[Freesurfer] 答复: Questions about surface coordanates

Thanks a lot! Just want to make sure that the “RAS”(FS cords?) and “MNI Talairach” is the MNI305 coords. 发件人: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 代表 Douglas Greve 发送时间: 2016年8月30日 21:21 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Re:

Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

Hi Matt I don't think that counts as a methods paper for the T2-based deformation. There is no validation or comparison with other methods in it, and really not enough detail to replicate what we did. cheers Bruce On Tue, 30 Aug 2016, Matt Glasser wrote: Sure there¹s a publication. See

Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

Sure there¹s a publication. See Figure 14: http://www.sciencedirect.com/science/article/pii/S1053811913005053 Peace, Matt. On 8/30/16, 10:21 AM, "Bruce Fischl" wrote: >Hi Don > >the T2 or FLAIR helps us avoid

[Freesurfer] About TRACULA results

Hi, I am trying to computer the changes of cortical parcellations and fiber pathways using FreeSurfer v5.3 and Tracula (2014/05/26 update) . I copied the anatomical and DWI images from the same scan session into five directories. Run recon-all and trac-all on the 5 same data sets, in order

Re: [Freesurfer] hippo sf segmentation 6.0 dev

Hi Renata, In general, mixing’n’matching is not a good idea, since different sequences bias the volumes in different directions. Now, if the differences in sequences were independent of whether subjects are patients or controls, it wouldn’t be *that* bad. But, if patients have different

Re: [Freesurfer] Brainstem nucleus

Hi Mohamad, For now, our brainstem module separates this structure into midbrain, pons, medulla and SCP - please see this link: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures If you want to segment more specific nuclei, we don’t have a tool capable of doing that yet. Cheers,

[Freesurfer] Brainstem nucleus

Hi Iglesias, Kindly, we would like to know if there are any methods in Freesurfer that can help to segment that brain stem nucleus. I mean output the nucleus automatically as a small masks, so these small masks can be used in other analyses (e.g. fMRI) I am thinking of creating masks for these

[Freesurfer] hippo sf segmentation 6.0 dev

Dear Eugenio, I have a couple of questions regarding the hippocampus subfields segmentation on the dev FS 6.0 which I hope you could help me with. We are comparing the volumes of hippocampal subregions of patients and controls, and we would like to be as consistent as possible with the input so

Re: [Freesurfer] Pial refinement with FLAIR

Hi Eelco we've made a bunch of improvements in the T2/FLAIR stream since 5.3 so you might check them out. Unfortunately I don't think they will be officially supported in 6.0 as we just don't have the resources to include it in our unit/system/regression test cycle. cheers Bruce On Tue,

Re: [Freesurfer] rfMRI and T2w image

Hi Vasudev probably not. What resolution are they? They are likely to be too low resolution to be useful and also quite significantly distorted w.r.t. the T1s. You can try it if you like, but my guess is it will hurt more than it helps sorry Bruce On Tue, 30 Aug 2016, Dev vasu wrote:

Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

Hi Don the T2 or FLAIR helps us avoid dura. It is still a beta version though as we don't have a ton of experience with it, and no, there is no reference for it yet (or maybe ever) :) Bruce On Tue, 30 Aug 2016, Krieger, Donald N. wrote: Dear list:   What are the advantages of including

Re: [Freesurfer] rfMRI and T2w image

Dear sir, I was checking for your reply about my question in Freesurfer Forum but unfortunately i could not your answer although ":Freesurfer Digest, Vol 150, Issue 43 " Today's topics section indicates that you have replied to my question. Following is my question : In order to run my

Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

FWIW, we’ve had good success with including the T2w scan as part of the FS 5.3-HCP release. cheers, -MH --  Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

Sure, any simulation can’t be exhaustive, but my understanding, chatting with Anderson, is that their 2014 paper simulated a quite large space of designs and Freedman-Lane is appropriate for the vast majority of the GLMs that we would encounter in neuroimaging. Also, again per Anderson, I

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

Hi all, In the presence of nuisance (orthogonal or not) the permutation test is only approximate, whatever is the method used. Regressing out the nuisance introduces dependencies between the residuals that render them strictly not exchangeable. However, in practice this is not an issue, and the

Re: [Freesurfer] Questions about surface coordanates

What is paraview? I would contact the developers. On 8/30/16 10:24 AM, Islem Rekik wrote: Hi all, I have a similar problem using Paraview: When I visualize the surface lh.pial and the anatomical image brainmask.mgz using FreeView they nicely overlap; however, after I convert lh.pial to

Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

Thank you - very helpful. Best - Don From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Tuesday, August 30, 2016 10:23 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] inclusion of both T1 and T2 in a

Re: [Freesurfer] Questions about surface coordanates

Hi all, I have a similar problem using Paraview: When I visualize the surface lh.pial and the anatomical image brainmask.mgz using FreeView they nicely overlap; however, after I convert lh.pial to lh.pial.vtk and brainmask*.mgz* to brainmask*.mha* and visualize them using Paraview, they are in

Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

ps. The 5.3 version is pretty buggy, so I'd wait until 6.0 to test it out On 8/30/16 10:12 AM, Krieger, Donald N. wrote: Dear list: What are the advantages of including a T2 scan when running recon-all –all ? Which results can it effect and to what extent? And how sensitive is

Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

Hi Don, the T2 stream is a work-in-progress, so we don't have a lot of these answers. In theory, a T2 will allow better placement of the pial surface allowing it to better exclude dura. No publication on this yet. doug On 8/30/16 10:12 AM, Krieger, Donald N. wrote: Dear list: What are

[Freesurfer] inclusion of both T1 and T2 in a recon-all run

Dear list: What are the advantages of including a T2 scan when running recon-all -all ? Which results can it effect and to what extent? And how sensitive is freesurfer to artifacts in the T2 scan? Is there a good reference for this/ Thanks and best - Don

Re: [Freesurfer] rfMRI and T2w image

You don't need T2w to run FreeSurfer/recon-all. There is an option to add a T2, but it is not necessary. In any event, you will not be able to use an fMRI scan for this purpose. On 8/30/16 7:50 AM, Dev vasu wrote: Dear Sir, In order to run my structural analysis pipeline , i require T2w

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

By "wrong" I meant that permutation no longer gives exact p-values in expectation with non-orthogonal designs. There is no theory to characterize the accuracy of Freeman-Lane of the other methods. In this sense, they are not approximations but ad hoc methods that people hope do a better job

Re: [Freesurfer] volume, surface area, and thickness

Hi Woo-Suk Just adding to Bruce's reply: area isn't a "technically more noisy and usually thus less sensitive" as the reviewer suggests. Area isn't noisier on its own right, and it's measured from the very same surfaces from which thickness is measured. However, there is a much larger variability

Re: [Freesurfer] Questions about surface coordanates

tksurfer always uses the ?h.orig coordinates. Also keep in mind that the vertex index is 0-based whereas matlab is 1-based. When you click on a point, you should see something like the following print out selected vertex 123491 out of 163842 current -39.11 15.65 11.26 orig -55.67 -10.37

[Freesurfer] rfMRI and T2w image

Dear Sir, In order to run my structural analysis pipeline , i require T2w images, but unfortunately we have not performed T2w scans , my colleague suggests we can use rfMRI instead T2w images Could you please let me know if i can use rfMRI image instead of T2w image?. Thanks Vasudev

[Freesurfer] Questions about surface coordanates

Dear Experts, I tried to extract vertex coordinates information from 'fsaverage/surf/lh.pial' file using matlab function 'read_surf', but I found that the coordinates returned by the function are different from what I saw in tksurfer, here are the screenshots: The vertex index starts from 0 in