Re: [Freesurfer] Chunks of missing WM
Hi, I have experienced this problem before also.So I have downloaded the script you provided but as a non-programmer I am wondering how I can incorporate this script into my work using Linux. Can I simply copy and paste this into the text editer and run it that way? Thanks, Deirdre On Fri, Dec 14, 2012 at 4:37 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: it doesn't, although the 5.2 mri_normalize should help as well cheers Bruce On Fri, 14 Dec 2012, Jonathan Holt wrote: OK this is great. Does this require the latest version of Freesurfer? I see recon-all v 5.2, we're running Freesurfer 5.0.0 for reference On Dec 14, 2012, at 1:16 PM, Alex Hanganu wrote: I think Emily is talking about this one: ftp://surfer.nmr.mgh.harvard.**edu/pub/dist/freesurfer/misc/** allplatforms/ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/ a. Le 14/12/2012 12:59 PM, Jonathan Holt a écrit : Emily, This is good news, can I find or download this revised version somewhere? jon On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote: We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are considered. Emily On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt whats...@umich.edu wrote: OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed... On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote: Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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 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] Chunks of missing WM
Hi Deirdre just copy the updated recon-all into $FREESURFER_HOME/bin and you should be all set cheers Bruce On Mon, 17 Dec 2012, Deirdre O Shea wrote: Hi, I have experienced this problem before also.So I have downloaded the script you provided but as a non-programmer I am wondering how I can incorporate this script into my work using Linux. Can I simply copy and paste this into the text editer and run it that way? Thanks, Deirdre On Fri, Dec 14, 2012 at 4:37 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: it doesn't, although the 5.2 mri_normalize should help as well cheers Bruce On Fri, 14 Dec 2012, Jonathan Holt wrote: OK this is great. Does this require the latest version of Freesurfer? I see recon-all v 5.2, we're running Freesurfer 5.0.0 for reference On Dec 14, 2012, at 1:16 PM, Alex Hanganu wrote: I think Emily is talking about this one: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/ a. Le 14/12/2012 12:59 PM, Jonathan Holt a écrit : Emily, This is good news, can I find or download this revised version somewhere? jon On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote: We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are considered. Emily On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt whats...@umich.edu wrote: OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed... On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote: Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Chunks of missing WM
We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are considered. Emily On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt whats...@umich.edu wrote: OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed... On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote: Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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 -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogal...@gmail.com ___ 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] Chunks of missing WM
Emily, This is good news, can I find or download this revised version somewhere? jon On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote: We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are considered. Emily On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt whats...@umich.edu wrote: OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed... On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote: Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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 -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogal...@gmail.com ___ 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] Chunks of missing WM
I think Emily is talking about this one: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/ a. Le 14/12/2012 12:59 PM, Jonathan Holt a écrit : Emily, This is good news, can I find or download this revised version somewhere? jon On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote: We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are considered. Emily On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt whats...@umich.edu mailto:whats...@umich.edu wrote: OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed... On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote: Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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] Chunks of missing WM
it doesn't, although the 5.2 mri_normalize should help as well cheers Bruce On Fri, 14 Dec 2012, Jonathan Holt wrote: OK this is great. Does this require the latest version of Freesurfer? I see recon-all v 5.2, we're running Freesurfer 5.0.0 for reference On Dec 14, 2012, at 1:16 PM, Alex Hanganu wrote: I think Emily is talking about this one: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/ a. Le 14/12/2012 12:59 PM, Jonathan Holt a écrit : Emily, This is good news, can I find or download this revised version somewhere? jon On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote: We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are considered. Emily On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt whats...@umich.edu wrote: OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed... On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote: Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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] Chunks of missing WM
Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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] Chunks of missing WM
OK will do... I'll upload both versions, before and after recon-all ran. I am beginning to think it's an issue with the script that I am running... I'm looking at another brain and there are areas I did not touch at all where white matter voxels are being added or removed... On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote: Hi Jon if you upload this subject we'll take a look Bruce On Wed, 12 Dec 2012, Jonathan Holt wrote: I've had this happen a handful of times and I'm wondering what I can do about it. For reference using Freesurfer 5.0.0. Edited a brain and ran recon-all -autorecon2 -autorecon3 -s subj_id which completed without error. The resulting brain had chunks of missing auxiliary volume in areas that I had not touched at all. This is bizarre and I am not sure what to do about it. Images of said issue attached of both main and auxiliary volumes. ___ 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
