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Hi,
I am new to recon-all and Freesurfer and I am having some difficulty tracking down the resulting outputs from when I re-run recon-all or they are not taking hold. So far I have edited two subjects after the initial run by lowering the ws height for the skullstrip in one and by adding white matter voxels by in the other. I followed all the tutorial instructions for both, starting with the edits and including the appropriate recon-all commands, which supposedly finished without error. However, after viewing the new volumes that were overwritten the day they were run, neither seem to have changed. For the wm.mgz, even, the wm voxel edits still exist as though recon-all did not run. If anyone has any tips for finding the proper outputs or what I might be doing incorrectly, I would greatly appreciate any advice.
Thanks
The first thing to do is to re-run you data using different subject names so that you have an unedited version. You can then use mri_diff, eg, mri_diff unedited/mri/wm.mgz edited/mri/wm.mgz to determine if there is a differenece that you are just not seeing
On 9/27/2021 7:16 PM, Kevin Miller wrote:
External Email - Use CautionHi,
I am new to recon-all and Freesurfer and I am having some difficulty tracking down the resulting outputs from when I re-run recon-all or they are not taking hold. So far I have edited two subjects after the initial run by lowering the ws height for the skullstrip in one and by adding white matter voxels by in the other. I followed all the tutorial instructions for both, starting with the edits and including the appropriate recon-all commands, which supposedly finished without error. However, after viewing the new volumes that were overwritten the day they were run, neither seem to have changed. For the wm.mgz, even, the wm voxel edits still exist as though recon-all did not run. If anyone has any tips for finding the proper outputs or what I might be doing incorrectly, I would greatly appreciate any advice.
Thanks
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The mri_diff command did show differences after re-running the wm and skullstrip commands under different names, but the differences were not related to the areas that I was troubleshooting. For example, I took the skullstrip ws height down to 10 for an adult brain in order to remove a piece of skull obscuring the temporal lobe, but it still exists in the brainmask.mgz and the mri_diff only caught one unrelated difference. Gcut missed the portion of skull as well. The same unrelated differences occurred for the wm edits and the wm.mgz still includes the wm edits from before I ran recon-all to correct it.
On Oct 1, 2021, at 11:02 AM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
The first thing to do is to re-run you data using different subject names so that you have an unedited version. You can then use mri_diff, eg, mri_diff unedited/mri/wm.mgz edited/mri/wm.mgz to determine if there is a differenece that you are just not seeing
On 9/27/2021 7:16 PM, Kevin Miller wrote: External Email - Use Caution
Hi,
I am new to recon-all and Freesurfer and I am having some difficulty tracking down the resulting outputs from when I re-run recon-all or they are not taking hold. So far I have edited two subjects after the initial run by lowering the ws height for the skullstrip in one and by adding white matter voxels by in the other. I followed all the tutorial instructions for both, starting with the edits and including the appropriate recon-all commands, which supposedly finished without error. However, after viewing the new volumes that were overwritten the day they were run, neither seem to have changed. For the wm.mgz, even, the wm voxel edits still exist as though recon-all did not run. If anyone has any tips for finding the proper outputs or what I might be doing incorrectly, I would greatly appreciate any advice.
Thanks
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1LdMfeu4JFsTIH46hB2dRaFccKvMDceI0wa1WvEZ9kurqMz...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1LdMfeu4JFsTIH46hB2dRaFccKvMDceI0wa1WvEZ9kurqMz... 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 Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1wbG0Fxry6mOJBs_6ev8X3E_3JeDZuIS2ENjNzQpbgLx7_At... . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
what were your recon-all commands?
On 10/2/2021 4:55 PM, Kevin Miller wrote:
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The mri_diff command did show differences after re-running the wm and skullstrip commands under different names, but the differences were not related to the areas that I was troubleshooting. For example, I took the skullstrip ws height down to 10 for an adult brain in order to remove a piece of skull obscuring the temporal lobe, but it still exists in the brainmask.mgz and the mri_diff only caught one unrelated difference. Gcut missed the portion of skull as well. The same unrelated differences occurred for the wm edits and the wm.mgz still includes the wm edits from before I ran recon-all to correct it.
On Oct 1, 2021, at 11:02 AM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
The first thing to do is to re-run you data using different subject names so that you have an unedited version. You can then use mri_diff, eg, mri_diff unedited/mri/wm.mgz edited/mri/wm.mgz to determine if there is a differenece that you are just not seeing
On 9/27/2021 7:16 PM, Kevin Miller wrote:
External Email - Use Caution
Hi,
I am new to recon-all and Freesurfer and I am having some difficulty tracking down the resulting outputs from when I re-run recon-all or they are not taking hold. So far I have edited two subjects after the initial run by lowering the ws height for the skullstrip in one and by adding white matter voxels by in the other. I followed all the tutorial instructions for both, starting with the edits and including the appropriate recon-all commands, which supposedly finished without error. However, after viewing the new volumes that were overwritten the day they were run, neither seem to have changed. For the wm.mgz, even, the wm voxel edits still exist as though recon-all did not run. If anyone has any tips for finding the proper outputs or what I might be doing incorrectly, I would greatly appreciate any advice.
Thanks
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 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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For skullstrip: recon-all -skullstrip -wsthresh 15 -clean-bm -subjid <insert subject> For wm: recon-all -autorecon2-wm -autorecon3 -subjid <insert subject>
On Oct 8, 2021, at 12:40 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
what were your recon-all commands?
On 10/2/2021 4:55 PM, Kevin Miller wrote:
External Email - Use CautionThe mri_diff command did show differences after re-running the wm and skullstrip commands under different names, but the differences were not related to the areas that I was troubleshooting. For example, I took the skullstrip ws height down to 10 for an adult brain in order to remove a piece of skull obscuring the temporal lobe, but it still exists in the brainmask.mgz and the mri_diff only caught one unrelated difference. Gcut missed the portion of skull as well. The same unrelated differences occurred for the wm edits and the wm.mgz still includes the wm edits from before I ran recon-all to correct it.
On Oct 1, 2021, at 11:02 AM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
The first thing to do is to re-run you data using different subject names so that you have an unedited version. You can then use mri_diff, eg, mri_diff unedited/mri/wm.mgz edited/mri/wm.mgz to determine if there is a differenece that you are just not seeing
On 9/27/2021 7:16 PM, Kevin Miller wrote:
External Email - Use CautionHi,
I am new to recon-all and Freesurfer and I am having some difficulty tracking down the resulting outputs from when I re-run recon-all or they are not taking hold. So far I have edited two subjects after the initial run by lowering the ws height for the skullstrip in one and by adding white matter voxels by in the other. I followed all the tutorial instructions for both, starting with the edits and including the appropriate recon-all commands, which supposedly finished without error. However, after viewing the new volumes that were overwritten the day they were run, neither seem to have changed. For the wm.mgz, even, the wm voxel edits still exist as though recon-all did not run. If anyone has any tips for finding the proper outputs or what I might be doing incorrectly, I would greatly appreciate any advice.
Thanks
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1t6c3QRHyOGeeis2bTOJZieIE6Bbb3C7p5aN-fQs2wL4mbC...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1t6c3QRHyOGeeis2bTOJZieIE6Bbb3C7p5aN-fQs2wL4mbC... 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 Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1fzfV_2ox0gCDZ_mDIvFv7ZJNz2NZE-xtKqgVAnWiXE5jDSN... . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1t6c3QRHyOGeeis2bTOJZieIE6Bbb3C7p5aN-fQs2wL4mbC...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1t6c3QRHyOGeeis2bTOJZieIE6Bbb3C7p5aN-fQs2wL4mbC... 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 Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1fzfV_2ox0gCDZ_mDIvFv7ZJNz2NZE-xtKqgVAnWiXE5jDSN... . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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Hello,
I just wanted to briefly follow up on this issue. Do you have any advice or suggestions for finding out why I am only receiving unrelated changes to volumes after re-running recon-all?
Thanks
On Oct 1, 2021, at 11:02 AM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
The first thing to do is to re-run you data using different subject names so that you have an unedited version. You can then use mri_diff, eg, mri_diff unedited/mri/wm.mgz edited/mri/wm.mgz to determine if there is a differenece that you are just not seeing
On 9/27/2021 7:16 PM, Kevin Miller wrote: External Email - Use Caution
Hi,
I am new to recon-all and Freesurfer and I am having some difficulty tracking down the resulting outputs from when I re-run recon-all or they are not taking hold. So far I have edited two subjects after the initial run by lowering the ws height for the skullstrip in one and by adding white matter voxels by in the other. I followed all the tutorial instructions for both, starting with the edits and including the appropriate recon-all commands, which supposedly finished without error. However, after viewing the new volumes that were overwritten the day they were run, neither seem to have changed. For the wm.mgz, even, the wm voxel edits still exist as though recon-all did not run. If anyone has any tips for finding the proper outputs or what I might be doing incorrectly, I would greatly appreciate any advice.
Thanks
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1urFbL4sg5fX80M7wSmBjt09HahoUDQOLmpe8YKlPhHXFFA...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1urFbL4sg5fX80M7wSmBjt09HahoUDQOLmpe8YKlPhHXFFA... 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 Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1Lr1vZaXmLsjwnD23-1Md9jhF46n-a0g7XX_szs-XcQGJcxo... . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Kevin Miller