[Freesurfer] minor edits to aseg lead to exist with errors in about 25% of my scans
Dear FS Wiki I run my scan in FS without any problem example: #@#%# recon-all-run-time-hours 8.342 recon-all -s 877 finished without error then I do some edits to the aseg in freeview edits include: relabelling correctly lateral ventricles voxels mostly in the posterior horn of the lateral ventricles; white matter hyperintensities around those voxels which are erroneously considered as cortex also more often in the posterior horn of the lateral ventricles; and correcting erroneous allocation of choroid plexus also typically in the posterior horn of the lateral ventricles Once done, I re-run using recon-all -s $i -autorecon2-noaseg example: /mridata/workingdata/HIV/subjects/877 /usr/local/FREESURFER/freesurfer5.3.0/bin/recon-all -s 877 -autorecon2-noaseg in 25% of cases, I get the following error message and the process exists example: # #@# Intensity Normalization2 Wed Dec 14 12:33:54 AEDT 2016 /mridata/workingdata/HIV/subjects/011/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz mri_normalize: aseg volume aseg.mgz must be conformed using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 011 exited with ERRORS at Wed Dec 14 12:33:56 AEDT 2016 in the other no problem example: #@#%# recon-all-run-time-hours 1.116 recon-all -s 877 finished without error at Thu Dec 1 14:42:27 AEDT 2016 ___ 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] minor edits to aseg lead to exist with errors in about 25% of my scans
sending this again as I have had no responses Thanks From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lucette Cysique Sent: Wednesday, December 14, 2016 12:52:11 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Madeleine Nichols (Redirection) Subject: [Freesurfer] minor edits to aseg lead to exist with errors in about 25% of my scans Dear FS Wiki I run my scan in FS without any problem example: #@#%# recon-all-run-time-hours 8.342 recon-all -s 877 finished without error then I do some edits to the aseg in freeview edits include: relabelling correctly lateral ventricles voxels mostly in the posterior horn of the lateral ventricles; white matter hyperintensities around those voxels which are erroneously considered as cortex also more often in the posterior horn of the lateral ventricles; and correcting erroneous allocation of choroid plexus also typically in the posterior horn of the lateral ventricles Once done, I re-run using recon-all -s $i -autorecon2-noaseg example: /mridata/workingdata/HIV/subjects/877 /usr/local/FREESURFER/freesurfer5.3.0/bin/recon-all -s 877 -autorecon2-noaseg in 25% of cases, I get the following error message and the process exists example: # #@# Intensity Normalization2 Wed Dec 14 12:33:54 AEDT 2016 /mridata/workingdata/HIV/subjects/011/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz mri_normalize: aseg volume aseg.mgz must be conformed using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 011 exited with ERRORS at Wed Dec 14 12:33:56 AEDT 2016 in the other no problem example: #@#%# recon-all-run-time-hours 1.116 recon-all -s 877 finished without error at Thu Dec 1 14:42:27 AEDT 2016 ___ 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] minor edits to aseg lead to exist with errors in about 25% of my scans
Please could someone consider my email question sent dec 14th? Email below Thanks Lucette A. Cysique, Ph.D. NHMRC Clinical Career Development Fellow / UNSW Medicine 2013-2017 NeuroHIV and Quantitative Neuropsychology Group Leader @ NeuRA Senior Lecturer SoMs, UNSW Medicine Affiliated senior researcher at the St. Vincent's Hospital Sydney, Applied Medical Research Centre, Peter Duncan Neuroscience Unit Postal Address: Neuroscience Research Australia PO Box 1165 (Street Address: 139 Barker Street) Randwick NSW 2031 Australia Office Ph: +61 2 9399 1880 Mobile Ph: (+61) (0)431 576 710 (text preferred) Emails: lcysi...@unsw.edu.au (primary) lucette.cysi...@svha.org.au (St. Vincent's Hospital Sydney, related project) lcysi...@ucsd.edu (HIV Neurobehavioral Research Center/UCSD related project) Twitter: @Lucette_C http://www.neura.edu.au/research/themes/cysique-group From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lucette Cysique Sent: Monday, December 19, 2016 12:37:13 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Madeleine Nichols (Redirection) Subject: Re: [Freesurfer] minor edits to aseg lead to exist with errors in about 25% of my scans sending this again as I have had no responses Thanks From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lucette Cysique Sent: Wednesday, December 14, 2016 12:52:11 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Madeleine Nichols (Redirection) Subject: [Freesurfer] minor edits to aseg lead to exist with errors in about 25% of my scans Dear FS Wiki I run my scan in FS without any problem example: #@#%# recon-all-run-time-hours 8.342 recon-all -s 877 finished without error then I do some edits to the aseg in freeview edits include: relabelling correctly lateral ventricles voxels mostly in the posterior horn of the lateral ventricles; white matter hyperintensities around those voxels which are erroneously considered as cortex also more often in the posterior horn of the lateral ventricles; and correcting erroneous allocation of choroid plexus also typically in the posterior horn of the lateral ventricles Once done, I re-run using recon-all -s $i -autorecon2-noaseg example: /mridata/workingdata/HIV/subjects/877 /usr/local/FREESURFER/freesurfer5.3.0/bin/recon-all -s 877 -autorecon2-noaseg in 25% of cases, I get the following error message and the process exists example: # #@# Intensity Normalization2 Wed Dec 14 12:33:54 AEDT 2016 /mridata/workingdata/HIV/subjects/011/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz mri_normalize: aseg volume aseg.mgz must be conformed using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 011 exited with ERRORS at Wed Dec 14 12:33:56 AEDT 2016 in the other no problem example: #@#%# recon-all-run-time-hours 1.116 recon-all -s 877 finished without error at Thu Dec 1 14:42:27 AEDT 2016 ___ 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] minor edits to aseg lead to exist with errors in about 25% of my scans
Dear Bruce Many thanks We are doing the aseg edits in Freeview. Is that an issue? I will use the command line you sent Many thanks Lucette From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of freesurfer-requ...@nmr.mgh.harvard.edu Sent: Friday, January 6, 2017 4:00:04 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 155, Issue 8 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. V6 beta freeview - stopped loading remaining files when one is missing (Antonin Skoch) 2. freeview V6beta - reposition surface option (Antonin Skoch) 3. Re: mri_convert error message (Bruce Fischl) 4. Re: V6 beta freeview - stopped loading remaining files when one is missing (Ruopeng Wang) 5. Re: 6.0.0 release (Tobias Granberg) 6. Problem with freeview (Jennifer Szeto) 7. Re: minor edits to aseg lead to exist with errors in about 25% of my scans (Lucette Cysique) 8. Re: minor edits to aseg lead to exist with errors in about 25% of my scans (Bruce Fischl) 9. Re: Problem with freeview (Ruopeng Wang) 10. Re: Problem with freeview (Jennifer Szeto) 11. Postdoctoral Fellow in Machine Learning in Neuroimaging (Thomas Yeo) 12. Postdoctoral fellow in mental disorder subtypes (Thomas Yeo) 13. Fwd: REMINDER: OHBM 2017 Call For Council Nominations (Douglas N Greve) -- Message: 1 Date: Wed, 4 Jan 2017 21:38:53 +0100 From: Antonin Skoch Subject: [Freesurfer] V6 beta freeview - stopped loading remaining files when one is missing To: freesurfer@nmr.mgh.harvard.edu Message-ID: <1798454155-32...@posta.medicon.cz> Content-Type: text/plain; charset="utf-8" Dear experts, with V6 beta version of freeview I encountered, that when some input file specified in command line is missing, the loading of remaining files is stopped. This was not the case with 5.3 version. I found this feature handy. Do you think that it would be good to implement this behavior also for V6 version of freeview? Regards, Antonin Skoch -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170104/b3a23719/attachment-0001.html -- Message: 2 Date: Wed, 4 Jan 2017 21:50:49 +0100 From: Antonin Skoch Subject: [Freesurfer] freeview V6beta - reposition surface option To: freesurfer@nmr.mgh.harvard.edu Message-ID: <1798681432-5...@posta.medicon.cz> Content-Type: text/plain; charset="utf-8" Dear experts, I have several questions regarding "reposition surface" tool in freeview (V6beta): 1. Are here any documentation how to use "reposition surface" tool? I would especially velcome the explanation of significance of "sigma", "size" and "gradient direction" parameter. I tried to play with the parameters by trial and error, but I could not get satisfactory results. 2. It seems to me that the selection of the active volume (i.e. the volume according to that the surface is repositioned) does not reflect the currently highlighted volume. It seems to always use the volume on top of the list of the volumes, but I am not sure given the unpredictive behaviour of this tool I got so far. 3. It would be maybe handy to include special flag to recon-all to rerun remaining recon-all pipeline after the reposition of the surface in freeview have been used. What do you think? 4. Do you think there is a chance to implement recon-all to preserve part of the surface which has been repositioned by this tool in case of recon-all rerun (similarly like it is done with other edits)? Regards, Antonin Skoch -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170104/167e137f/attachment-0001.html -- Message: 3 Date: Wed, 4 Jan 2017 16:18:42 -0500 (EST) From: Bruce Fischl Subject: Re: [Freesurfer] mri_convert error message To: Freesurfer support list Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Robert disk space and permissions are really the only two things I can think of. Can you try writing it somewhere else? Or using .mgz as output (or .nii without the .gz)? cheers Bruce On Wed, 4 Jan 2017, W
[Freesurfer] Freesurfer 6.0 and 5.3 differences in eTIV but not in supratentorial volume
Hello all FYI I have found non-negligeable differences in eTIV for 5.3 versus 6.0 in my healthy young sample It is probably due to the cerebellum computation changes (presented in released notes for 6.0) Unsurprisingly the supratentorial volumes 5.3 versus 6.0 are very similar (all was checked by simple correlations) Could people who have good knowledge of cerebellum studies comment on the reliability of freesurfer 5.3 in assessing size of the cerebellum versus manual tracing? This may need to be redone for version 6.0. Regards Lucette Lucette A. Cysique, Ph.D. NHMRC Clinical Career Development Fellow / UNSW Medicine 2013-2017 NeuroHIV and Quantitative Neuropsychology Group Leader @ NeuRA Senior Lecturer SoMs, UNSW Medicine Affiliated senior researcher at the St. Vincent's Hospital Sydney, Applied Medical Research Centre, Peter Duncan Neuroscience Unit Postal Address: Neuroscience Research Australia PO Box 1165 (Street Address: 139 Barker Street) Randwick NSW 2031 Australia Office Ph: +61 2 9399 1880 Mobile Ph: (+61) (0)431 576 710 (text preferred) Emails: lcysi...@unsw.edu.au (primary) lucette.cysi...@svha.org.au (St. Vincent's Hospital Sydney, related project) lcysi...@ucsd.edu (HIV Neurobehavioral Research Center/UCSD related project) Twitter: @Lucette_C http://www.neura.edu.au/research/themes/cysique-group ___ 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] How to obtain stats on custom anatomical ROI in freeview/freesurfer
Dear Ruopeng and colleagues, I am interested in following same tracing protocol for the amygdala as in "Neuroimage. 2012 April 2; 60(2): 1226–1235: "A reliable protocol for the manual segmentation of the human amygdala and its subregions using ultra-high resolution MRI” I would like as they did use freeview because it has some versatility and resolution that other programs do not have. I have however one issue Once I have created my ROI in freeview it ends up being by default a .label file. I create my ROI using ROIs and edit ROI tools and simply save it. I have tried to use “mri_label2vol” to get my ROI file (e.g., right_amygdala.label) into a volume file from which I thought I could then compute stats using “mri_segstats” But it does not work, as it seems that the initial .label file does not have the current format? Or required info? My command line output that it cannot read my .label file Thanks for your assistance Lucette ___ 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.
