Re: [Freesurfer] hello freesurfer developer~

On 8/25/15 9:35 AM, A-reum Min wrote: Hello developers I have some question to you. 1.In fig.png, how many vertices were composed of cluster at least? I'm not sure what you mean. it does not look like there are any clusters there 2. How to change Area Threshold(fig.png)? The area is contro

Re: [Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

Run recon-all -aparc2aseg On 8/24/15 7:00 PM, fmri wrote: Hello FreeSurfer, How do I get edits made on aseg.mgz to reflect onto the aparc+aseg.mgz? I have tried the *recon-all -autorecon2-noaseg -subjid mysubject* * * but the aparc+aseg.

Re: [Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

Should we run this after recon-all autorecon2-noaseg -subjid ? On Aug 25, 2015, at 7:43 AM, Douglas Greve wrote: > Run recon-all -aparc2aseg > > On 8/24/15 7:00 PM, fmri wrote: >> Hello FreeSurfer, >> >> How do I get edits made on aseg.mgz to reflect onto the aparc+aseg.mgz? >> >> I have tried

[Freesurfer] extract values of individual cluster

Dear FS experts, I have run two group comparison on qdec and I get differences in a number of clusters, which also survive cluster wise correction. I would like to extract the values for each of my subjects (to run further stats) on each of these clusters. Is there a way to do this rather than d

[Freesurfer] converting ROI .labels to MNI space

Dear Freesurfers, I'm hoping you can help me resolve an issue I'm having with regard to converting my ROI labels from freesurfer space (Taliarach) to MNI space in prep for using these as seeds for a functional connectivity analysis. I created several ROIs labels (.label files), which I hand drew o

[Freesurfer] TRACULA and eddy (FSL)

Dear TRACULA experts and developers, I am wondering whether TRACULA will allow usage of eddy, the newer eddy-correction tool from FSL in a newer version? Alternatively, it seems it would be possible to use the eddy corrected nifti plus bvec and bval as the original input to TRACULA and turn off

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

Reposting my question: This happens for all the segments that I've tried to extract using mri_extract_label. They all show up as 128 nerve after mri_extract_label. Is this a bug in the dev version? Any help is greatly appreciated! On Thu, Aug 20, 2015 at 3:45 PM, Priyanka wrote: > This happen

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

Hi Priyanka that is what mri_extract_label is designed to do. This facilitates making density maps in a common space. If you want to get the original label # back you can use something like: mri_binarize --match 128 --binval or something like that cheers Bruce On Tue, 25 Aug 2015, Priyank

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

Thanks Bruce. Just wanted to make sure I've got the correct output. Really appreciate the help. Thanks again, Priyanka Mehta > On Aug 25, 2015, at 4:44 PM, Bruce Fischl wrote: > > Hi Priyanka > > that is what mri_extract_label is designed to do. This facilitates making > density maps in a

Re: [Freesurfer] FreeSurfer 6.0 dev version Output

of course On Tue, 25 Aug 2015, Priyanka wrote: > Thanks Bruce. Just wanted to make sure I've got the correct output. > > Really appreciate the help. > > Thanks again, > Priyanka Mehta > >> On Aug 25, 2015, at 4:44 PM, Bruce Fischl wrote: >> >> Hi Priyanka >> >> that is what mri_extract_label is d

Re: [Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

yes On 08/25/2015 01:11 PM, fmri wrote: > Should we run this after recon-all autorecon2-noaseg -subjid ? > > On Aug 25, 2015, at 7:43 AM, Douglas Greve wrote: > >> Run recon-all -aparc2aseg >> >> On 8/24/15 7:00 PM, fmri wrote: >>> Hello FreeSurfer, >>> >>> How do I get edits made on aseg.mgz to r

Re: [Freesurfer] TRACULA and eddy (FSL)

Hi Barbara - Yes, just correct with the method of your choice, apply the rotation to the gradient vectors, pass the corrected images and gradient vectors to tracula, and turn off the default eddy correction (then it won't rotate anything, either). I'll probably make it an option in the upcomin

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

Hi Joe what version are you using? That looks a lot like a bug I fixed a month or two ago (the hippocampal stuff). The cortex I'm not so sure about. Some of it might be dura cheers Bruce On Tue, 25 Aug 2015, fmri wrote: > Dear Freesurfer experts, > > on aparc+aseg.mgz there is Hippocampus lab

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

wasn't this brought up on the list a few weeks back? On 08/25/2015 06:08 PM, fmri wrote: > Dear Freesurfer experts, > > on aparc+aseg.mgz there is Hippocampus labeled over WM regions. > > There are cortex "Unknown" voxels that persist through out all of our scans. > > What files should be edited a

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

Version freesurfer-Darwin-lion-dev-20150701 On Aug 25, 2015, at 3:11 PM, Bruce Fischl wrote: > Hi Joe > > what version are you using? That looks a lot like a bug I fixed a month > or two ago (the hippocampal stuff). The cortex I'm not so sure about. Some > of it might be dura > cheers > Bru

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

sorry, what was ? On Aug 25, 2015, at 3:18 PM, Douglas N Greve wrote: > wasn't this brought up on the list a few weeks back? > > On 08/25/2015 06:08 PM, fmri wrote: >> Dear Freesurfer experts, >> >> on aparc+aseg.mgz there is Hippocampus labeled over WM regions. >> >> There are cortex "Unknow

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

that's probably the reason the hippocampus (and maybe cortex) doesn't look that good. Try grabbing a new dev version and see if it improves. Doug: has the new atlas been put into the dev recon-all? I think it has, hasn't it? On Tue, 25 Aug 2015, fmri wrote: > Version > > freesurfer-Darwin-lion

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

The non-labeled voxels in the aparc+aseg near hippocampus. I think the resolution was that they were labeled as cortex in the aseg but as "unknown" in the aparc, so they get labeled as "unkown" in the aparc+aseg (since that is what they are) On 08/25/2015 06:42 PM, fmri wrote: > sorry, what was

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

which "new" atlas? On 08/25/2015 06:44 PM, Bruce Fischl wrote: > that's probably the reason the hippocampus (and maybe cortex) doesn't > look that good. Try grabbing a new dev version and see if it improves. > Doug: has the new atlas been put into the dev recon-all? I think it has, > hasn't it? >

Re: [Freesurfer] Hippocampus in WM region, Unknown voxels still persist

I have already processed 88 subjects in this version, would it matter if I process or re-process subjects with another version? On Aug 25, 2015, at 3:44 PM, Bruce Fischl wrote: > that's probably the reason the hippocampus (and maybe cortex) doesn't > look that good. Try grabbing a new dev vers