Re: [Freesurfer] Extracting structural measures from trend-level PET clusters

Hi, A bit more info: the stack of thickness maps consists of lh.thickness.fwhm15.fsaverage.mghs that were created after -qcache. I used mri_concat --f --o to create the stack of mghs. I also noticed that the vertex values are in the range of 20-30, whereas those in the lh.thickness.fsvaerage

Re: [Freesurfer] Extracting structural measures from trend-level PET clusters

Thanks, Doug. It works but I am not sure if the values I'm getting are correct. Is this supposed to be reporting the mean cortical thickness of each cluster? I have pasted the output below from the avgwf below. The names of the clusters correspond to the regions from the "summary" text, am I

Re: [Freesurfer] recon all

Thank you very much Doug, Kindly, what do you suggest me to use instead of fslswapidim. What is your choice in this case? I highly appreciate your experience !   Bests, John   Sent: Friday, November 11, 2016 at 4:42 PM From: "Douglas N Greve" To: 

Re: [Freesurfer] recon all

I don't think that you need to do anything. If the tal reg checks out ok, then you can turn off the check when you run recon-all by adding -no-tal-check On 11/11/2016 05:40 PM, John Anderson wrote: > Thank you very much Doug, > Kindly, what do you suggest me to use instead of fslswapidim.

[Freesurfer] How to view overlapping voxels across multiple sig.mgh files?

Hi Freesurfer Team, I am just wondering if there is a neat way to derive .mgh files containing cluster information about spatially overlapping voxels across various sig.mgh? Thank you. Best Wishes, Elijah ___ Freesurfer mailing list

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Is it better to compute mean to weight by number of vertices or surface area ? Best, Matthieu Le 11 nov. 2016 11:33 PM, "Douglas N Greve" a écrit : > Vertices do not have equal areas and are not equally spaced > > > On 11/11/2016 05:11 PM, Matthieu Vanhoutte wrote: >

Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

I guess I'm not sure what the problem is. If you need to go from a surface coordinate to scanner coord, then get the tkr2scanner matrix and multiply it by the surface coord. The volumes are not transformed to tkr coords. The various xform matrices are kept with the volume. What are you trying

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Vertices do not have equal areas and are not equally spaced On 11/11/2016 05:11 PM, Matthieu Vanhoutte wrote: > > Thank you Douglas for giving me a way to compute area from segmented > surface data. > > Are vertices equally spaced along cortex or do triangles all have same > area ? > > Best, >

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Thank you Douglas for giving me a way to compute area from segmented surface data. Are vertices equally spaced along cortex or do triangles all have same area ? Best, Matthieu Le 11 nov. 2016 10:55 PM, "Douglas N Greve" a écrit : If you want to do it on fsaverage,

Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

Now I don't understand. Here's the situation: Someone has given me a bunch of MEG's with freesurfer runs which were run using both a T1 and a T2 scan with -T2pial . Mri_info --tkr2scanner gives the same transform for aparac+aseg.mgz, T1.mgz, and T2.mgz . I will be coregistering the MEG which

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

If you want to do it on fsaverage, then mris_segstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.area.mgh --seg lh.sign_clust.bin.mgh --excludeid 0 --sum lh.bin.area.sum --accumulate On 11/11/2016 04:48 PM, Matthieu Vanhoutte wrote: > > Dear Douglas, > > Yes I would like to in order to

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Dear Douglas, Yes I would like to in order to compute mean of some means. Maybe not if it is equivalent to number of vertices (are vertices distributed equaly distant on the cortical surface ?) In case I need surface area, do I have to convert overlay to annotation file to be used with

Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

If the head has not moved, then they will share a scanner RAS, ie, a given scanner RAS will be at the same place in the head in the two scans, though they will map to different col,row,slice in their respective volumes. If the head has moved, then you will need to perform a registration to

Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

Thanks for getting back, Doug. I understand - but if there are two scans, aren't there two scanner RAS's since the head presumably moved at least a little from one to the other or the scans could have been done on different scanners? Don From:

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

NVox is the number of vertices. The Volume_mm3 is not meaningful. Do you want area? On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote: > Dear Douglas, > > I come back to you concerning stats made from binary .mgh surface data > file: > > mri_segstats --i lh.fsaverage.sm10.mgh --seg

Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

-tkr2scanner gives the transform that takes "tkregister RAS" and converts it to scanner RAS. "tkregisterRAS" is the RAS system used by surfaces (it, a vertex xyz is in tkregisterRAS). See http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 11/10/2016 09:33 PM, Krieger, Donald N.

Re: [Freesurfer] recon all

This can also happen if the head is oriented in a strange way. This can happen with older patients that tend to tilt their head back. On 11/10/2016 08:27 PM, Bruce Fischl wrote: > Hi John > > it means that the talairach transform that was computed was extremely > unlikely and deemed to be

Re: [Freesurfer] CVS repository

This page should be more helpful for you. http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page -Zeke > I am trying to checkout the development version of Freesurfer from the CVS > repository. I need to build against VTK 7.1 instead of 5.6 for freeview > and am using

Re: [Freesurfer] differences between OS recon all output, longitudinal data

> Hi > > I am using recon-all in some longitudinal data on a ubuntu 16.04, and > using > the development version of freesurfer as I was told here, because the > other > current version doesnt work on ubuntu 16.04. > > The problem is that the first scans were probablly processed using >

Re: [Freesurfer] AAL atlas

Yes, mri_label2vol is the right command for this On 11/11/2016 12:20 PM, stella maris sanchez wrote: > Hi Doug, thanks for your response. > > I have one question more. I was reading the mail archive and I found a > few messages that talk about the mri_label2vol, vol2surf and surf2surf >

Re: [Freesurfer] FSL View in the virtual box version?

Hi Jeffrey I think this question is one for the FSL list, not for us. cheers Bruce On Fri, 11 Nov 2016, Jeffrey Crawford wrote: Hello there!   I currently use the virtualbox version of freesurfer on my windows and the CentOS 4 (32b) version on a linux computer. I noticed today that the

[Freesurfer] FSL View in the virtual box version?

Hello there! I currently use the virtualbox version of freesurfer on my windows and the CentOS 4 (32b) version on a linux computer. I noticed today that the Virtual box version does not seem to have fsl view. I found this link to a blog where this person has a virtual box that contained

Re: [Freesurfer] AAL atlas

Hi Doug, thanks for your response. I have one question more. I was reading the mail archive and I found a few messages that talk about the mri_label2vol, vol2surf and surf2surf commands. Specially the first one (mri_label2vol) the user said that with it he moved the AAL to the subject's space. Do

[Freesurfer] differences between OS recon all output, longitudinal data

Hi I am using recon-all in some longitudinal data on a ubuntu 16.04, and using the development version of freesurfer as I was told here, because the other current version doesnt work on ubuntu 16.04. The problem is that the first scans were probablly processed using virtualbox in a windows and

Re: [Freesurfer] Large Ventricles

Hi Tamara not really. The older versions didn't handle them that well, which I guess means you have to manually edit the asegs. cheers Bruce On Fri, 11 Nov 2016, Tamara Tavares wrote: Hello, I have a participant who has very large ventricles and as a result, there are substantial errors

[Freesurfer] ERROR: make_roi_paths did not complete successfully!

Hi Freesurfer experts, I was working on to conduct the local gyrification index analysis. I am getting the following error message when I used the option -localGI in recon-all. Improper assignment with rectangular empty

[Freesurfer] Large Ventricles

Hello, I have a participant who has very large ventricles and as a result, there are substantial errors in the aseg output. Looking at the mailing list, I see that the newest version of Freesurfer is suppose to be better at handling large ventricles; however, I want to be consistent with the

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Dear Douglas, I come back to you concerning stats made from binary .mgh surface data file: mri_segstats --i lh.fsaverage.sm10.mgh --seg lh.sign_clust.bin.mgh --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt In the output file « lh.bin.sum » all is considered as volume input/output as