[Freesurfer] Processing Freesurfer thickness files in SPM for ANOVA

Dear Experts, Is it possible to process the FreeSurfer thickness files of T1-MRI data in SPM for ANOVA testing? Waiting for a precise reply. Thank you. Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical Syst

[Freesurfer] DODS/DOSS

Hi mailinglist, I have a question regarding DOSS/DODS. In the mailinglist I read that if you do a group analysis, you have to check for interaction between your continuous variable and categorical variable in DODS, and if there's no interaction, you can use DOSS. This however leaves a few qu

[Freesurfer] DOSS in FS 5.3 QDEC

Dear Experts, Hi, I have already done my data analysis having group as fixed factor and age as nuisance factor in QDEC FS 5.3. I also need to run it with DOSS. Would you please advise how to run the same analysis with DOSS from terminal and if it is possible to look at the results in QDEC Display a

Re: [Freesurfer] T1 data on 1yr-old subjects

Just wondering if anyone has attempted to process T1-mpr data for a 1yr-old subject or if this is possible with FS. Our data is of reasonable spatial resolution (1mm isotropic), however the flip in gm/wm intensities is still occurring at this age. I presume these data would also be problematic d

Re: [Freesurfer] T1 data on 1yr-old subjects

Hi Jim, Using the current FS recon pipeline with your data is indeed not feasible. We are in the process of creating another pipeline geared towards that age range. Lilla On Thu, 10 Oct 2013, Alexopoulos, Dimitrios wrote: > Just wondering if anyone has attempted to process T1-mpr data for a

[Freesurfer] QDEC issues

Dear FreeSurfers, While running analyses in QDEC, it only allows me to select one continuous variable at a time instead of the usual two –so running analyses in QDEC is extremely limited. I have used QDEC before, and this is a new issue. Has anyone else encountered this problem? Thanks, Prapt

Re: [Freesurfer] New Atlas Creation

Hi Liv, What you are asking for is quite ambitious. As you have noticed, most of the image processing tools fail on the infant data sets as they are usually of much lower SNR, they have changing GM/WM contarst, higher noise and a much smaller anatomy. So it is not only a question of creating

[Freesurfer] Gender as a nuisance factor

Dear Freesurfer experts, I'm performing a group analysis in Qdec correlating a biological marker and the CTh, and I would like to covariate the gender and age effect, i.e. ideally get rid of both effects and isolate the biological marker effect. So, I understand that the age effect is (at least

Re: [Freesurfer] trac-all -tensor error

Hi Jenn - Can you please send the scripts/trac-all.log and your tracula.cfg? I don't have permission to access them. Thanks, a.y On Mon, 7 Oct 2013, Jennifer Segawa wrote: Hello! I'm having problems running the trac-all -tensor step.  dtifit appears to run correctly; the problem seems to be

Re: [Freesurfer] Problem with DWI and structural coregistration

Do the surfaces from recon-all look ok? Bbregister uses the surface to register the DWI to the structural. On Tue, 8 Oct 2013, std...@virgilio.it wrote: Hi list, I'm performing trac-all but I'm noting some coregistration error. I have try to run separately each step. When -masks was finishe

Re: [Freesurfer] TRACULA question

Hi Lars - Just like you have to do before you run any freesurfer programs, you'll have to run a script that comes with freesurfer and sets up all the necessary environment variables. See: http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration Hope this helps, a.y PS: Please send e

Re: [Freesurfer] brain.mgz and control.dat attached

how do you know that they have not taken effect? The log is cumulative, so if you ran once with 23 then added more that's what you would see On Tue, 8 Oct 2013, Francesco Siciliano wrote: > My recon-all log says that 53 control points were read. However, the same > control points still have not

[Freesurfer] mri_glmfit-sim without talairach.xfm, orig.mgz and aparc

Hi Freesurfer experts, I am running a group analysis of functional data on a custom template/average subject for which I do not have a talairach.xfm file, an orig.mgz nor aparc data (it is a primate dataset). I ran into some error messages when trying to use mri_glmfit-sim. 1) I get an error messa

Re: [Freesurfer] Tracula

- Original Message - From: ebell...@uwm.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:14:06 PM Subject: Tracula Hello, I had a question regarding batch processing in trac all. When you batch process and put in multiple subjects in your subject list in your

Re: [Freesurfer] FSL masks applied to Freesurfer surfaces?

Hi, Douglas Just to check if I correctly understood you, when you said "mri_label2vol can go in both directions" did you mean it can also create a label from a volume or a binary mask? If so, could you please explain how? I read documentation on wiki and help from the command itself and could not s

Re: [Freesurfer] Tracula

Hi Emily - The first version of tracula was in freesurfer 5.1. However, I would *highly* recommend using the newer version of tracula, now in 5.3, as it has improvements in both performance and speed. The processing in trac-all is supposed to happen in parallel for each of the subjects include

Re: [Freesurfer] Tracula

Hello Anastasia, Is it okay to run my DTI data on Freesurfer 5.3 when all my recon-all scripts for the structural data were run in Freesurfer 5.0? And I can download the tracula program straight from the tracula Wiki? And it will work for Linux? Thanks so much! Emily - Original Message -

Re: [Freesurfer] Tracula

Hi Emily - You can't download tracula separately from the rest of freesurfer, you'll have to download freesurfer 5.3. It works on any platform that the rest of freesurfer works. The one thing that tracula uses from the freesurfer recon is the aparc+aseg.mgz. I have never tried running tracula

[Freesurfer] using multiple functional ROIs in fcseed-config

Hi, I know that we can have multiple segments (segIDs) in fcseed-config. Is there anyway to use multiple ROIs (functionally defined) in fcseed-config? If no, what is the alternative? Is there anyway to average the .dat output files generated by separate fcseed commands? Is it OK to manuall