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 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.

[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

[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

[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

[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

[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

[Freesurfer] make_average_subject label files

Dear Freesurfer experts, I have a question related to make_average_subject command and Freesurfer versions. When I used to create my average subject with Freesurfer 5.3, I got lh.cortex.label and rh.cortex.label files inside label folder with 149955 vertexs. Moreover, lh.Medial_Wall.label

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Thanks you anyway, Douglas ___ 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

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Thanks you for your reply. I have used surfreg script and now it runs correctly. However, my subject list is very long, I have 100 subjects and running surfreg with all subject takes 13 hours (using all my cpus in a parallel way). Is there any option to reduce this long time? Any cuda file?

[Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Dear FreeSurfer experts, I am using mris_preproc command with following options: mris_preproc --s s_001 --s s_002 --s s_003 --target my_subject_average --hemi lh --meas my_input_surf.mgh --out /my_output_path/output_file I observe mris_preproc uses mri_surf2surf. My question is related

[Freesurfer] Brain without skull and manual edits

Dear all, I would like an accurate segmentation of the brain without skull in native space. I am running a recon-all with Freesurfer 6 and Ubuntu 16.04. When it finishes, I find mistakes and I erase some skull voxels from brainmask.mgz. I run recon-all again and it finished without errors.