Re: [Freesurfer] How to avoid overlaps between volume labels?
Hi Yuko I think you can use multiple label tags when using mri_label2vol like below: mri_label2vol --subject $subject_name --hemi $hemi --label $label1 --label $label2 --label $label3 --temp $template --o $output --fillthresh 0.3 --proj frac 0 1 0.1 --identity The output volume would have non-zero voxels, marked with three different values. Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea ___ 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] [FREESURFER] atlas applicability. (fwd)
Dear Lilla I appreciate your answers. It was very helpful. Just another follow-up question. I think freesurfer itself ended without errors and the skull-stripped and surfaces look okay. I think in the recommended reconstruction Pipeline, check segmentation is related to checking atlas worked. Still, I wonder there is a gold standard to check the atlas (Deksian atlas) works okay. . Thanks again! Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea On Fri, Mar 30, 2012 at 2:46 AM, Lilla Zollei lzol...@nmr.mgh.harvard.eduwrote: Hi Cheol, I am using freesurfer for patients with various neural disease. I wonder the the freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB), epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies already used freesurfer for some of the diseases in the list,) I believe epilepsy patients with lobectomy cannot be applicable. If the malformation or the difference between normal control acquisitions and your scans is significant the FS pipeline, using the FS atlas is not going to be successful. Withuot seeing your data I cannot tell which population from the above is going to be affected, but if in doubt just try processing one or two representative samples from the different populations and assess how successful the processing is. Also is there age limit for the freesurfer atlas? How young can the atlas work for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper bound? 80 year-old? The lower bound, in our experience, is about 4-5 yrs. Of course, it depends on your data quality but we had success all the way down to that age. I am not aware of any upper limits. Again, if you are processing these kind of extreme populations, make sure that you inspect the outcome of the FS recon pipeline carefully before proceeding with any type of analysis. Lilla 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/**compliancelinehttp://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.
Re: [Freesurfer] [FREESURFER] atlas applicability. (fwd)
Dear Lilla Yes, It is clear now! Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea On Fri, Mar 30, 2012 at 8:40 AM, Lilla Zollei lzol...@nmr.mgh.harvard.eduwrote: Hi Cheol, I am a bit confused by your question. The atlases that we use help with the segmentation on the surface rec onstruction steps when we process a new volume. If the outcomes look resonable to you, then all is good. Did I answer your question? Lilla On Fri, 30 Mar 2012, Cheol Han wrote: Dear Lilla I appreciate your answers. It was very helpful. Just another follow-up question. I think freesurfer itself ended without errors and the skull-stripped and surfaces look okay. I think in the recommended reconstruction Pipeline, check segmentation is related to checking atlas worked. Still, I wonder there is a gold standard to check the atlas (Deksian atlas) works okay. . Thanks again! Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea On Fri, Mar 30, 2012 at 2:46 AM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Cheol, I am using freesurfer for patients with various neural disease. I wonder the the freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB), epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies already used freesurfer for some of the diseases in the list,) I believe epilepsy patients with lobectomy cannot be applicable. If the malformation or the difference between normal control acquisitions and your scans is significant the FS pipeline, using the FS atlas is not going to be successful. Withuot seeing your data I cannot tell which population from the above is going to be affected, but if in doubt just try processing one or two representative samples from the different populations and assess how successful the processing is. Also is there age limit for the freesurfer atlas? How young can the atlas work for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper bound? 80 year-old? The lower bound, in our experience, is about 4-5 yrs. Of course, it depends on your data quality but we had success all the way down to that age. I am not aware of any upper limits. Again, if you are processing these kind of extreme populations, make sure that you inspect the outcome of the FS recon pipeline carefully before proceeding with any type of analysis. Lilla 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/**compliancelinehttp://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.
[Freesurfer] [FREESURFER] atlas applicability.
Hello freesurfers I am using freesurfer for patients with various neural disease. I wonder the the freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB), epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies already used freesurfer for some of the diseases in the list,) I believe epilepsy patients with lobectomy cannot be applicable. Also is there age limit for the freesurfer atlas? How young can the atlas work for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper bound? 80 year-old? Thanks for reading and your time! Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea ___ 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] Freesurfer for stroke subjects?
Hi Bruce. Thanks for your answer. What should I do for a larger one like removal of almost all of temporal lobe or prefrontal cortex. Modifying wm.mgz is not enough? Best, Han. On Wed, May 19, 2010 at 8:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Han, it depends on the size of the resection/stroke. For small ones it should be okay, but larger ones can require a lot of work (or be close to impossible). cheers Bruce On Wed, 19 May 2010, Cheol Han wrote: Hello Freesurfers We are going to handle some subjects with stroke or subjects who receives a surgery to remove brain tumors. I just wonder whether it is possible to use freesurfer for those subjects and how the surface registration is affected. Best, Han 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. -- Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea ___ 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.
