[Freesurfer] NeuroHackademy 2019

External Email - Use Caution We are happy to announce a call for applications to participate in Neurohackademy 2019! This two-week hands-on workshop held at the University of Washington eScience Institute in Seattle, July 29th - August 9th, 2019, focuses on tools and techniques us

[Freesurfer] How to make grey matter edits

External Email - Use Caution Dear FreeSufer team, I have been working with MS patients using T1 lesion filled images. I corrected pial surface and I did control points for white matter. However, I have not found how to edit gray matter segmentation. I would much appreciate if you

[Freesurfer] LME MATLAB Tools

External Email - Use Caution Dear Freesurfer Experts, I have a question about how to interpret cortical thickness difference between groups using LME MATLAB tools. I have three groups(g0, g1, and g2) and five time points(t= 0,0.5, 1,2,3). I am trying to use LME model wi

Re: [Freesurfer] Large cluster size significant clusters

Try raising the threshold On 1/10/19 1:42 PM, Azeez, Azeezat wrote: > > External Email - Use Caution > > > Hello , > I have results for my mri_glmfit-sim. I find a significant results in > my cache.th20abs.sig.cluster.summary. > Yet, the cluster size of the significant cluster is almost t

[Freesurfer] Large cluster size significant clusters

External Email - Use Caution Hello , I have results for my mri_glmfit-sim. I find a significant results in my cache.th20abs.sig.cluster.summary. Yet, the cluster size of the significant cluster is almost the size of the total cortical surface area. I am not sure what to make of thi

Re: [Freesurfer] fsaverage, brainstem and cerebellum

External Email - Use Caution Ah! great!! thank you so much for the great help!! Have a good day, John Sent with ProtonMail Secure Email. ‐‐‐ Original Message ‐‐‐ On Thursday, January 10, 2019 1:03 PM, Bruce Fischl wrote: > Hi John > > we distribute an aseg.mgs with fs

Re: [Freesurfer] fsaverage, brainstem and cerebellum

Hi John we distribute an aseg.mgs with fsaverage I believe. You can just tesselate that. cheers Bruce On Thu, 10 Jan 2019, john Anderson wrote: External Email - Use Caution Hi Dr Bruce, I highly appreciate your guidance. I would like to load the cerebellum and brain stem st

Re: [Freesurfer] fsaverage, brainstem and cerebellum

External Email - Use Caution Hi Dr Bruce, I highly appreciate your guidance. I would like to load the cerebellum and brain stem structures as an average structure similar to "fsaverage" , I usually use the command tksurferfv fsaverage lh pial -overlay mri_tessellate or mri_mc w

Re: [Freesurfer] MRI sequence parameter difference and effect on cortical thickness values

I imagine it will have some systematic effect. If your design is such that the two scan types are divided across your contrast of interest (eg, diagnosis), then including it as a nuisance regressor is probably fine. On 1/3/19 4:31 PM, Arsenije Subotic wrote: > External Email - Use Caut

Re: [Freesurfer] Questions About Effect Sizes in Vertexwise GLM Anlaysis

On 1/9/19 10:35 AM, Max Owens wrote: > > External Email - Use Caution > > Hi, > > I just wanted to follow up and see if there was anyone who could > answer my questions: > > 1.What is the unit of effect size for the gamma.mgh file created by > vertexwise GLM Analysis using mri_glmfit? S

Re: [Freesurfer] Subcortical divide parcellation

Hi Huifang sorry, we don't have tools for dividing up the subcortical segmentations. For cortical parcels we find the first eigenvector and divide it along that cheers Bruce On Thu, 10 Jan 2019, WANG Huifang wrote: External Email - Use Caution Hi Bruce, Thank you so

Re: [Freesurfer] fsaverage, brainstem and cerebellum

Hi John you could use mri_tessellate or mri_mc to create a surface for those structures, then smooth them with mris_smooth and load them into freeview. Shouldn't be too hard. cheers Bruce On Thu, 10 Jan 2019, john Anderson wrote: External Email - Use Caution Dear FS ex

Re: [Freesurfer] Pial surface error (failing dura removal)

Dear Douglas, This is just a friendly reminder concerning the data I send you. I'd much appreciate if there is any advice on how to advance our pial surfacing other than manual editing. Thanks! Johann From: Rusche, Johann Sent: Monday, January 07, 2019 1:03 P

Re: [Freesurfer] Help with Reviewer Comment

Hi Shane that's a pretty tough one to answer. Certainly some developmental conditions (e.g. dramatic FCDs) can mess up the thickness. It really depends on the details. sorry I don't have a better answer Bruce On Thu, 10 Jan 2019, Shane Schofield wrote: External Email - Use Caution

Re: [Freesurfer] segmentation problem

Hi Manuela you can certainly do manual editing in freeview cheers Bruce On Thu, 10 Jan 2019, Manuela Costa wrote: External Email - Use Caution Dear all, We have a subject for whom we would like to do hippocampal subfield and amygdalar nuclei segmentation.  Unfortunately,

Re: [Freesurfer] Subcortical divide parcellation

External Email - Use Caution Hi Bruce, Thank you so much for your response. I would like to divide them into two/three uniformed parts, not considering the subfields. Now I made some python codes to do it. I am trying to test it with the more datasets now. If you have tools

[Freesurfer] fsaverage, brainstem and cerebellum

External Email - Use Caution Dear FS experts, For visualization purposes, is there any way to show the cerebellum and brain stem regions (similar to the attached figure), this figure was published used CONN toolbox but I am not sure how they were able to map functional data in b

[Freesurfer] Help with Reviewer Comment

External Email - Use Caution Hi Freesurfer A reviewer asked whether there are concerns about whether Freesurfer may obtain accurate cortical thickness data in people with developmental conditions - the main focus in my study. I did a search and could not find any validation stud

[Freesurfer] Problem with checking registration quality using tkregister-sess: if: Expression Syntax.

External Email - Use Caution Hi I’m having a problem that I’m hoping someone could help me with. I’m trying to check the quality of the alignment of structural and functional data, using the command: tkregister-sess -s 20_1 -fsd bold -per-run where 20_1 is the subject ID. N

[Freesurfer] segmentation problem

External Email - Use Caution Dear all, We have a subject for whom we would like to do hippocampal subfield and amygdalar nuclei segmentation. Unfortunately, this subject has a large lesion in the right hemisphere. Looking at the aseg, the segmentation of the bilateral amygdala a