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 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.
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. I have realized mri_aparc2aseg is not working fine because I get an error log. I've attached it. I can send you to our ftp server whole average subject folder if you consider it appropiate. Many thanks, Cheers, M del Mar error.log Description: error.log recon-all.log Description: recon-all.log ___ 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.
[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 same problem because we want to do statistic tests just over the cortex (without medial wall). It also happens with left hemisphere. Could you please take a look at that issue? Thanks very much, M del Mar ___ 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.
[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 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.
[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 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.
[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 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.
[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 5.3 and there is not any problem, all 116 subjects works fine. Best, M del Mar ___ 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.
[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 related with previous issue becuase label files are generated before. All the best, M del Mar error.log Description: error.log recon-all.log Description: recon-all.log ___ 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.
[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 and rh.Medial_Wall.label had 13887 vertexs. However, with new Freesurfer 6, I get 163841 vertexs for cortex and only one vertex for medial wall. That's why I have problems with mri_glmfit when I use rh or lh.cortex.label files as label mask. I am considering all vertexs, and I would like to use only real cortex vertexs. Are label files outputs from make_average_subject wrong? How can I fit this problem? Thanks in advance, M del Mar ___ 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.
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 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.
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? Thanks in advance, M del Mar ___ 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.
[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 to Freesurfer version. Using FreeSurfer 5.3, mri_surf2surf takes sphere.reg as srcsurfreg, while with Freesurfer 6 script mri_surf2surf has changed. It takes my_subject_average.sphere.reg (target of mris_preproc) as srcsurfreg. I get an error because my_subject_average.sphere.reg file doesn't exist inside s_001 folder. Why Freesurfer 6 changes srcsurfreg to $target.sphere.reg? What can I do in order to be coherent with my script which was designed using Freesurfer 5.3? Thanks in advance, M del Mar ___ 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.
[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. When I used to do that proccess with Freesurfer 5.1, I masked rawavg.mgz with brain.mgz to get the final segmented brain: mri_mask rawavg.mgz brain.mgz brainraw.mgz mri_convert -odt float brainraw.mgz brain.nii In that case, deleted voxels are set to background in brain.mgz (my manual changes affect to brain.mgz). Now I am using Freesurfer 6 and my manual erased voxels appears in brain.mgz (they are not black). So, what output from Freesurfer should I use to the above goal? Should I use brain.finalsurfs.mgz? Thanks you in advance M del Mar ___ 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.
