Re: [Freesurfer] Hanging or running at 'SubCort Seg'?
hmmm, looks like it is almost finished with mri_cc but doesn't complete. It usually only takes like 2 minutes for this process, so something must be wrong. Can you send me aseg.auto_noCCseg.mgz and norm.mgz for this subject? You can probably just email them. cheers Bruce On Mon, 17 Oct 2011, Irwin, William wrote: Hi Bruce- It is still running, but the recon-all.log as it stands is attached. Thanks for your help. Regards, Wil From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Sunday, October 16, 2011 6:27 PM To: Irwin, William Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William Subject: Re: [Freesurfer] Hanging or running at 'SubCort Seg'? Hi Wil Can you send us the full recon-all.log? Cheers Bruce On Oct 16, 2011, at 3:53 PM, Irwin, William wir...@memory.ucsf.edu wrote: Hi- I?m a bit stumped by a cased. The input volume looks very good. The first error was the Talairach transform would not complete, so I used the ?-notal-check? flag. As I have been focused on other things, I just let the job run, but after 2 weeks, it is stuck (I assume) as indicated. It is running on a fast processor with plenty of memory, so system constraints are not the issue #@# SubCort Seg Sun Oct 9 16:41:44 PDT 2011 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca as eg.auto_noCCseg.mgz mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz ?lta /media/ClusterData2/data/localdata2/FreeSurfer/wirwin/wirwin_subject s/FT047-5/mri/transforms/cc_up.lta FT047-5 Any suggestions as to what might be the problem? Thanks much, Wil ___ 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 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.
Re: [Freesurfer] Hanging or running at 'SubCort Seg'?
Hi Bruce- We'll this was insightful: The norm.mgz file was empty and when I looked at the original input after (after MRI convert) the sagittal view was rotate by 90 degrees. I'm not sure what caused this, as the input is correctly oriented. The discrepancy between input and conversion to .mgz seem likely to explain why the Talairach transform failed. Suggested on what would cause this glitch? Thanks, Wil |-Original Message- |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] |Sent: Monday, October 17, 2011 6:27 AM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: RE: [Freesurfer] Hanging or running at 'SubCort Seg'? | |hmmm, looks like it is almost finished with mri_cc but doesn't complete. |It usually only takes like 2 minutes for this process, so something must be |wrong. Can you send me aseg.auto_noCCseg.mgz and norm.mgz for this |subject? You can probably just email them. | |cheers |Bruce | | |On Mon, 17 Oct 2011, Irwin, |William wrote: | | | Hi Bruce- | | | | It is still running, but the recon-all.log as it stands is attached. | | | | Thanks for your help. | | | | Regards, | | Wil | | | | From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] | Sent: Sunday, October 16, 2011 6:27 PM | To: Irwin, William | Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William | Subject: Re: [Freesurfer] Hanging or running at 'SubCort Seg'? | | | | Hi Wil | | Can you send us the full recon-all.log? | | Cheers | | Bruce | | | On Oct 16, 2011, at 3:53 PM, Irwin, William wir...@memory.ucsf.edu |wrote: | | Hi- | | | | I?m a bit stumped by a cased. The input volume looks very good. The first |error was the Talairach transform would not complete, so I used the | ?-notal-check? flag. As I have been focused on other things, I just let the |job run, but after 2 weeks, it is stuck (I assume) as indicated. It | is running on a fast processor with plenty of memory, so system | constraints are not the issue | | | | #@# SubCort Seg Sun Oct 9 16:41:44 PDT 2011 | | | | mri_ca_label -align -nobigventricles norm.mgz | transforms/talairach.m3z | /usr/local/freesurfer/average/RB_all_2008-03-26.gca as | | eg.auto_noCCseg.mgz | | | | mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz ?lta | /media/ClusterData2/data/localdata2/FreeSurfer/wirwin/wirwin_subject | | s/FT047-5/mri/transforms/cc_up.lta FT047-5 | | | | Any suggestions as to what might be the problem? | | | | Thanks much, | | Wil | | ___ | 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
Re: [Freesurfer] Hanging or running at 'SubCort Seg'?
what is your input format? Is it analyze? On Mon, 17 Oct 2011, Irwin, William wrote: Hi Bruce- We'll this was insightful: The norm.mgz file was empty and when I looked at the original input after (after MRI convert) the sagittal view was rotate by 90 degrees. I'm not sure what caused this, as the input is correctly oriented. The discrepancy between input and conversion to .mgz seem likely to explain why the Talairach transform failed. Suggested on what would cause this glitch? Thanks, Wil |-Original Message- |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] |Sent: Monday, October 17, 2011 6:27 AM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: RE: [Freesurfer] Hanging or running at 'SubCort Seg'? | |hmmm, looks like it is almost finished with mri_cc but doesn't complete. |It usually only takes like 2 minutes for this process, so something must be |wrong. Can you send me aseg.auto_noCCseg.mgz and norm.mgz for this |subject? You can probably just email them. | |cheers |Bruce | | |On Mon, 17 Oct 2011, Irwin, |William wrote: | | | Hi Bruce- | | | | It is still running, but the recon-all.log as it stands is attached. | | | | Thanks for your help. | | | | Regards, | | Wil | | | | From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] | Sent: Sunday, October 16, 2011 6:27 PM | To: Irwin, William | Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William | Subject: Re: [Freesurfer] Hanging or running at 'SubCort Seg'? | | | | Hi Wil | | Can you send us the full recon-all.log? | | Cheers | | Bruce | | | On Oct 16, 2011, at 3:53 PM, Irwin, William wir...@memory.ucsf.edu |wrote: | | Hi- | | | | I?m a bit stumped by a cased. The input volume looks very good. The first |error was the Talairach transform would not complete, so I used the | ?-notal-check? flag. As I have been focused on other things, I just let the |job run, but after 2 weeks, it is stuck (I assume) as indicated. It | is running on a fast processor with plenty of memory, so system | constraints are not the issue | | | | #@# SubCort Seg Sun Oct 9 16:41:44 PDT 2011 | | | | mri_ca_label -align -nobigventricles norm.mgz | transforms/talairach.m3z | /usr/local/freesurfer/average/RB_all_2008-03-26.gca as | | eg.auto_noCCseg.mgz | | | | mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz ?lta | /media/ClusterData2/data/localdata2/FreeSurfer/wirwin/wirwin_subject | | s/FT047-5/mri/transforms/cc_up.lta FT047-5 | | | | Any suggestions as to what might be the problem? | | | | Thanks much, | | Wil | | ___ | 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 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] Hanging or running at 'SubCort Seg'?
Hi- I'm a bit stumped by a cased. The input volume looks very good. The first error was the Talairach transform would not complete, so I used the '-notal-check' flag. As I have been focused on other things, I just let the job run, but after 2 weeks, it is stuck (I assume) as indicated. It is running on a fast processor with plenty of memory, so system constraints are not the issue #@# SubCort Seg Sun Oct 9 16:41:44 PDT 2011 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca as eg.auto_noCCseg.mgz mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /media/ClusterData2/data/localdata2/FreeSurfer/wirwin/wirwin_subject s/FT047-5/mri/transforms/cc_up.lta FT047-5 Any suggestions as to what might be the problem? Thanks much, Wil ___ 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.
Re: [Freesurfer] Hanging or running at 'SubCort Seg'?
Hi Wil Can you send us the full recon-all.log? Cheers Bruce On Oct 16, 2011, at 3:53 PM, Irwin, William wir...@memory.ucsf.edu wrote: Hi- I’m a bit stumped by a cased. The input volume looks very good. The first error was the Talairach transform would not complete, so I used the ‘-notal-check’ flag. As I have been focused on other things, I just let the job run, but after 2 weeks, it is stuck (I assume) as indicated. It is running on a fast processor with plenty of memory, so system constraints are not the issue #@# SubCort Seg Sun Oct 9 16:41:44 PDT 2011 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca as eg.auto_noCCseg.mgz mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz –lta /media/ClusterData2/data/localdata2/FreeSurfer/wirwin/wirwin_subject s/FT047-5/mri/transforms/cc_up.lta FT047-5 Any suggestions as to what might be the problem? Thanks much, Wil ___ 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.
