Re: [Freesurfer] question about aseg.mgz

just visually. If we knew a way to automatically check it we would use that to correct it :) On Sat, 2 Jul 2016, Jasmin Alves wrote: Hi Bruce, Thank you for clarifying, this makes more sense, is there a way to check the subcortical segmentation?  Thanks! Jasmin  On Sat, Jul 2, 2016 at 7:28 PM

Re: [Freesurfer] question about aseg.mgz

Hi Bruce, Thank you for clarifying, this makes more sense, is there a way to check the subcortical segmentation? Thanks! Jasmin On Sat, Jul 2, 2016 at 7:28 PM, Bruce Fischl wrote: > Hi Jasmin > > the norm.mgz isn't a voxel labeling - it's an intensity volume. We > typically check the aseg.mgz

Re: [Freesurfer] question about aseg.mgz

Hi Jasmin the norm.mgz isn't a voxel labeling - it's an intensity volume. We typically check the aseg.mgz display *over* the norm.mgz to see if the labels make sense w.r.t. the intensities. cheers Bruce On Sat, 2 Jul 2016, Jasmin Alves wrote: Dear Freesurfer support, I noticed in previous

Re: [Freesurfer] Any updates on recon-all GPU support?

Hi Richard, Thanks anyway for taking a look. Despite a number of further tweaks to our cuda libraries, we have made no further progress with this. Any chance you could pass along your cuda binaries so that I can see whether they might just "work"? Very curious. -Derek

[Freesurfer] question about aseg.mgz

Dear Freesurfer support, I noticed in previous threads, people have inquired about how to check the quality of the aseg.mgz segmentation using the norm.mgz as a reference. When I did this, there were several mislabeled regions according to the norm.mgz ie. voxels labeled as white matter on the nor

Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

Hi Lars, I had the same problem. You can notice in your bvec file that there are some unusual blank spaces sometimes. Try to look at each space between two numbers and make sure it’s fine. You can also make sure about the number of entries by running wc -w on each of your bvec or bval file. Hop

Re: [Freesurfer] tksufer got the opposite direction of image

how do you know it is the right hemi and not the left? Also, we don't use or support tksurfer anymore. Try freeview instead cheers Bruce On Sun, 3 Jul 2016, 李琬 wrote: Dear all,   I've been trying to use "tksufer" to check the surface images according to the instruction of "Inspectio

[Freesurfer] Qdec-correction for multiple comparison

Hi Doug, I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison. In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend to correct the results of cortical

Re: [Freesurfer] Order of overlays

Yes, you can. If I remember correctly, you can goto view->configure overlay, then find the item to specify that you want the labels under the activation. On 6/29/16 5:22 AM, Reza Rajimehr wrote: Hi, In Tksurfer, we want to show functional activity map and borders of aparc on a surface. The

[Freesurfer] tksufer got the opposite direction of image

Dear all, I've been trying to use "tksufer" to check the surface images according to the instruction of "Inspection of Freesurfer Oupt". I could get the images, but the direction is opposite. Like if I typed "tksurfer fsaverage lh inflated ", but I got the right one. W

Re: [Freesurfer] controlling for total gray matter volume

Hi Clara, If I am understanding your question correctly, you don't need to control for brain volume when looking at thickness analyses. See quote below from this link: http://www.freesurfer.net/fswiki/eTIV "Note that this correction is only useful in situations where the structure scales with h

Re: [Freesurfer] cotrolling for total gray matter volume

Hi Clara I would use the stats from the long as they are most stable, and yes I believe you should control for total volume when looking at surface area. cheers Bruce On Thu, 30 Jun 2016, Clara Kühn wrote: Dear FreeSurfer experts, I would like to look at longitudinal thickness data and

[Freesurfer] cotrolling for total gray matter volume

Dear FreeSurfer experts, I would like to look at longitudinal thickness data and want to control for total gray matter volume. Should I use that information from the CROSS before anything has been registered and smoothed or from the LONG after they have been registered to the BASE? Also I was

[Freesurfer] controlling for total gray matter volume

Dear FreeSurfer experts, I would like to look at longitudinal thickness data and want to control for total gray matter volume. Should I use that information from the CROSS before anything has been registered and smoothed or from the LONG after they have been registered to the BASE? Also I was w

[Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

Hi, Trying to run trac-all -c dmric_file -prep, I get an error message stating that there are different numbers of entries in the bval and bvec files. I don't understand why, since both have the same number of rows (64). OS = Ubuntu 14.04.4 Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5