Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Yes, it solves medial_wall label problem but not mri_aparc2aseg error.log. I attached you in a previous message: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56610.html Many thanks, M del Mar ___ Freesurfer mailing list

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi M del Mar, I think I’ve discovered the source of this issue. It’s tough to troubleshoot it without access to the subject set, but I think I have a working fix. The patch link (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface) is updated with the new

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi Andrew, My test in December with last version of make_average_surface worked correctly. However, now I am trying to make another average subject and medial_wall.label is not created. I am using the last patch as last time. It is unusual because last time label folder was correctly created.

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi M del Mar, Okay, I just updated the script at https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface. Let me know if the issue continues. best, Andrew On Dec 22, 2017, at 9:25 AM, M del Mar Velasco >

[Freesurfer] [Re] medial wall label in Freesurfer 6

Hi, I am sorry for insisting, but I have found a new mistake in your new version of make_average_surface. rh.medial_wall.label contains 13733 vertex, it is a desired result. However, rh.cortex.label contains all 163842 vertex, i.e, it covers medial wall area too. That's why we still have the

[Freesurfer] [Re] medial wall label in Freesurfer 6

Hi Andrew, Thanks very much! I have tried the new version of make_average_surface and it works fine. I am very gratefull. Best, M del Mar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi M del Mar, Sorry for the delay, I’ve uploaded the fix to https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface. If you copy this new version of make_average_surface to $FREESURFER_HOME/bin, this should hopefully solve the problem. Let me know if these

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Hi M del Mar, I think I’ve found the cause - it’s due to a small bug in make_average_surface. I should have a fix for you soon (today or tomorrow). best, Andrew > On Dec 7, 2017, at 3:47 PM, M del Mar Velasco wrote: > > Hi, > > Have you take a look at our data? Have

[Freesurfer] [Re] medial wall label in Freesurfer 6

Hi, Have you take a look at our data? Have you find any possible cause? We need to continue with our analysis and it is now stopped. Thanks you in advance, M del Mar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Thanks, I just received it - I’ll take a look Andrew On Dec 1, 2017, at 5:10 AM, M del Mar Velasco > wrote: Hello, I have upload the data. Recipient mail was ahoo...@mgh.harvard.edu. Please, check you have

[Freesurfer] [Re] medial wall label in Freesurfer 6

Hello, I have upload the data. Recipient mail was ahoo...@mgh.harvard.edu. Please, check you have received it. Thanks very much, M del Mar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

Okay, can you upload the compressed average subject to our ftp server (https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange) and I will take a look? thanks, Andrew On Nov 30, 2017, at 12:30 PM, M del Mar Velasco > wrote: Hi, I have

[Freesurfer] [Re] medial wall label in Freesurfer 6

Hi, I have installed the patch and it doesn't fix the label files problem. We have tried make_average_subject with the other 56 subjects and Medial_wall.label contains about 300 vertexs. It is very different from the other 60 subjects. Nevertheless, we have also repeated the test with

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

The make_average_subject patch can be downloaded here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ The readme file contains some instructions. This patch will definitely fix your recon-all error, but I don’t think it’s related to the labeling issue. Though, it’s worth a

[Freesurfer] [Re] medial wall label in Freesurfer 6

Hi, We are not using the make_average_subject 6.0.0-patch. Do you think it would be a possible solution? Where can I find that patch? On the other hand, we've noticed that recon-all, which is a final make_average_subject step, fails. I send you the recon-all.log. However, maybe it is not

Re: [Freesurfer] [Re] medial wall label in Freesurfer 6

I’ve tested a few different (large) sets of subject data and still been unable to replicate this problem, so tough to say what’s causing it. Are you using the make_average_subject 6.0.0-patch? Have you also tried running the command with a subgroup containing the other 56 subjects (maybe it’s a

[Freesurfer] [Re] medial wall label in Freesurfer 6

Hi, User M del Mar and me belong to same investigation group, so the problem is common. We have 116 subjects and we detected this trouble. However, we tried to repeat the make_average_subject command using a subgroup (only 60 subjects) and label files were correctly created. Maybe, number of