Hi Bruce,I am editing aseg to correct the boundaries that excluded the lateral ventricle. The problem with lateral ventricle has been solved after running the process with -noaseg flag. But the boundaries in the middle, is crossing to the other hemesphere in some cases. I even tried -autorecon2-cp, the problem still exists. aparc+aseg has not been updated after running the process.
Does Celine's case apply to mine? Here is your answer to Celine: Hi Celine the only existing way to correct this would be to create two volumes in addition to brain.finalsurfs.mgz (say, lh.brain.finalsurfs.mgz and rh.brain.finalsurfs.mgz) and edit each of them to remove voxels in the contralateral hemisphere that are causing problems, then rerun mris_make_surfaces for each hemi, using the appropriate volume. At some point I guess we should put an intersection check into it for the contra hemicheers Bruce Could you help me with the exact command line? Thank you in advance for your help,Maryam
Hi Maryam
I guess, although it's hard to say without looking at your data. I think the upcoming V6 does much better on the midline. If you upload your data I can take a look. For the command line you can check out the recon-all help and just rerun the pial surface generation
cheers Bruce On Mon, 7 Mar 2016, maryam koochaki wrote:
Hi Bruce, I am editing aseg to correct the boundaries that excluded the lateral ventricle. The problem with lateral ventricle has been solved after running the process with -noaseg flag. But the boundaries in the middle, is crossing to the other hemesphere in some cases.
I even tried -autorecon2-cp, the problem still exists. aparc+aseg has not been updated after running the process.
Does Celine's case apply to mine? Here is your answer to Celine:
Hi Celine the only existing way to correct this would be to create two volumes in addition to brain.finalsurfs.mgz (say, lh.brain.finalsurfs.mgz and rh.brain.finalsurfs.mgz) and edit each of them to remove voxels in the contralateral hemisphere that are causing problems, then rerun mris_make_surfaces for each hemi, using the appropriate volume. At some point I guess we should put an intersection check into it for the contra hemi cheers Bruce
Could you help me with the exact command line?
Thank you in advance for your help, Maryam
Hi Bruce,Thanks, I uploaded my subject in your ftp site.case name: train_emc_010.tar.gz Best,Maryam
On Monday, March 7, 2016 5:26 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Maryam
I guess, although it's hard to say without looking at your data. I think the upcoming V6 does much better on the midline. If you upload your data I can take a look. For the command line you can check out the recon-all help and just rerun the pial surface generation
cheers Bruce On Mon, 7 Mar 2016, maryam koochaki wrote:
Hi Bruce, I am editing aseg to correct the boundaries that excluded the lateral ventricle. The problem with lateral ventricle has been solved after running the process with -noaseg flag. But the boundaries in the middle, is crossing to the other hemesphere in some cases.
I even tried -autorecon2-cp, the problem still exists. aparc+aseg has not been updated after running the process.
Does Celine's case apply to mine? Here is your answer to Celine:
Hi Celine the only existing way to correct this would be to create two volumes in addition to brain.finalsurfs.mgz (say, lh.brain.finalsurfs.mgz and rh.brain.finalsurfs.mgz) and edit each of them to remove voxels in the contralateral hemisphere that are causing problems, then rerun mris_make_surfaces for each hemi, using the appropriate volume. At some point I guess we should put an intersection check into it for the contra hemi cheers Bruce
Could you help me with the exact command line?
Thank you in advance for your help, Maryam
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Hi Maryam
I'm looking at it now - it's very noisy and has a huge I/S bias field (brainstem WM is almost twice as bright as superior WM). Can you send me the coords of the crossing and also tell me something about the acquisition (coil, sequence, field-strength)?
cheers Bruce
On Tue, 8 Mar 2016, maryam koochaki wrote:
Hi Bruce, Thanks, I uploaded my subject in your ftp site. case name: train_emc_010.tar.gz
Best, Maryam
On Monday, March 7, 2016 5:26 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Maryam
I guess, although it's hard to say without looking at your data. I think the upcoming V6 does much better on the midline. If you upload your data I can take a look. For the command line you can check out the recon-all help and just rerun the pial surface generation
cheers Bruce On Mon, 7 Mar 2016, maryam koochaki wrote:
Hi Bruce, I am editing aseg to correct the boundaries that excluded the lateral ventricle. The problem with lateral ventricle has been solved after
running
the process with -noaseg flag. But the boundaries in the middle, is crossing to the other hemesphere in some cases.
I even tried -autorecon2-cp, the problem still exists. aparc+aseg has not been updated after running the process.
Does Celine's case apply to mine? Here is your answer to Celine:
Hi Celine the only existing way to correct this would be to create two volumes in addition to brain.finalsurfs.mgz (say, lh.brain.finalsurfs.mgz and rh.brain.finalsurfs.mgz) and edit each of them to remove voxels in the contralateral hemisphere that are causing problems, then rerun mris_make_surfaces for each hemi, using the appropriate volume. At some point I guess we should put an intersection check into it for the contra hemi cheers Bruce
Could you help me with the exact command line?
Thank you in advance for your help, Maryam
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.
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