[Freesurfer] Application of Default Surface Based Registration to Surfaces Other than the Sphere

Hi, I am wondering if there is a way to apply the default surface based registration that is done during recon-all to surfaces other than the sphere so that the nodes are all lined up? I am wanting to have registered white matter surfaces that I can map data from the volume to the surface to a

Re: [Freesurfer] Covariates in qdec

And for the comparison to be appropriate, you further have to make sure that you are using the exact same main and interaction terms in SPSS as are being used in QDEC. The mere presence of interaction terms in a model can have big effects on the significance (or lack thereof) of the main effects.

[Freesurfer] continue longitudinal processing...

Hi: I was processing a longitudinal processing using a command line like: recon-all -base -tp -tp ... -all but it couldn't finished because the power cut produced by a 8.8 magnitude earthquake here in Chile... How can I continue the processing without starting again from the beginning ?...

Re: [Freesurfer] mri_convert dicom conversion

Try creating a file with the list of files that should be converted, then run mri_convert with --sdcmlist file-with-list If that does not work, you can always just copy the files to a new directory. doug Satrajit Ghosh wrote: > hi, > > mri_convert TrioTim/123456-10-1.dcm test.nii.gz > > wil

[Freesurfer] mri_convert dicom conversion

hi, mri_convert TrioTim/123456-10-1.dcm test.nii.gz will scan all files in the dicom directory to get at series 10. in the above scenario, i know that the files corresponding to the run are 123456-10-*.dcm. is there a way to leverage this information, so that it does not scan the entire directory

Re: [Freesurfer] Optseq2 - Incorporate sequential order of trials as a factor

Optseq2 does not have the ability to change the identity of the stimuli during the run. doug Gaber, Tilman wrote: > Thank you for your quick response. Initially I had the same idea. > Unfortunately, this easy solution does not work. All trials are successor of > the previous and predecessor o

Re: [Freesurfer] ICV Error fs 4.3.1

It's hard to tell from the coronal, but it looks ok. The problem is more visible in the sagittal. doug Jeff Sadino wrote: > Hello Doug, > > I loaded up the tkregister2 program and I think I see some poor > transformations. I've never really used it before though. Am I just > looking at wheth

Re: [Freesurfer] ROI extraction based on t-values

If you use mri_surfcluster, it will output an annotation of the clusters. You can then use mris_anatomical_stats to compute the mean value inside those clusters. doug Cindy Eckart wrote: > Dear FreeSurfers, > > is there an easy way to extract the mean cortical thickness of clusters > according

Re: [Freesurfer] Covariates in qdec

Depends on some of the details. Is spss demeaning the age? If so, are you passing qdec demeaned ages? It can also be that it shows up better in the ROI analysis (ROI analyses are often more powerful than map-based). doug Dankner, Nathan (NIH/NIMH) [F] wrote: > Hi all, > > I've covaried age in a

Re: [Freesurfer] design matrix problem in qdec

The last column in the matrix is all 0s. This means that there are no members of that group (PTSDPTSD-diagnostikKG). doug =?iso-8859-1?q?=22br=f...@nmr.mgh.harvard.edu wrote: > Hi to All, > > I have come across a problem using qdec, specified below. What I am trying to > do is to look for an int

[Freesurfer] Covariates in qdec

Hi all, I've covaried age in a group difference analyses on cortical thickness data both in qdec for vertex-based and in spss for the gyral-based data. For the vertex-based data, covarying age has almost no effect, and if anything intensifies the group differences. However, when run in qdec,

[Freesurfer] a question about FS longitudinal stream

Hi, there, I have a question about FS longitudinal stream, I have data from two time points which have been processed by FreeSurfer cross-sectional stream. I also built the base template using recon-all -base command, everything looks fine. When I ran the longitudinal stream, one of them stop

[Freesurfer] conitnue longitudinal processing...

Hi: I was processing a longitudinal processing (previous the 8.8 earthquake) using a command line like: recon-all -base -tp -tp ... -all but it couldn't finished because the power cut... How can I continue the processing without starting again from the beginning ?... Sincerely, Gonzalo

[Freesurfer] ROI extraction based on t-values

Dear FreeSurfers, is there an easy way to extract the mean cortical thickness of clusters according to a predefined t-value threshold? I performed a cortical thickness analysis between 3 groups and found some clusters where the groups differed significantly. Now, I would like to extract the mea

[Freesurfer] design matrix problem in qdec

Hi to All, I have come across a problem using qdec, specified below. What I am trying to do is to look for an interaction between two discrete variables (diagnostik and PTSD). It is my understanding that this appears to be a common problem. However, is there a way around it, such as conceptuali