[Freesurfer] ALICE overlay files conversion

Hello, My lab group has some scans with overlays identifying hemorrhages that were made using ALICE (the files have a .oly extension) that we'd really like to be able to use with FreeSurfer Obviously mri_convert won't do anything with these files, but I was hoping that perhaps you have some o

[Freesurfer] CT registration

Does FreeSurfer (or FSL) have any commands that support CT registration? -- ___ 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 th

[Freesurfer] recon-all -all -long error

While running the following command: recon-all -all -long 2615_12202006 2615_12202006 -i .../dicom_raw/01.dcm I'm getting this error durring the Cortical Ribbon mask: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon -

[Freesurfer] mris_register error

Hello, So I'm attempting to use the V1_predict script to generate a primary visual cortex label and had been receiving an error message. I was able to track down the error to the mris_register command: mris_register -inflated -a 4096 -dist 10.0 -parea 1.0 \ /surf/lh.sphere \ /label/lh

[Freesurfer] surface label values

Hi, I'm trying to use a surface label (generated by V1 predict) to extract values that have been painted onto a surface using mri_vol2surf. Is there a FreeSurfer tool that will do this? I've been looking but nothing is popping out at me. Thanks, Greg --

Re: [Freesurfer] mris_expand problem

Greve wrote: > Sorry, it looks like it is the thickness file, not the white surface, it is > having problems with. Can you load the thickness as an overlay? > > Gregory Dierksen wrote: >> >> Yes, I can view both the left and right white matter surfaces in tksurfer. >>

Re: [Freesurfer] mris_expand problem

e with something else? Eg, can you load it > with tksurfer? > > doug > > Gregory Dierksen wrote: >> Hi, >> >> I'm trying to make a "midgray" surface by inflating the white surface of a >> subject by 5% using the following command: >>

[Freesurfer] mris_expand problem

Hi, I'm trying to make a "midgray" surface by inflating the white surface of a subject by 5% using the following command: mris_expand -thickness rh.white 0.5 rh.midgray.05 I am getting the following output: using distance as a & of thickness expanding surface rh.white by 0.50% of thickness an

[Freesurfer] mri_vol2surf error

Hi, I'm trying to paint functional data onto a cortical "midgray" surface. The surface was generated using mris_expand to expand the WM surface to 50% of the pial surface. The data I want to paint onto this surface is in a 96 x 96 x 17 x 512 dimension NIFTI file generated using the feat comma

[Freesurfer] surfaces in slicer3

Hi, I'm trying to convert a binary volume to a surface that can be viewed with slicer3. I've used the following commands: mri_tesselate microbleeds.mgz 1 lh.microbleeds mris_smooth lh.microbleeds -n 5 lh.microbleeds-smooth When I attempt to ope the lh.microbleeds-smooth surface using slicer

[Freesurfer] ADC units after dt_recon

Hi All, After running the dt_recon processing stream on a standard diffusion tensor image, does any body know the units on the resulting adc.nii volume? Thanks Greg -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh

Re: [Freesurfer] smoothing with mri_surf2surf

the mask regardless of whether I masked the input or not. One thing that I did find is that it will smooth the vertices that are outside the mask but immediately adjacent to it. This should be a small effect but it might be misinterpreted as differences inside the mask. doug Gregory Dier

Re: [Freesurfer] smoothing with mri_surf2surf

ouglas N Greve wrote: mri_surf2surf will not change the values outside of the mask (those will be left unsmoothed). Is there an actual difference in the mask? doug Gregory Dierksen wrote: Hi, I want to smooth a cortical thickness map using values only in a specific area. Basically I want t

[Freesurfer] smoothing with mri_surf2surf

Hi, I want to smooth a cortical thickness map using values only in a specific area. Basically I want to mask out all other segmentations, for example smooth with fwhm of 20 only in the postcentral region. I've used quite a few combinations of the -label-src and -label-trg flags and noticed

[Freesurfer] mri_volcluster

Hi, I'm trying to use the mri_volcluster command to make label files from a single volume of binary voxel clusters. Once I have split the volume into individual label files I want to convter the label files back into individual cluster volumes (I am trying to use mri_label2vol to do this). T

[Freesurfer] mri_volcluster

Hi, I'm trying to use the mri_volcluster command to make label files from a single volume of binary voxel clusters. Once I have split the volume into individual label files I want to convter the label files back into individual cluster volumes (I am trying to use mri_label2vol to do this). T