On the brainmask the intensity within the STG wm is either slightly lower than 110 or slightly higher, though at the exact location of the control points it is 110. Similarly on the wm.mgz the intensities range around 110. I am not sure what the intensity was at these points before the cp's were added and reprocessed.
On 17/01/2012, at 1:36 PM, Bruce Fischl wrote:
Can you cc the list so others can answer? Is the wm in the brain.mgz in those regions darker than 110? Does putting control points there increase the intensity? It looks like a topological defect, but control points should help
On Jan 16, 2012, at 9:34 PM, Alana Shepherd alana.shepherd@unsw.edu.au wrote:
Hi Bruce, Thanks for your fast reply. Sorry - I realise I may have been unclear in my explanation. The sections are not missing from the brainmask mgz file - as if they had been cut out during skull stripping - they are actually missing from the surfs and aseg definitions (see attached screen shot). Regarding skull stripping - I have been changing the skull strip parameters on an 'as-need' basis - so some of the subjects have a lowered ws thresh, others I have needed to use gcut to remove excess dura, and some have been fine with the default ws thresh. I hope this clarifies the issue, Cheers Alana
<cp fail Screen shot 2012-01-17.png>
On 17/01/2012, at 1:17 PM, Bruce Fischl wrote:
Hi Alana
Have you tried changing the skull strip parameters?
Cheers Bruce
On Jan 16, 2012, at 6:33 PM, Alana Shepherd alana.shepherd@unsw.edu.au wrote:
Hello, I am running version 5.0, and am finding in a few cases that some areas (most commonly STG) are missing from the original brainmask - after adding control points and re-running the pipeline, these regions are still not being picked up in the surfs or in the aseg. Can you suggest any other way of remedying this? Many thanks Alana Shepherd _______________________________________________ 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.
Hmmm. If you upload the subject we will take a look Bruce
On Jan 16, 2012, at 9:53 PM, Alana Shepherd alana.shepherd@unsw.edu.au wrote:
On the brainmask the intensity within the STG wm is either slightly lower than 110 or slightly higher, though at the exact location of the control points it is 110. Similarly on the wm.mgz the intensities range around 110. I am not sure what the intensity was at these points before the cp's were added and reprocessed.
<cp fail Screen shot 2012-01-17.png>
On 17/01/2012, at 1:36 PM, Bruce Fischl wrote:
Can you cc the list so others can answer? Is the wm in the brain.mgz in those regions darker than 110? Does putting control points there increase the intensity? It looks like a topological defect, but control points should help
On Jan 16, 2012, at 9:34 PM, Alana Shepherd alana.shepherd@unsw.edu.au wrote:
Hi Bruce, Thanks for your fast reply. Sorry - I realise I may have been unclear in my explanation. The sections are not missing from the brainmask mgz file - as if they had been cut out during skull stripping - they are actually missing from the surfs and aseg definitions (see attached screen shot). Regarding skull stripping - I have been changing the skull strip parameters on an 'as-need' basis - so some of the subjects have a lowered ws thresh, others I have needed to use gcut to remove excess dura, and some have been fine with the default ws thresh. I hope this clarifies the issue, Cheers Alana
<cp fail Screen shot 2012-01-17.png>
On 17/01/2012, at 1:17 PM, Bruce Fischl wrote:
Hi Alana
Have you tried changing the skull strip parameters?
Cheers Bruce
On Jan 16, 2012, at 6:33 PM, Alana Shepherd alana.shepherd@unsw.edu.au wrote:
Hello, I am running version 5.0, and am finding in a few cases that some areas (most commonly STG) are missing from the original brainmask - after adding control points and re-running the pipeline, these regions are still not being picked up in the surfs or in the aseg. Can you suggest any other way of remedying this? Many thanks Alana Shepherd _______________________________________________ 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.
Great, thanks. Do you need the brainmask plus surf ?h orig and/or aparc/aseg?
Alana
On 17/01/2012, at 2:09 PM, Bruce Fischl wrote:
Hmmm. If you upload the subject we will take a look Bruce
On Jan 16, 2012, at 9:53 PM, Alana Shepherd alana.shepherd@unsw.edu.au wrote:
On the brainmask the intensity within the STG wm is either slightly lower than 110 or slightly higher, though at the exact location of the control points it is 110. Similarly on the wm.mgz the intensities range around 110. I am not sure what the intensity was at these points before the cp's were added and reprocessed.
<cp fail Screen shot 2012-01-17.png>
On 17/01/2012, at 1:36 PM, Bruce Fischl wrote:
Can you cc the list so others can answer? Is the wm in the brain.mgz in those regions darker than 110? Does putting control points there increase the intensity? It looks like a topological defect, but control points should help
On Jan 16, 2012, at 9:34 PM, Alana Shepherd alana.shepherd@unsw.edu.au wrote:
Hi Bruce, Thanks for your fast reply. Sorry - I realise I may have been unclear in my explanation. The sections are not missing from the brainmask mgz file - as if they had been cut out during skull stripping - they are actually missing from the surfs and aseg definitions (see attached screen shot). Regarding skull stripping - I have been changing the skull strip parameters on an 'as-need' basis - so some of the subjects have a lowered ws thresh, others I have needed to use gcut to remove excess dura, and some have been fine with the default ws thresh. I hope this clarifies the issue, Cheers Alana
<cp fail Screen shot 2012-01-17.png>
On 17/01/2012, at 1:17 PM, Bruce Fischl wrote:
Hi Alana
Have you tried changing the skull strip parameters?
Cheers Bruce
On Jan 16, 2012, at 6:33 PM, Alana Shepherd alana.shepherd@unsw.edu.au wrote:
Hello, I am running version 5.0, and am finding in a few cases that some areas (most commonly STG) are missing from the original brainmask - after adding control points and re-running the pipeline, these regions are still not being picked up in the surfs or in the aseg. Can you suggest any other way of remedying this? Many thanks Alana Shepherd _______________________________________________ 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.
Hi Bruce, Sorry for the multitude emails. I have attempted to upload via both FTP and Martinos file drop. The martinos site keeps dropping out, and FTP is giving the following error:
230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd transfer/incoming 250 Directory successfully changed. ftp> put /users/alana/Ashepherd.zip local: /users/alana/Ashepherd.zip remote: /users/alana/Ashepherd.zip 229 Entering Extended Passive Mode (|||37857|) 553 Could not create file. ftp>
This occurs whether I attempt to transfer a zipped folder or an individual mgz file.
Thanks for any suggestions, Alana
On 17/01/2012, at 2:09 PM, Bruce Fischl wrote:
Hmmm. If you upload the subject we will take a look Bruce
On Jan 16, 2012, at 9:53 PM, Alana Shepherd alana.shepherd@unsw.edu.au wrote:
On the brainmask the intensity within the STG wm is either slightly lower than 110 or slightly higher, though at the exact location of the control points it is 110. Similarly on the wm.mgz the intensities range around 110. I am not sure what the intensity was at these points before the cp's were added and reprocessed.
<cp fail Screen shot 2012-01-17.png>
On 17/01/2012, at 1:36 PM, Bruce Fischl wrote:
Can you cc the list so others can answer? Is the wm in the brain.mgz in those regions darker than 110? Does putting control points there increase the intensity? It looks like a topological defect, but control points should help
On Jan 16, 2012, at 9:34 PM, Alana Shepherd alana.shepherd@unsw.edu.au wrote:
Hi Bruce, Thanks for your fast reply. Sorry - I realise I may have been unclear in my explanation. The sections are not missing from the brainmask mgz file - as if they had been cut out during skull stripping - they are actually missing from the surfs and aseg definitions (see attached screen shot). Regarding skull stripping - I have been changing the skull strip parameters on an 'as-need' basis - so some of the subjects have a lowered ws thresh, others I have needed to use gcut to remove excess dura, and some have been fine with the default ws thresh. I hope this clarifies the issue, Cheers Alana
<cp fail Screen shot 2012-01-17.png>
On 17/01/2012, at 1:17 PM, Bruce Fischl wrote:
Hi Alana
Have you tried changing the skull strip parameters?
Cheers Bruce
On Jan 16, 2012, at 6:33 PM, Alana Shepherd alana.shepherd@unsw.edu.au wrote:
Hello, I am running version 5.0, and am finding in a few cases that some areas (most commonly STG) are missing from the original brainmask - after adding control points and re-running the pipeline, these regions are still not being picked up in the surfs or in the aseg. Can you suggest any other way of remedying this? Many thanks Alana Shepherd _______________________________________________ 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@nmr.mgh.harvard.edu
-
Alana Shepherd -
Bruce Fischl