caution > > when i run recon all it creates all the subfolders but they're empty. the > only thing that is actually generated is orig.mgz and rawavg.mgz in the mri > subfolder. i didn't get any errors when running recon all so was hoping > someone could shed some light on this. > > Many thanks > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1pv0QRKxHHm3bK95pbGMtqIVB26pP3kYoNfmyodrdaZ5YBK5DqXeXuJWOM6OcK_ljpNhflF8kTem02uOZuJ4HwhzFzAy80ffLKB3JTufvAYmtGJwy8lrzvlVbiehfYYjBcD6cyqPa5QaoIoIJ2-L-EZFGNLElJby5pcSXF-luj3ZOWYJnGfrjtR5v9sYGxjaTphwgIH8Tsv1bkGIa2Vp6snWZBYE2uDFNFP0y6mYkGnJrSHy-mLciEcyXAMEgtuagLKOdcN3oM_3Ymv1zhhROBcgqSCr-U6tJOkm5kKEDwHZzg_zlf_U-nyQaEDqhKE0z2i285YvnxVTdIl6r95_4FQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesu rfer <https://secure-web.cisco.com/1pv0QRKxHHm3bK95pbGMtqIVB26pP3kYoNfmyodrdaZ5YBK5DqXeXuJWOM6OcK_ljpNhflF8kTem02uOZuJ4HwhzFzAy80ffLKB3JTufvAYmtGJwy8lrzvlVbiehfYYjBcD6cyqPa5QaoIoIJ2-L-EZFGNLElJby5pcSXF-luj3ZOWYJnGfrjtR5v9sYGxjaTphwgIH8Tsv1bkGIa2Vp6snWZBYE2uDFNFP0y6mYkGnJrSHy-mLciEcyXAMEgtuagLKOdcN3oM_3Ymv1zhhROBcgqSCr-U6tJOkm5kKEDwHZzg_zlf_U-nyQaEDqhKE0z2i285YvnxVTdIl6r95_4FQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1ac1v8vDVEStKdGxbXhRU86UENFU1Wy0erfYeMr0ZrBu_k0Q2azo3leEbEiSkvEBauht-pFSITeqSyQiwPvDLyh4psjX52C0WMCBtUEmi9WPkn5GwHdh825HUpF08NPcDxCO3uS1y60RMv6efR0TrdbiMpQ-xplURRKKtz7oMNTLq1SvE8VXGn6nSpNHGxcNAjUFEBgQPf5x2jMuELdhka7FmqGjdKxscav9-CryBuhIHwusas25LiMlnbP7-zrNQxSeoND3HCSwpZRHSfcfBbAiLnoYbPoK-mM6YP1V4EVdnIo4uOfqDpAAnPLTdwree/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1Na-myl1E0RJGh5pxYM0ADIGQlH_fv8739vZUlYPjl79JJtqjp1IrqDxwLxY1Zln76oUsSP0eD023Pn_K8XpQsxn5RhuaeIzzxUSgRkePqi1siqKDomGSKB5eiEt_SOV30cYe8rV1iJtw5_ZbHVVVb3r9LxNx7hxpe77Dkaw-Az55CXeDmrcM7ZUwYiTVl_t0XWXDNXR1HINfdbaltbxPY5Q5HRu9CSIWyuXdH22nzfL_nfE0pdrzaSjcpZJXSk7cVXaktxOxxrgkNXQBiJuyhqzvjOC48Qjj4tC47_ygPYSwJUYLLIBrJONFocqfjUpS/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1Na-myl1E0RJGh5pxYM0ADIGQlH_fv8739vZUlYPjl79JJtqjp1IrqDxwLxY1Zln76oUsSP0eD023Pn_K8XpQsxn5RhuaeIzzxUSgRkePqi1siqKDomGSKB5eiEt_SOV30cYe8rV1iJtw5_ZbHVVVb3r9LxNx7hxpe77Dkaw-Az55CXeDmrcM7ZUwYiTVl_t0XWXDNXR1HINfdbaltbxPY5Q5HRu9CSIWyuXdH22nzfL_nfE0pdrzaSjcpZJXSk7cVXaktxOxxrgkNXQBiJuyhqzvjOC48Qjj4tC47_ygPYSwJUYLLIBrJONFocqfjUpS/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/13t0Q-qbL5YzBZXNd-QS28f33Llh1ydbxT_yRq0mm01Vp6mfGP7akI6hz9Oh2t3sD42e245IacP3VcJzyF0FQJvzwoX3_NHdtmv7CMIS_Ye_-_3lFLRiDbhLKjEtk_uW4ZfPIgo7OkGYxQMKqpmia6wg_nYI85dwyfChlhXcHixB6PXz1A-pf0eDHzLHPdC3LeELAde5DLBTpr2mbhyp5jOPiKZHayNy3DxfC6nuI2ego6kiWfTG-CgfOt4eFKHM4AJJ5aMATQzvpyXL-0EzDkqUrjZNgBmgR4W6-Q-uOMSwAT82ErUv61FuShvi4S3nI/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Alison McDonnell -
Douglas N. Greve -
Tim Schäfer