Re: [Freesurfer] Surface area in aparc stats

Hi Zhuangming by default we use the interior ("?h.white") surface for computing area, but you can specify the pial to mris_anatomical_stats if you want instead. cheers Bruce On Fri, 7 Mar 2014, 沈庄明 wrote: Hi Doug,    Sorry for forgetting to post to the list. The figure attached to this ema

Re: [Freesurfer] Surface area in aparc stats

By default, just the interior, though it is possible to get measures from the exterior doug On 3/7/14 1:09 AM, 沈庄明 wrote: Hi Doug,     Sorry for forgetting to post to the list. The figure attached to this email could illustrate my qu

Re: [Freesurfer] Longitudinal analysis - the effect of FS release?

Hi Sasa, no time frame for 6.0 release as far as I know. since you only processed the first time point, I'd recommend to re-process everything with 5.3. Never process one time point with one version and the other with a different version! Theoretically you could run the second time point with

Re: [Freesurfer] Convert expert segmentation to FreeSurfer space

I have a expert segmentation and i want to transform this file to GCA space. However, i first need to have the segmentation in conformed space cause the segmentation is 256x256x278 1mm and has a different origin. I tried the following: >> mri_convert -rl orig.mgz -rt nearest mySeg.nii.gz mySeg_con

[Freesurfer] Group Analysis Age slopes

Hi Doug, I ran a group analysis comparing a trait between two groups (Diseased vs Controls) with one continuous variable (age), with the following design matrices [1 -1 0 0] and [0 0 1 -1]. When I loaded the significance map and the descriptor file, the age slope of the trait in Controls was posit

Re: [Freesurfer] OpenMP and non-OpenMP output is different at mri_ca_register

Hello Chris, Extremely coincidentally I just recently started researching subtle variations between recon-all when run on OSX vs Linux, and just yesterday found the EXACT same thing. The OSX build does not support openmp whereas the Linux build does and I get very minor but detectable differen

Re: [Freesurfer] OpenMP and non-OpenMP output is different at mri_ca_register

Do you get the same difference if you run an open MP version but force it to use only one thread? doug On 03/07/2014 03:52 PM, Z K wrote: > Hello Chris, > > Extremely coincidentally I just recently started researching subtle > variations between recon-all when run on OSX vs Linux, and just > ye

Re: [Freesurfer] Group Analysis Age slopes

Was the difference in the age slopes significant? Ie, and interaction between age and group. If so, then you have to proceed with caution (at least one statistician told me not to proceed at at:) because the difference in the intercepts between the two groups will depend on age making it very

Re: [Freesurfer] Convert expert segmentation to FreeSurfer space

none of our tools use the nifti origin (and we don't have a way to set it). Do you need it for something else? FSL or SPM may have tools that can set it On 03/07/2014 02:40 PM, Oualid Benkarim wrote: > I have a expert segmentation and i want to transform this file to GCA > space. However, i fi

Re: [Freesurfer] Large areas of white matter ignored, even with control points

Hi Andrea, You can use the contour tool in the voxel edit mode to quickly and roughly fill in wm. Use the tool with the wm.mgz selected in the volume layer list but set the brainmask (or T1) as the reference. Set brush value to 255, and then do crtl+alt+leftbutton while dragging the mouse to a

Re: [Freesurfer] tkmedit edit voxel tcl script

Hi Pfannmoe, I don't believe it is possible to edit a voxel via tcl scripts. If so the command would be listed on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMeditScripting -Louis On Wed, 5 Mar 2014, Joerg Pfannmoeller wrote: > Hello, > > if I have sel

Re: [Freesurfer] cannot sign white matter area by control point and white matter edit

Hi Rujing, You might try drawing in the wm thicker than it is already. Also, check there are no disconnects between the wm voxels in the wm.mgz. -Louis On Tue, 4 Mar 2014, charujing123 wrote: Hi all. In troubleshooting, I want to sign some area as white matter by control point and wm edit.

Re: [Freesurfer] OpenMP and non-OpenMP output is different at mri_ca_register

The openmp version did use only one thread. I used the vtk build in the tarball of precompiled support libraries on the Freesurfer ftp site. I tried building vtk 5.8 and still had the same issues. It is not a big deal because this exercise was more to do with the computational components rather

Re: [Freesurfer] Group comparisons

Thanks Doug. I wasn't clear in my DOSS question, I meant to ask why are categoricalXcontinuous interactions (e.g. such as the one probed by the contrast "Does the thickness-age correlation differ between group A and B?") still created in DOSS analyses, when by definition DOSS imposes that (e.g.) th

Re: [Freesurfer] Group comparisons

On 03/07/2014 06:45 PM, Tudor Popescu wrote: > Thanks Doug. I wasn't clear in my DOSS question, I meant to ask why > are categoricalXcontinuous interactions (e.g. such as the one probed > by the contrast "Does the thickness-age correlation differ between > group A and B?") still created in DOSS

Re: [Freesurfer] Group Analysis Age slopes

Hi Doug, Thanks for your reply. Yes there were areas of significant difference reported in the age slopes maps, after the mri_glmfit command was run. However, I haven't checked to see yet whether there are surviving clusters after correction for multiple comparisons. I see, yes that definitely mak