[Freesurfer] Qdec Analysis Interpretation

Dear Freesurfers, in my qdec analysis I want to compare my patients group with a control group. The analysis should be corrected for age effects, so I used group as discrete factor and age as covariate. If I choose „Does the average thickness differ between the two groups“, how can I

[Freesurfer] within subject regression analysis and qdec

Hi, I'm still trying to figure out how to run a regression analysis using functional data. I found the information in using qdec, however, the example uses a between subject design (with age/gender) and looks at thickness measures. I tried creating a qdec.table.dat, but I am unsure how to do

[Freesurfer] brainmask/wm edits

Hi, I have a similar questionto the one listed below. After I edit brainmask.mgz and wm.mgz, my understanding was that I could run autorecon2-wm and would not have to run autorecon2-pial because -wm will run everything else through the end of -autorecon2. However, if brainmask.mgz is run at

Re: [Freesurfer] CentOS 5.1 and freesurfer and tksurfer

Dear FS experts, I am using CentOS 5.4. When I run tkmedit, the data looks fine. In tksurfer, it just appears as a sliver of surface without an error message. In console, it sticks on reading vertex. Somebody said this could be resolved by simply removing the package xserver-xgl. How can I do

[Freesurfer] w file conversion

Hi, Is it possible to convert a .w file to another format? Thanks, Yigal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the

Re: [Freesurfer] w file conversion

sure, mris_convert will do this, or you can load it into matlab and do what you want with it. cheers Bruce On Thu, 11 Mar 2010, Yigal Agam wrote: Hi, Is it possible to convert a .w file to another format? Thanks, Yigal ___ Freesurfer mailing

Re: [Freesurfer] brainmask/wm edits

Hi Helen, That's a good question. You don't have to start at autorecon1, however. When you run -autorecon2-wm or -autorecon2-pial one of the first steps is: mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz which is changing the brain.finalsurfs.mgz to take into account the changes

Re: [Freesurfer] Qdec Analysis Interpretation

You have done the right thing, but you need to know a little more. When QDEC says mean thickness it really means the thickness at age=0, so it is extrapolating the results back to age=0. Since you have a covariate and you are using DODS, you have to specify an age at which to do the test (you

Re: [Freesurfer] within subject regression analysis and qdec

It looks like you have 1 discrete variable with two levels and three covariates. Three is too many for qdec, so you'll have to set up your own FSGD. See the wiki for how to set up an FSGD. There are examples there for many different designs. doug Katie Bettencourt wrote: Hi, I'm still

[Freesurfer] downsampling 4D volume

Hi, I am trying to downsample a 4D volume using mri_convert. However, it seems to be killing the 4 dimension. For example, if I do mri_convert -voxsize 4 4 4 tmp.mgz tmp444.mgz The original volume which is 256 x 256 x 256 x 120 becomes 64 x 64 x 64. Thanks, Thomas

Re: [Freesurfer] downsampling 4D volume

This is a bug in the released version of FS. Our development version is fixed. I've put a version here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert ythomas wrote: Hi, I am trying to downsample a 4D volume using mri_convert. However, it seems to be killing the

Re: [Freesurfer] bbregister

It depends on why it failed, which is usually for one of two reasons. The first is that the initialization failed. You can check this by saving the initial registration by passing --init-reg-out init.reg.dat, then viewing this reg with tkregister2. If this is more than 5 mm or 5 deg off, then

Re: [Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgz

Liang, mri_annotation2label will separate all the ROIs in the ?h.aparc.a2009s.annot - is this what you need? I'm not sure what you mean by mask image based on this image using 1, 2. You can merge or split labels as well. To display aparc.a2009s+aseg.mgz in tkmedit, you can do: tkmedit subjid

Re: [Freesurfer] modification made to longitudinal results

Derin OK, Allison discovered it in the depth of recon-all :-) The control points are copied from the cross sectional by default (and should be edited there). There is an optional flag to get them from the base, but that has never been really tested. It only makes sense if there is very little

Re: [Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgz

Hi Allison, Thanks. I have used the command line below to separately create many label files, each of which include vertex number and XYZ coordinates. mri_annotation2label --subject BNC006 --hemi lh --labelbase aparc.a2009 Sorry for not declaring my intention previously. What I actually want

[Freesurfer] problem on recon-all

Hi all, When we do recon-all, we usually do autorecon1, autorecon2, and autorecon3 in sequence. But now suppose I have already have a very good skull-stripped subject. I mean I don't need to do skull-stripping with freesurfer. But I want to get greymatter and white matter, which are generated