[Freesurfer] nifti1Read(): unsupported slice timing pattern 5 -- mri_convert fix?

Hi, I'm analyzing data from a collaborator who used SPM to generate some niftis, and freesurfer is unable to read these. I get the following error: nifti1Read(): unsupported slice timing pattern 5 Someone previously had

[Freesurfer] fsfast: using an empirically derived HRF with mkanalysis-sess

hi freesurfers, i would like to use an empirically derived HRF with mkanalysis-sess. i have derived the HRF i want [via an FIR model], but it's not obvious how i can use my custom HRF with mkanalysis-sess. one option, it seems, is to feed in my own regressors with the -taskreg flag and then not

Re: [Freesurfer] fsfast: using an empirically derived HRF with mkanalysis-sess

and one point of clarification: i only care about beta weights for each condition of interest, so i don't care that -taskreg would only run an F-test for significance maps and wouldn't give me t maps for each regressor of interest. thanks again, alex On Sun, Sep 14, 2014 at 1:55 PM, Alex Kell

[Freesurfer] reading writing surface files in python

hi freesurfers, i'm looking to read and write freesurfer surface files in python -- like MRIread.m MRIwrite.m but for surfaces and in python. i'm happy to write the code myself, but it seems like the kind of thing that has been done before and i don't want to reinvent the wheel if i don't have

[Freesurfer] segfault during rfx with mri_glmfit

hi freesurfers, i am running into a segfault whenever i try to use mri_glmfit to run a random effects analysis. (this is in the volume, not on the surface.) here's my call: mri_glmfit \ --y $ces_fpath \ --X $design_mat_fpath \ --C $c1_fpath \ --C $c2_fpath \ --C $c3_fpath \ --mask

Re: [Freesurfer] segfault during rfx with mri_glmfit

drop I'll take a look. doug On 05/07/2013 10:24 AM, Alex Kell wrote: hi freesurfers, i am running into a segfault whenever i try to use mri_glmfit to run a random effects analysis. (this is in the volume, not on the surface.) here's my call: mri_glmfit \ --y $ces_fpath

[Freesurfer] denominator of the t-test in fsfast?

freesurfers, i have a question about how t-tests are computed in fsfast. so t = ces/sqrt(cesvar), but how exactly is cesvar calculated? i thought it would be: cesvar = variance_of_residual *c*(X' * X)^-1*c' where X is the stim matrix and c is the contrast vector and ' denotes transpose

Re: [Freesurfer] Two questions: autocorrelation correction and vertex distance

Hi Doug, Thanks for the information about how FS whitens the data. Is there a way to temporally whiten data without running a GLM (i.e., without running selxavg3-sess)? Alex On Tue, Jan 22, 2013 at 9:58 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: On 01/19/2013 03:18 PM, Alex Kell

Re: [Freesurfer] Two questions: autocorrelation correction and vertex distance

Whoops, I just saw your response in your response. My bad -- please ignore. Alex On Fri, Jan 25, 2013 at 10:37 AM, Alex Kell alexk...@mit.edu wrote: Hi Doug, Thanks for the information about how FS whitens the data. Is there a way to temporally whiten data without running a GLM (i.e

[Freesurfer] Two questions: autocorrelation correction and vertex distance

Hi Freesurfers, I have two unrelated questions. 1. I want to pre-whiten some functional data without running a GLM on them (we're going to run the GLM in matlab). It looks like fsfast does autocorrelation correction as a part of the selxavg3-sess wrapper. I tried poking around on the wiki and

[Freesurfer] how is fsnr computed?

in the whole brain mask (i.e., gm and wm)? separately, random other question: what are the h.dat, h.nii.gz, and h-offset.nii.gz file/volumes? thanks in advance! alex kell ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] moving volumetric masks to surface labels within subject

to the orig.mgz's. alex On Fri, Aug 17, 2012 at 11:07 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Alex when you say it is in the native anatomical space can you elaborate? How did you create the mask? Bruce On Fri, 17 Aug 2012, Alex Kell wrote: hi freesurfers, i'm trying to move a volume

Re: [Freesurfer] moving volumetric masks to surface labels within subject

is in the right place (hit the compare button to flip back and forth). doug On 08/17/2012 11:02 AM, Alex Kell wrote: hi freesurfers, i'm trying to move a volume from a subject's native anatomical space to that subject's surface space, and i'm running into some difficulty. we have binary masks

Re: [Freesurfer] moving volumetric masks to surface labels within subject

), then it will try to read it as a surface and fail. To look at it in tksurfer, load it as an overlay, eg tksurfer subject lh inflated -overlay surf_name.mgz doug On 08/17/2012 02:26 PM, Alex Kell wrote: hi doug, i can't visualize it. when i try to use tksurfer (or even mris_info) i get the following

[Freesurfer] Smart concatenation in selxavg3-sess?

Hi Freesurfers, The selxavg3-sess's help and Freesurfer documentation say that selxavg3-sess creates a design matrix for each run, fits the glm for each run, and then combines the runs together to give summary data for the subject's whole session. Some of the fsfast 5 slides say it uses smart

[Freesurfer] Flags to align per-run motion-corrected functional volumes?

Hi Freesurfers, I am using preproc-sess in Freesurfer/Fsfast 5 with per-run motion correction (these subjects have a lot of between-run motion), and I want to analyze the volumes in each subject's individual space (I'd prefer native functional space, but I am happy to do it in each subject's

[Freesurfer] mri_vol2vol not downsampling when applying a morph and a rigid registration matrix

, Alex Kell Kanwisher Lab Manager ___ 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 person to whom it is addressed. If you believe