Re: [Freesurfer] CUDA in FS6?

On 1 February 2017 at 05:47, Chris Adamson wrote: > Are the CUDA binaries still being developed in FS6? Are they compatible with > the CPU only versions? > I remember asking questions about this a while ago and apparently the cuda > binaries were no longer being developed in favour of openmp. I

Re: [Freesurfer] ROIs in midline for cortical thickness

I see. Have you run recon-all on each hemi? If so, use bbregister to register the surfaces to the fmri data, then use mri_vol2surf to map the activations on to the left and right surfaces and draw your ROIs that way. cheers Bruce On Wed, 1 Feb 2017, Sahil Bajaj wrote: Hi Dr. Fischl, Thank y

Re: [Freesurfer] ROIs in midline for cortical thickness

Hi Sahil can you clarify what you mean. Do you have the left hemi SMA labeled in MNI space and it (incorrectly) extends into the right hemi? Or are you trying to draw both the left and the right SMA? Bruce On Wed, 1 Feb 2017, Sahil Bajaj wrote: Hi everyone, I have supplementary motor area

[Freesurfer] ROIs in midline for cortical thickness

Hi everyone, I have supplementary motor area (SMA) defined in standard MNI volume space and I would like to extract cortical thickness for this area. I have 80% of SMA in left hemisphere and 20% on right hemisphere. So I am stuck at the command mri_vol2surf before proceeding to mri_segstats. In m

Re: [Freesurfer] Fwd: Cortical thickness from ROI in volume format

did you check whether the registration was accurate using that tkmedit command? On 02/01/2017 02:19 PM, Martin Juneja wrote: > > Hi, > > I am really sorry for re-sending this message. I would really > appreciate any response. > > Thanks. > > > Hi FreeSurfer experts, > > My goal is to extract co

Re: [Freesurfer] mri_cvs_register: how to read/import .m3z warp file

Hi Stefano, You can try to use the attached matlab file for reading the m3z file. Lilla On Mon, 30 Jan 2017, Stefano Zappalà wrote: Dear FreeSurfer Developers, I am trying to visualize and modify the output warp field (in .m3z) of a mri_cv_registration call aimed at aligning a T1w scan to

[Freesurfer] Fwd: Cortical thickness from ROI in volume format

Hi, I am really sorry for re-sending this message. I would really appreciate any response. Thanks. Hi FreeSurfer experts, My goal is to extract cortical thickness of several ROIs, which are in volume space. I am following instructions from this page: https://surfer.nmr.mgh.harvard.edu/fswiki/V

Re: [Freesurfer] extract values uncorrected clusters

You can run mri_surfcluster using the sig.mgh as the input and specifying a --minarea and --thmin .001. --minarea takes a surface area in mm2, not number of vertices, so you'll have to compute what the approx area is of 150 vertices. Include a --ocn output and --sum sumfile, then use mri_segsta

[Freesurfer] Announcing HCP Course 2017 at UBC in Vancouver June 19-23!

We are pleased to announce the *2017 HCP Course: "Exploring the Human Connectome"* , to be held *June 19 – 23, 2017* at the University of British Columbia (UBC) , in Vancouver, BC, Canada.

[Freesurfer] Converstion of Wavefront .obj files into Nifti

Dear all, Could you please suggest me some method where i can possibly convert Wavefront .obj files into Nifti files, is such conversion technically relevant ?. Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

[Freesurfer] extract values uncorrected clusters

Dear FreeSurfer experts, I did a group analysis in QDEC for the symmetric percent change from pre to post and have a couple of clusters that don't survive the Monte Carlo correction. I want to extract the values for each time point per subject for those clusters that are bigger than 150 vertice

Re: [Freesurfer] [FSFAST] Contrast percent map

you have the right idea, but it is cespct = 100*contrast/baseline The baseline is the mean offset of the fMRI, the contrast is the deviation from baseline On 2/1/17 4:49 AM, Seung-Goo KIM wrote: Dear all, I wish to know how “cespct.nii.gz” is computed in selxavg3-sess. I thought it comput

Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (REPOST)

Hi Doug, This seems correct. What do you mean by "not so great"? Could you send files to look at? Lilla On Tue, 31 Jan 2017, Douglas Merkitch wrote: Hello, I'm reposting the following just in case anyone has any ideas. Any input would be greatly appreciated! Thank you very much for the sugge

Re: [Freesurfer] QDEC - Controlling for gender

I'd probably normalize everyting On 2/1/17 7:44 AM, Jennifer Szeto wrote: > Thank you very much Doug! > > It works when I include only normalized age and BDI in the qdec.table.dat > file, but not when I include also all the other variables of interest in the > file. > > As normalizing w

Re: [Freesurfer] QDEC - Controlling for gender

Thank you very much Doug! It works when I include only normalized age and BDI in the qdec.table.dat file, but not when I include also all the other variables of interest in the file. As normalizing works for BDI, will I have to normalize all the variables of interest as well? Or just the

[Freesurfer] CUDA in FS6?

Freesurfer devs, Are the CUDA binaries still being developed in FS6? Are they compatible with the CPU only versions? I remember asking questions about this a while ago and apparently the cuda binaries were no longer being developed in favour of openmp. Thanks in advance, Dr Chris Adamson Res

[Freesurfer] [FSFAST] Contrast percent map

Dear all, I wish to know how “cespct.nii.gz” is computed in selxavg3-sess. I thought it computes something like a relative change like: cespct = (contrast-baseline)/baseline*100, but I cannot figure out what was taken for the baseline. I thought it could be mean beta for constant terms (0-th