[Freesurfer] Export Functional Data Overlayed Onto Sphere

Hello, I've specifically adopted Freesurfer for its ability to map a brain into a sphere. I've ran a subject's structural data through the recon-all pipeline using the -all option. With this reconstruction completed, I'd like to overlay functional data on the sphere. More specifically, I'd l

Re: [Freesurfer] Export Functional Data Overlayed Onto Sphere

Hi Luis if your functional data is mapped onto the surface (i.e. with mri_vol2surf) then it is already on the sphere. All the surfaces for a given subject's hemisphere are topologically equivalent, so you can simply look up the same vertex index on the ?h.sphere (for the metrically optimal sph

Re: [Freesurfer] fsgd

I exactly tried that. I typed: mris_preproc --fsgd \ --cache in thickness.fwhm.10.fsaverage \ --target fsaverage \ --hemi lh \ --out .mgh everytime I am running this it says that my fsgd file cannot be found. So I wonder where I have to save it so that FreeSurfer can find it. Thanks for any he

Re: [Freesurfer] fsgd

Did you pass it the full path to the fsgd file, not just it's name? If so, please send the full command line. Also, run it with ---debug and send me the full terminal output. doug On 6/7/12 9:39 AM, Marie Schneider wrote: I exactly tried that. I typed: mris_preproc --fsgd \ --cache in thick

Re: [Freesurfer] 回复: Re: /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory

Hi Xiangzhen - Currently mri_convert does not support extracting gradients and b-values from dicom files. If you can get the gradients and b-values from the dicom header yourself, that's great. Save them in text files and enter the path in your dmrirc file. a.y On Thu, 7 Jun 2012, Xiangzhen

Re: [Freesurfer] Mris_anatomical_stats: smoothing does not work with surface area maps

Use "--sval lh.area". Also, why do you want to smooth it before averaging over the ROI? doug On 06/07/2012 01:29 AM, Jürgen Hänggi wrote: > Hi Doug > > This is my command line: > > mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area > -nsmooth 15 -f $s/stats/lh.aparc.a2005s.sta

[Freesurfer] Creating DMPFC ROIs in Freesurfer

I was wondering whether anyone here has used Freesurfer to create ROIs for the Dorsomedial Prefrontal Cortex, or if anyone knows citations of articles that have. Thanks, Paula Paula Wu Postbaccalaureate Intramural Research Training Associate Section on Functional Imaging Methods Laboratory of B

Re: [Freesurfer] MNI to RAS surface coordinates

Here are instructions to go from a surface RAS to the mni305 RAS, so just invert them. doug I have an RAS point on the surface (tkrR tkrA tkrS) ("Vertex RAS" from tksurfer) and want to compute the MNI305 RAS that corresponds to this point: MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'

[Freesurfer] Using an ROI and not correcting/"fixing" the rest of the image

Hi, I am planning on looking at a specific region of interest, and I am wondering it is possible to only "quality check" this region and leave the rest of the brain as is. Meaning, can I save the time of going through every slice and re-assigning voxels for the entire brain and just focus on m

Re: [Freesurfer] Using an ROI and not correcting/"fixing" the rest of the image

Hi Anson yes, that's ok as long as you make sure that the registration (sphere.reg) is ok for group results. cheers Bruce On Thu, 7 Jun 2012, Kairys, Anson wrote: Hi,   I am planning on looking at a specific region of interest, and I am wondering it is possible to only ?quality check? t

Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

Hi Leon, I found the problem. mris_make_face_parcellation was actually merging several units together. You can get a fixed version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux Let me know how it goes doug On 06/04/2012 02:44 PM, Leon w

[Freesurfer] loading surface in freeview

hi doug n fellow fs users, whenever we try to load a fsaverage surface in freeview, it shows me following message: "Surface does not contain valid volume geometry information. It may not align with volumes and other surfaces" this message is limited only to fsaverage surfaces. was just wo

[Freesurfer] mri_fill problem

Hi, I am having problem getting mri_fill to run on one of my volumes (it did work with another monkey, so I assume I am running things right). I am using v5.0 (but it also happens on 5.1). The input is a monkey wm file with specified coordinates for the corpus callosum. The error I get is: "could

Re: [Freesurfer] mri_fill problem

What's your command line? Are you using voxel coords? On Jun 7, 2012, at 9:52 PM, Shay Ohayon wrote: > Hi, > > I am having problem getting mri_fill to run on one of my volumes (it did work > with another monkey, so I assume I am running things right). > I am using v5.0 (but it also happens o

Re: [Freesurfer] mri_fill problem

Hi Bruce, Yes. I am using voxel coordinates. The command line is: mri_fill /space/data/shayo/cooked/test2/mri/wm.nii /space/data/shayo/cooked/test2/mri/filled.nii -CV 122 116 91 (I also gave the pons values, but it didn't seem to change anything). -- Shay Tsao lab Caltech On Thu, Jun 7, 2012 a

Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

Hi, Douglas Thank you very much for taking care of it. The ROIs ending with 2 and 5s have been correctly labeled and have volumes now after running the fixed version of mris_make_face_parcellation.  However, there is still one ROI missing in the volume data that is located at the top of the po

Re: [Freesurfer] Mris_anatomical_stats: smoothing does not work with surface area maps

Hi Doug I correlated a behavioural measure with cortical thickness and surface area using mri_preroc, mri_surf2surf and mri_glmfit. Now I would like to extract the individual values of the clusters that correlated with the behavioural measure. Because the individual values should be comparable wi