[Freesurfer] load_nifti.m - empty header

Dear Freesurfers, I am struggling with a very basic step at the very beginning of my processing pipeline. This is what I've done: registered BOLD to anatomical data using bbregister, results checked with tkregister2 - all seems fine. Then I want to project BOLD data to the surfaces using mri_vol2s

Re: [Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal

Hi Yoon - The update is here: http://freesurfer.net/fswiki/Tracula#Updates There will also be a new freesurfer release in the next couple of months, but I don't anticipate making more changes to longitudinal tracula before that, so this should be the same as in the future 5.4 version.

Re: [Freesurfer] Tracula : Path not entirely in the white matter

Hi Emily - Yes, this is fine. I just meant that it shouldn't look like a single line. a.y On Thu, 24 Jul 2014, ebell...@uwm.edu wrote: > Hi Anastasia, > > Just to be clear, is this what you mean by a more diffuse volumetric > distribution. Here is a snapshot of the right inferior longitudinal

Re: [Freesurfer] dmri_trk2trk issue

Hi Tommi - The input reference volume (--inref) should be in the same space as the input .trk file, i.e., your individual's diffusion space. It seems that you're using the individual's T1 space instead? a.y On Fri, 25 Jul 2014, r...@nmr.mgh.harvard.edu wrote: > Hi, > > I am attempting to morp

Re: [Freesurfer] Diffusion analysis qs

Hi Rotem - It's hard to tell without zooming into some key areas, like corpus callosum and cingulum for example. The colors look ok (red and green, respectively) but it's hard to see how the lines look. a.y On Mon, 28 Jul 2014, Rotem Saar wrote: Dear Anastasia, I followed your suggestion:

Re: [Freesurfer] trac-all -prep problem

Hi Shantanu - It's stuck trying to initialize one of the tracts. You can check which tract it is, and then check the data to see if there's something wrong that would affect that particular tract (for example, if part of the brain that this tract goes through is cut off in the mask). a.y On F

Re: [Freesurfer] Tracula Missing Statistics

Hi Emily - The weighted average is the most reliable in practice, and it is also the proper statistical definition of mean (expected) value. It weighs the value of FA etc at each voxel with the probability of the tract going through that voxel. The cases that are missing stats may need to be r

Re: [Freesurfer] DTI Statistics

Weighted average recommended, see my previous email. On Tue, 5 Aug 2014, Emily Louise Belleau wrote: ​Hello all, I was just wondering if in publications/papers it is more common to report the average FA statistics, the weighted average statistics, or the center statistics (the average of

Re: [Freesurfer] tracula longitudinal

Hi Kevin - The names should be the cross-sectional IDs, i.e., without the .long.basename suffix. Note that the version of longitudinal tracula originally included in freesurfer 5.3 uses the cross-sectional aparc+aseg from freesurfer, whereas the latest updated version (recommended) uses the

Re: [Freesurfer] Steps for Longitudinal trac-all

Hi Yoon - Sorry, the config file is necessary for anything that doesn't use default settings for trac-all, and that includes running it in longitudinal mode. What kind of cluster do you have? I'm working on making running trac-all easier on clusters that are not currently supported, as part of

[Freesurfer] Cortical thickness via freesurfer

Dear all. I have a question concerning the estimation of cortical thickness in freesurfer. My overall goal is the comparison of a patient and matched control group with VBM and cortical thickness. My first try was the recon-all with masked MP2RAGE UNI-Images. Unfortunately it executed with error

[Freesurfer] Checking in about FLAIR Registration Problem

Good morning, I wrote several weeks ago about a bbregister problem that we’ve encountered (I’ve attached the original email below). I’d like to check back in about the status of the patch that was being developed. Thank you for your time and assistance! Marta Zamroziewicz MD/PhD Candidate Deci

[Freesurfer] None region label number (color) not in FreeSurferColorLUT.txt

I am trying to make a custom label color scheme and wanted to change the None. Region but the FreeSurferColorLUT.txt only lists the unknown region (0) rather than None. I replaced the unknown region label name with None. to no avail like this. Is the None. region a different label number and c

[Freesurfer] mismatch between FWHM data in fwhm.dat & specified smoothing kernel

Dear Surfers, While running a mri_glmfit-sim (monte carlo simulation) for roi analyses generated using mri_glmfit, I encountered the following error code: ERROR: cannot find /Applications/MRI/freesurfer_5.30_x86_64/average/mult-comp-cor/fsaverage/lh/cortex/fwhm31/abs/th13/mc-z.csd I checked the

Re: [Freesurfer] mismatch between FWHM data in fwhm.dat & specified smoothing kernel

The fwhm.dat is computed from your data and reflects all the spatial correlation in your data, not just the smoothing you imposed. It is usually the case that there is some inherent smoothness and so the total smoothness is more than what you apply. This may be due to an outlier or just that

[Freesurfer] FreeSurfer platform/performance questions

Hello FreeSurfer mailing list, First off, I am not a scientist and I have no experience running FreeSurfer. I have installed it, and seen it run, but that's it. I work for the IT department in the Beckman Institute, part of the University of Illinois. We support a computer lab here called the "

Re: [Freesurfer] FreeSurfer platform/performance questions

Nevermind question 2, I was just shown this from the FreeSurfer website: Important Note! When processing a group of subjects for your study, it is essential to process all your subjects with the same version of freesurfer, on the same OS platform and vendor, and for safety, even the same version

[Freesurfer] download link broken?

Hi, Trying to download freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz . Link gives 550 error and terminal error is: No such directory 'pub/dist/freesurfer/5.3.0' Please ad

Re: [Freesurfer] download link broken?

Hi Wynn - There is a scheduled outage of the Martinos Center storage cluster today and tomorrow. a.y On Mon, 18 Aug 2014, Wynn Legon wrote: Hi,Trying to download freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz. Link gives 550 error and terminal error is: No such directory 'pub/dis

[Freesurfer] no improvement for recon-all result after edits

Hi Freesurfer experts, I was doing some manual editing on our subjects which are patients with lesions. I managed to correct most of them, however, 4 subjects have the same problem that I can't fix no matter what edits I tried. So, the 4 subjects, they all have the same problem, which is: frontal