Hi Bruce, rh.aparc.stats looks good and also rh.aparc.a2009s.stats looks correct. However, both aparc+aseg.mgz and aparc.a2009s+aseg.mgz have the issue with missing parcellation labels in right hemisphere.

Also I suspect the issues starts occurring in rh.ribbon.mgz and ribbon.mgz (missing labels). (lh.ribbon.mgz is fine)

I tried to recreate the rh.ribbon.mgz and ribbon.mgz files using the command below and I am able to reproduce the issue. mris_volmask http://freesurfer.net/fswiki/mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid>

I can upload the data if you would like to take a look. Thanks Mehul

On Fri, Aug 15, 2014 at 1:54 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

How does the rh.aparc look?

On Aug 14, 2014, at 8:13 PM, Mehul Sampat mpsampat@gmail.com wrote:

Hi Folks, We have a strange error for one case. For one case there are missing cortical parcellation labels in aparc+aseg.mgz file in the right hemisphere (see screenshots)

I looked at the recon-all.log file and no errors are reported. Also I recreated aparc+aseg.mgz file using the following command but the issue persists: mri_aparc2aseg --s subjid --volmask I looked at the rh.white and rh.pial and those look good. I cannot figure out what would cause such an issue ? I was wondering if anyone has seen something similar ? Thanks Mehul

<missing-parcellation-10591037.png>

<s3061-s10591037-img3.png>

<s3061-s10591037-img2.png>

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.

Thank Bruce. I have uploaded the case to transfer/incoming in surfer.nmr.mgh.harvard.edu My file is missingRightParcLabels.tar.gz Mehul

On Fri, Aug 15, 2014 at 3:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Sure, upload it and one of us will take a look

Bruce

On Aug 15, 2014, at 10:28 me PM, Mehul Sampat kmpsampat@gmail.com wrote:

Hi Bruce, rh.aparc.stats looks good and also rh.aparc.a2009s.stats looks correct. However, both aparc+aseg.mgz and aparc.a2009s+aseg.mgz have the issue with missing parcellation labels in right hemisphere.

Also I suspect the issues starts occurring in rh.ribbon.mgz and ribbon.mgz (missing labels). (lh.ribbon.mgz is fine)

I tried to recreate the rh.ribbon.mgz and ribbon.mgz files using the command below and I am able to reproduce the issue. mris_volmask http://freesurfer.net/fswiki/mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid>

I can upload the data if you would like to take a look. Thanks Mehul

On Fri, Aug 15, 2014 at 1:54 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

How does the rh.aparc look?

On Aug 14, 2014, at 8:13 PM, Mehul Sampat mpsampat@gmail.com wrote:

Hi Folks, We have a strange error for one case. For one case there are missing cortical parcellation labels in aparc+aseg.mgz file in the right hemisphere (see screenshots)

I looked at the recon-all.log file and no errors are reported. Also I recreated aparc+aseg.mgz file using the following command but the issue persists: mri_aparc2aseg --s subjid --volmask I looked at the rh.white and rh.pial and those look good. I cannot figure out what would cause such an issue ? I was wondering if anyone has seen something similar ? Thanks Mehul

<missing-parcellation-10591037.png>

<s3061-s10591037-img3.png>

<s3061-s10591037-img2.png>

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.