Freesurfer August 2019

freesurfer@nmr.mgh.harvard.edu

100 participants
144 discussions

Using Freesurfer Commands for Neonate
by Mahshid Fouladivanda 02 Aug '19

02 Aug '19

External Email - Use Caution Dear Experts, I have a neonate MRI Image which its parcellation file, surface files and the ribbon are not created by freesurfer. I have created an annotation file for it using "write_annotation". Now, for further processing I need to use freesurfer commands like "mri_aparc2aseg". Now I have a general question. Can these commands be used for neonate images?? Regards, Mahshid

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How to Divide the Brain Surface Parcells to more regions
by Mahshid Fouladivanda 01 Aug '19

01 Aug '19

External Email - Use Caution Dear Freesurfer Experts, I would like to divide the surface parcellations of the neonatal brain. The parcells were extracted using Draw_EM (Developing brain Region Annotation With Expectation-Maximization), an atlas based segmentation, from cortical and sub-cortical. As I understand from help comments, mris_divide_parcellation would help, but it needs annotation file to be imported as input. I do not have the annotation file. I would appreciate it if you could help me how to divide my parcells in more regions? Regards, Mahshid

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How to Create Cortex Parcellation Using "mri_aparc2aseg"?
by Mahshid Fouladivanda 01 Aug '19

01 Aug '19

External Email - Use Caution Dear experts, I have a segmentation file of all the tissues in the brain and the ribbon file which were extracted by another toolbox rather than freesurfer. Also, I have created the annotation file using "write_annotation.m". Now, I wanna create a parcellation file based on the segmentation and annotation files using "mri_aparc2aseg" in freesurfer. Bellow is the command I entered in the terminal and extract the parcels: mri_aparc2aseg --s subject name --annot annotation name --o output name and I used the segmentation file as the "aseg.mgz" for the above command. Now, I am wondered that do I select the right aseg file or not?? Any help would be appreciated. Regards, Mahshid

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Re: [Freesurfer] Running FSL randomise on FS cortical thickness data
by Antonin Skoch 01 Aug '19

01 Aug '19

External Email - Use Caution Dear Mark, I would suggest to use PALM instead: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide PALM supports surface-based data. Each vertex has different area, which has to be accounted when the cluster size is computed. Antonin Skoch Dear Freesurfer experts,Hi. We are analyzing cortical thickness data in Freesurfer, longitudinal data in 55 subjects using the linear mixed effects package. We are finding a number of siginificant clusters, and would like to correct for multiple comparisons with permutation testing. We have already run about 2000 permutations, and would like to use TFCE available in randomise rather than empirical methods to set parameters such as the cluster forming threshold. So, the simple question is, how do we convert our FS format data (these are F statistics at each vertex) into a format which can be read into randomise? Thanks for any advice you can provide. Best, Mark

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Freesurfer August 2019