Re: [Freesurfer] Aseg missing frontal portions - subcortical okay?
External Email - Use Caution Okay, thank you very much! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Tuesday, March 16, 2021 11:03 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aseg missing frontal portions - subcortical okay? Then it is probably ok On 3/8/2021 1:46 PM, Laurel Quinlan wrote: External Email - Use Caution The subcortical structures do look okay to me. -Laurel From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <mailto:dgr...@mgh.harvard.edu> Sent: Monday, March 8, 2021 9:48 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Aseg missing frontal portions - subcortical okay? Hard to say from a description. If you look at the subcortical structures, do they look like they are accurate? On 3/1/2021 4:36 PM, Laurel Quinlan wrote: External Email - Use Caution Hi Freesurfer Team, I am checking over the aseg on one of my subjects and notice that there are large portions of cortex missing anteriorly. The omission does not seem to affect any subcortical structures. Do you think that the subcortical values extracted from this subject are okay, even if there is cortex missing? Thanks! Laurel Quinlan Research Specialist Center for Healthy Minds University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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/10idtRXSHyTwmjyIQerrZT9JruXWx2B6IvTKeOrShRhrGnWWIgPhROB8apwD0j16GtIURfugADBv4dc2fTenzTXbC-9_jAiNhCY1XbxkKXP9zXKjV5jSl7sMu_gK24yqqCBfmWc-O_4jBO5OkQX1LsVgNPi8ap3vuphriNf703NPIe2jslcOzmX99N7jeFshWkvaOI7jCl-S6mWgTdWhwNAhVXZaGCbrYvYxg1oFOMBXkt2HWZJ9XWkNnNrrIk1vwsKEZpuOuchHjxrQNep3KSA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1Dc5_5WHRzq3HjN6XPT1-K5hTg_UysfcGjDZxRdbrhu_3FOCZ1JOgAN9qFZzg1mBw1dxCFBsrhA3corCseU5dr8bQ3w33ujCQ1ickhI0HDVi3coOGLxXlshVNFkBkGPeN0mgTYpO3h5p4xUmLyok-P7wJLW1cMcsrT9Hr0mhBJJ0Sor66W58_AiLRgHQYsYFlRH3_wYFLPgx7dBXjSNGogqhwWYg5EU6SaK401leRLGT_TBcjkRxobf227solYWwHXt_Y0C49n1Kug7hMpQ1j3Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/10idtRXSHyTwmjyIQerrZT9JruXWx2B6IvTKeOrShRhrGnWWIgPhROB8apwD0j16GtIURfugADBv4dc2fTenzTXbC-9_jAiNhCY1XbxkKXP9zXKjV5jSl7sMu_gK24yqqCBfmWc-O_4jBO5OkQX1LsVgNPi8ap3vuphriNf703NPIe2jslcOzmX99N7jeFshWkvaOI7jCl-S6mWgTdWhwNAhVXZaGCbrYvYxg1oFOMBXkt2HWZJ9XWkNnNrrIk1vwsKEZpuOuchHjxrQNep3KSA/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
Re: [Freesurfer] Aseg missing frontal portions - subcortical okay?
External Email - Use Caution The subcortical structures do look okay to me. -Laurel From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Monday, March 8, 2021 9:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aseg missing frontal portions - subcortical okay? Hard to say from a description. If you look at the subcortical structures, do they look like they are accurate? On 3/1/2021 4:36 PM, Laurel Quinlan wrote: External Email - Use Caution Hi Freesurfer Team, I am checking over the aseg on one of my subjects and notice that there are large portions of cortex missing anteriorly. The omission does not seem to affect any subcortical structures. Do you think that the subcortical values extracted from this subject are okay, even if there is cortex missing? Thanks! Laurel Quinlan Research Specialist Center for Healthy Minds University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1Dc5_5WHRzq3HjN6XPT1-K5hTg_UysfcGjDZxRdbrhu_3FOCZ1JOgAN9qFZzg1mBw1dxCFBsrhA3corCseU5dr8bQ3w33ujCQ1ickhI0HDVi3coOGLxXlshVNFkBkGPeN0mgTYpO3h5p4xUmLyok-P7wJLW1cMcsrT9Hr0mhBJJ0Sor66W58_AiLRgHQYsYFlRH3_wYFLPgx7dBXjSNGogqhwWYg5EU6SaK401leRLGT_TBcjkRxobf227solYWwHXt_Y0C49n1Kug7hMpQ1j3Q/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
[Freesurfer] Aseg missing frontal portions - subcortical okay?
External Email - Use Caution Hi Freesurfer Team, I am checking over the aseg on one of my subjects and notice that there are large portions of cortex missing anteriorly. The omission does not seem to affect any subcortical structures. Do you think that the subcortical values extracted from this subject are okay, even if there is cortex missing? Thanks! Laurel Quinlan Research Specialist Center for Healthy Minds University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities
External Email - Use Caution Hi Bruce, Thank you for your help! I removed the IsRunning.lh+rh script as well and reran the recon. Everything seems to have worked! -Laurel From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Tuesday, January 28, 2020 3:37 PM To: Freesurfer support list Cc: Greve, Douglas N.,Ph.D. Subject: Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities Hi Laurel if a subject dir already exists recon-all will exit unless you specify -force. Alternatively you can try using the -make all flag, which should rerun only the steps that are needed (assuming the reboot didn't happen e.g. in the middle of writing a file) cheers Bruce On Tue, 28 Jan 2020, Laurel Quinlan wrote: > > External Email - Use Caution > > Hi Doug, > > Thanks for looking over that file. It is the correct recon-all file for one > of the problem brains. I discovered that there was a system reboot of some > sort when the recon-all was processing for these problem brains, so that is > likely what caused the process to stop. How can I restart the recon-all > process for these brains? I have tried just rerunning the recon-all command > but the process exits within a few moments each time. I am wondering if > there is something I need to delete that was partially processed during the > first attempt. > > Thanks, > > Laurel > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > Sent: Friday, January 24, 2020 9:34 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon-all errors - mri_segstats and > mri_relabel_hypointensities > It did not look like there was an explicit error in that log file, it just > stops at mris_volmask. Is that the right recon-all? Also, please just send > the text file so that we don't have to unzip it. > > On 1/22/2020 4:39 PM, Laurel Quinlan wrote: > > External Email - Use Caution > > Hi FS Support, > > I have two brains for which recon-all exited with errors after I > edited the wm.mgz volume. It seems that the problem occurs during the > mri_segstats and mri_relabel_hypointensities steps (if I'm reading the > output of the command "tail scripts/recon-all.log" correctly). I > attached one of the recon-all.log files as a zipped txt file. Please > let me know if you have troubleshooting suggestions. > > Thank you for your help! > > Laurel Quinlan > Research Specialist > Center for Healthy Minds > University of Wisconsin-Madison > > > ___ > 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] recon-all errors - mri_segstats and mri_relabel_hypointensities
External Email - Use Caution Hi Doug, Thanks for looking over that file. It is the correct recon-all file for one of the problem brains. I discovered that there was a system reboot of some sort when the recon-all was processing for these problem brains, so that is likely what caused the process to stop. How can I restart the recon-all process for these brains? I have tried just rerunning the recon-all command but the process exits within a few moments each time. I am wondering if there is something I need to delete that was partially processed during the first attempt. Thanks, Laurel From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Friday, January 24, 2020 9:34 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities It did not look like there was an explicit error in that log file, it just stops at mris_volmask. Is that the right recon-all? Also, please just send the text file so that we don't have to unzip it. On 1/22/2020 4:39 PM, Laurel Quinlan wrote: External Email - Use Caution Hi FS Support, I have two brains for which recon-all exited with errors after I edited the wm.mgz volume. It seems that the problem occurs during the mri_segstats and mri_relabel_hypointensities steps (if I'm reading the output of the command "tail scripts/recon-all.log" correctly). I attached one of the recon-all.log files as a zipped txt file. Please let me know if you have troubleshooting suggestions. Thank you for your help! Laurel Quinlan Research Specialist Center for Healthy Minds University of Wisconsin-Madison ___ 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] surfaceholes in aseg.stats
External Email - Use Caution Hi Doug, Thank you! Yes, their control point edits were different. Are the number of ?h.orig.nofix defects calculated after reconstruction with control point edits? -Laurel From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Tuesday, December 3, 2019 2:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surfaceholes in aseg.stats Those are the number of defects in the ?h.orig.nofix. Not sure why the two people see different numbers. Are you totally sure they are being run in exactly the same way? If they made different edits (control points, brain mask) then it could result in different number of holes On 12/3/2019 2:38 PM, Laurel Quinlan wrote: External Email - Use Caution Hi Freesurfer Support, I'm wondering how ?h.surfaceholes prior to fixing and "Total number of defect holes in surfaces prior to fixing" are calculated in the aseg.stats file for each brain. I compared aseg.stats files for the same brain edited by two different people, and I noticed that there were different numbers of holes listed for each person, despite the brain being the same. For example: lhSurfaceHoles 130 vs 61 rhSurfaceHoles 102 vs 80 Total number of defect holes 232 vs 141 Why would those numbers be so different? Thanks, Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison ___ 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
[Freesurfer] surfaceholes in aseg.stats
External Email - Use Caution Hi Freesurfer Support, I'm wondering how ?h.surfaceholes prior to fixing and "Total number of defect holes in surfaces prior to fixing" are calculated in the aseg.stats file for each brain. I compared aseg.stats files for the same brain edited by two different people, and I noticed that there were different numbers of holes listed for each person, despite the brain being the same. For example: lhSurfaceHoles 130 vs 61 rhSurfaceHoles 102 vs 80 Total number of defect holes 232 vs 141 Why would those numbers be so different? Thanks, Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
