[Freesurfer] Correcting for multiple comparisons using clustering and external data

Dear free surfer experts, I was wondering if someone could give me some general guidance on controlling for multiple comparisons using clustering and FDR. This the situation. I completed an analysis of functional data by first dividing the cortex into parcellations using the icosahedron 5 

[Freesurfer] mris_make_surfaces in longitudinal stream - explanation of parameters

Dear experts, I am trying to understand how the pial and white surfaces are generated in longitudinal stream using information from the reconstructed base template (freeSurfer development version). In longitudinal stream, apart from the -orig, -orig_pial and -orig_white there are also

Re: [Freesurfer] Getting combined bvals/bvecs

Hi Anatasia, Thank you for your reply, I'm sorry for responding so later, I have been trying a few different things in order to get tracula to work. I did what you suggested and compiled the bvals and bvecs into one file, in the same order as the images. This got me further, but the trac-all

Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

Thank you very much Doug. You are so awsome :)   Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419     Sent: Monday, November 14, 2016 at

Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

Hi, I just found a bug in mri_glmfit-sim in regards to GRF on volume-based data. I put a fixed version at the same location. Please use the new version On 11/04/2016 10:25 AM, Douglas N Greve wrote: > oops, sorry, > > download these files > >

Re: [Freesurfer] nuisance dichotomous variables

That is usually not the way you want to handle dichotomous variables. For example, if you use Male=1 and Female=2, you are implying that Females have a factor of two greater thickness (or whatever) relative to males. Maybe it works if the factor only has two levels. But why not set it up as a

Re: [Freesurfer] mri_convert issue

Thanks a lot for your reply. Also, my apologies about giving you a hard time. Again, thanks for the reply. Best regards, DaWoon > 2016. 11. 15. 오전 12:54, Douglas N Greve 작성: > > Hi, we do not support a tool to do this, sorry. I think you can do it in > FSL with

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

You can use fscalc to multiply the pet and area maps,eg fscalc pet.lh.nii.gz mul lh.white.avg.area.mgh -o weighted.nii.gz On 11/14/2016 11:53 AM, Matthieu Vanhoutte wrote: > Ok I will try both. > > Best, > Matthieu > > 2016-11-14 17:50 GMT+01:00 Douglas N Greve

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

If you did not smooth them explicitly, then there will be only a little vertex-like smoothing. As to which weighting is better, I'm not sure. If the ROI is big, it probably won't make much difference. Can you try both and see? On 11/14/2016 11:39 AM, Matthieu Vanhoutte wrote: > Dear Douglas,

Re: [Freesurfer] Longitudinal surface analysis of PET data

Thank you ! Best regards, Matthieu 2016-11-14 17:48 GMT+01:00 Douglas N Greve : > Rigid. > > > On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote: > > Still using rigid-body registration on --long subject directory ? > > > > Or is affine registration in this case

Re: [Freesurfer] Longitudinal surface analysis of PET data

Rigid. On 11/14/2016 11:43 AM, Matthieu Vanhoutte wrote: > Still using rigid-body registration on --long subject directory ? > > Or is affine registration in this case needed ? > > Best regards, > Matthieu > > 2016-11-14 17:12 GMT+01:00 Douglas N Greve

Re: [Freesurfer] complement of a label

or do it in matlab. Should only be 4-5 lines of matlab code On Mon, 14 Nov 2016, Douglas N Greve wrote: > I don't know of a single way to do it. I would probably use > mri_label2label to output a mask of the label, then use mri_binarize to > invert it, then mri_cor2label to convert it back to a

Re: [Freesurfer] Longitudinal surface analysis of PET data

Still using rigid-body registration on --long subject directory ? Or is affine registration in this case needed ? Best regards, Matthieu 2016-11-14 17:12 GMT+01:00 Douglas N Greve : > I would just register the pet to the closest (in time) anatomical > > > On

Re: [Freesurfer] Surface-Edges

what do you mean the edges? On 11/14/2016 11:18 AM, Foteini Protopapa wrote: > Dear FS experts, > > I have a volume with specific clusters and I project it to a surface > using mri_vol2surf. How can I determine the edges of my clusters now? > > Thanks in advance, > Foteini. > > >

[Freesurfer] Surface-Edges

Dear FS experts, I have a volume with specific clusters and I project it to a surface using mri_vol2surf. How can I determine the edges of my clusters now? Thanks in advance, Foteini. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Longitudinal surface analysis of PET data

I would just register the pet to the closest (in time) anatomical On 11/14/2016 07:20 AM, Matthieu Vanhoutte wrote: > Dear Freesurfer's experts, > > I come back to you concerning questions of registrations. > > Since during the longitudinal process each --long subject directory > has been

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

Good question. I'm not sure as there could be reasons to do either. I guess if you are not smoothing your data, then weighting by area would be the most appropriate doug On 11/11/2016 05:41 PM, Matthieu Vanhoutte wrote: > > Is it better to compute mean to weight by number of vertices or >

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

Hi Elijah, can you repost with previous correspondence included? We get a lot of emails here and can't keep track of each person's issue. thanks! doug On 11/11/2016 08:06 PM, Elijah Mak wrote: > Hi, > > A bit more info: the stack of thickness maps consists of >

Re: [Freesurfer] complement of a label

I don't know of a single way to do it. I would probably use mri_label2label to output a mask of the label, then use mri_binarize to invert it, then mri_cor2label to convert it back to a label On 11/14/2016 10:53 AM, Eryilmaz, H. Hamdi wrote: > Dear FreeSurfers, > > I was wondering if there is

Re: [Freesurfer] mri_convert issue

Hi, we do not support a tool to do this, sorry. I think you can do it in FSL with fslswapdim. Try contacting the FSL list On 11/14/2016 07:52 AM, DaWoon Heo wrote: > Dear Freesurfer experts, > > I would like to use the ‘mir_convert --out_orientation LAS’ to change the > orientation of my data

[Freesurfer] complement of a label

Dear FreeSurfers, I was wondering if there is a standardized way to construct a label that is the complement of a regional label on freesurfer. For example, I have a customized DLPFC label and would like to create another label that encompasses the entire cortex except that DLPFC region.

[Freesurfer] Invalid FreeSurfer license key problem

Hi, Anyone has solved a similar problem with 'Invalid FreeSurfer license key'? I have just got a license though email, and put the four-line code in a file named license.txt. Now the file is in the folder where I installed freesurfer. It should work well but it didn't. When I used tksurfer,

[Freesurfer] mri_convert issue

Dear Freesurfer experts, I would like to use the ‘mir_convert --out_orientation LAS’ to change the orientation of my data (i.e. fMRI T1 data). From several materials, I could find it is not a good idea to change the orientation. However, to improve the efficacy of ‘bet’, it seems converting the

Re: [Freesurfer] Longitudinal surface analysis of PET data

Dear Freesurfer's experts, I come back to you concerning questions of registrations. Since during the longitudinal process each --long subject directory has been registered onto the common --base template, shouldn't I: 1) Register PET data onto the subject cross-sectional directory (native

Re: [Freesurfer] nuisance dichotomous variables

Hi Prof. Greve, Thanks for the response and sorry for the confusion. I mean can we use dichotomous variables in the "Nuisance Factors" box of qdec? i.e., if we don't explicitly define them as categorical variables. I was thinking that if it's a GLM then it should be ok? We want to do this