[Freesurfer] How to threshold an input mutli-volume?

Hi, all. Can mri_threshold threshold an input mutli-volume file? With a seven volumes NIFTI file, all voxels other than in the first volume are set to zero. In addition, the help for mri_threshold options is very limited. There is nothing about the options. Usage: mri_threshold [options] in vol

Re: [Freesurfer] make_average_subject error about limit

Hi, I copied the default average subject from $FREESURFER_HOME/subjects dir to my analysis dir. Then, I make a FSGD file and some contrast matrices and put them into my analysis dir. After that, I start to run group analysis. But, when I type the following commands: mris_preproc

[Freesurfer] Re: Melodic results on Freesurfer average subject

great, thanks Christian. I think Doug has some tools that can be used for this. cheers Bruce On Tue, 7 Jul 2009, Christian F. Beckmann wrote: Hi Bruce Martina, Yes, the easiest is to run melodic temporal concatenation on data pre- processed and warped into a common space by freesurfer.

[Freesurfer] WM-hypointensities

Hi all, I don't kown what is WM-hypointensities Is it a volume? I suppose this because WM-hypointensities is in the aseg.stats. thanks Anita di Iasio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] WM-hypointensities

they are voxels with abnormal appearing white matter On Tue, 7 Jul 2009, Anita di Iasio wrote: Hi all, I don't kown what is WM-hypointensities Is it a volume? I suppose this because WM-hypointensities is in the aseg.stats. thanks Anita di Iasio

[Freesurfer] ROI

Dear Experts: I am trying to create a cortical mask of M1 (Precentral cortex) for each hemisphere to use it for tractography in FSL. First I register the subject to the space I am using (Talairach or MNI), then I save the label from tksurfer and then use mri_vol2roi to create the ROI which is all

Re: [Freesurfer] ROI

Hi Natalia, at what stage is it misaligned? Note that we do everything in native space, so unless you apply a transform to the ROI it will not be in tal coords. Also, you might consider using our estimate of M1 from the Zilles/Amunts data instead of drawing it (e.g. lh.BA4a.label). cheers,

Re: [Freesurfer] Gaussian random field correction

I've actually implemented that already, but I have not been satisfied with how well the grf results match the simulations. doug jorge luis wrote: There is a very good implementation of surface-based Gaussian Random Field theory (GRF) correction from Keith J. Worsley at:

Re: [Freesurfer] make_average_subject error about limit

Is there a space between -- and hemi? caching is just a way to speed some analyses by pre-smoothing and sampling to the standard space. doug Feng-Xian wrote: Hi, I copied the default average subject from $FREESURFER_HOME/subjects dir to my analysis dir. Then, I make a FSGD file and

Re: [Freesurfer] Re: Melodic results on Freesurfer average subject

Use the registration matrix found in $FREESURFER_HOME/average/mni152.register.dat doug Bruce Fischl wrote: great, thanks Christian. I think Doug has some tools that can be used for this. cheers Bruce On Tue, 7 Jul 2009, Christian F. Beckmann wrote: Hi Bruce Martina, Yes, the easiest is

Re: [Freesurfer] ROI

Sounds like there are a lot of places where something could have gone wrong. Have you checked the output each step of the way or just the final result? doug Natalia Sanchez wrote: Dear Experts: I am trying to create a cortical mask of M1 (Precentral cortex) for each hemisphere to use it for

[Freesurfer] citation for appropriateness of using freesurfer with children

Hello- I am using Freesurfer to obtain cortical parcellations for both children (aged 8-11 years) and adults. A reviewer asked for evidence that the parcellation works equally well in children and adults. Has this been tested empirically and published anywhere? I found a post saying not too

Re: [Freesurfer] How to Fitting Tensors in dt_recon?

you can apply it to the raw data. The tensor is just assembled from the regression coefficients (betas) in the standard way, ie, a design matrix is constructed with 7 columns. Each column consists of [gx gy gz gx*gy gx*gz gy*gz 1], and the 1st 6 coefficients for the tensor. doug 李猛 wrote:

Re: [Freesurfer] citation for appropriateness of using freesurfer with children

Hi Anthony, Peng Yu had a relatively recent IEEE TMI paper in which we parcellated neonates. The citation (and paper) are on the wiki. cheers, Bruce On Tue, 7 Jul 2009, Anthony Dick wrote: Hello- I am using Freesurfer to obtain cortical parcellations for both children (aged 8-11

[Freesurfer] Re: BUG in multiple comparisons correction for ABS

Hello Doug, Thanks so much for fixing this bug. I tried it and it works perfectly fine and it solves the problem that I had. Many thanks again, Nasim Nasim and Judith (and everyone else), I've found and fixed a bug that was causing the surfcluster results for the mc and perm simulations

[Freesurfer] Citing QDEC

Hello, Could you advise me on how to cite QDEC please? Thank you, Nasim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Within group analysis

I am trying to run glm for two different scans of same subjects, ie first year scan vs second year scan. I ran the mris_prepoc and mri_surf2surf and it completed without error. When i run mri_glmfit it gives me error ERROR: gdfReadV1: Input line 1, subjid = 0049_05102006 Found 1

Re: [Freesurfer] Within group analysis

looks like you have a variable on the input line that you did not declare. Check to make sure that your fsgd file has the proper format. Muhammad Ayaz wrote: I am trying to run glm for two different scans of same subjects, ie first year scan vs second year scan. I ran the mris_prepoc and

Re: [Freesurfer] Citing QDEC

It's just a GLM, so you only need to say that you used QDEC and cite our web site (www.surfer.nmr.mgh.harvard.edu) doug nmal...@mclean.harvard.edu wrote: Hello, Could you advise me on how to cite QDEC please? Thank you, Nasim

[Freesurfer] restarting after edits to brainmask.mgz and wm.mgz

Hi, I was just wondering if I should use -autorecon2-wm or -autorecon2-pial after making adjustments to both the brainmask.mgz and wm.mgz when restarting freesurfer. -Mira Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401

Re: [Freesurfer] restarting after edits to brainmask.mgz and wm.mgz

autorecon2-wm which is a superset of autorecon2-pial. cheers Bruce On Tue, 7 Jul 2009, Mira Michelle Raman wrote: Hi, I was just wondering if I should use -autorecon2-wm or -autorecon2-pial after making adjustments to both the brainmask.mgz and wm.mgz when restarting freesurfer. -Mira

Re: [Freesurfer] How to threshold an input mutli-volume?

I guess it would be pretty easy to fix to work on multi-frame images. What hardware/software platform are you using? Bruce On Tue, 7 Jul 2009, [UTF-8] ?? wrote: Hi, all. Can mri_threshold threshold an input mutli-volume file? With a seven volumes NIFTI file, all voxels other than in the

Re: [Freesurfer] How to threshold an input mutli-volume?

Thank you in advance for your help. We installed the freesurfer on a ubuntu 8.04 i686 machine. On Wed, Jul 8, 2009 at 9:57 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: I guess it would be pretty easy to fix to work on multi-frame images. What hardware/software platform are you using?