[Freesurfer] ico4 parcellation and mri_segstats

missing something? Thanks, -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 ___ Freesurfer

[Freesurfer] BOLD vol2surf dimension mismatch

for height (1, usually 256) in volume structure I should probably use mri_vol2vol first, but which target volume should I then use? Or is there something else I'm doing wrong? Thanks for your help! -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center

Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10

and mri_segstats To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5025264e.3030...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed what are your command lines? doug On 08/09/2012 01:21 PM, Linda Douw wrote: Dear Freesurfers, I'm trying to extract the average waveforms

Re: [Freesurfer] ico4 parcellation and mri_segstats

not have any voxels in your parcellation. Eg, #82: 8282 ic4.tri_vertex_82 0 So the problem appears to be with mris_make_face_parcellation, not with mri_segstats. doug On 09/10/2012 10:56 AM, Linda Douw wrote: Hi Doug, Output and sumfile are attached. Any ideas? Linda Message: 10

[Freesurfer] manual parcellation

to check it out. Thanks so much, -- Linda Douw, Ph.D. Research fellow ___ 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

[Freesurfer] label transformation to MNI space

But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Linda Douw, PhD. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

Re: [Freesurfer] label transformation to MNI space

: mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --inv doug Linda Douw wrote: Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do

Re: [Freesurfer] label transformation to MNI space

in the aparc+aseg since it fills in the ribbon: mri_binarize --i aparc+aseg.mgz --match 1006 --o lh_entorhinal.nii.gz 1006 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt doug Linda Douw wrote: Hi Doug, Thanks for the reply. This cmd makes it slightly better I guess, but still definetely

[Freesurfer] dimensions of input and annot for mri_segstats

Hi all, I have nifti files containing the surface-projected time series data of a subject (obtained using procsurffast), both lh and rh. These time series are projected onto fsaverage5, and are 3414 x 1 x 3 time points, where 3414*3 = 10242 are the number of vertices for each hemisphere. Now, I

[Freesurfer] custom making an overlay

, but you need the coordinates of the labels for that. In my case, I've made my own parcellation by using mris_divide_parcellation, so then I would have to know where to find the coordinates (I don't). And do you think this is the most efficient method? Thanks! -- Linda Douw, Ph.D

[Freesurfer] label shape with mris_divide_parcellation

to get a different result? Thanks! -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 ___ Freesurfer

Re: [Freesurfer] label shape with mris_divide_parcellation

, Linda Douw wrote: Hi all, I would like to make a fine-grained surface parcellation from aparc - let's say 500 labels, and I would like the labels to be more or less isometric. When subdividing the parcellation with mris_divide_parcellation, the labels become very stretched instead

[Freesurfer] template to dicoms

going from a template to dicoms is not that easy. I'd appreciate any tips! -- Linda Douw, Ph.D. Branco Weiss fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129

[Freesurfer] citation for FsFast

Hi Doug, What is your preferred citation for FsFast (used for resting-state)? I couldn't really find a clear answer in the Zotero library or mail archives. Thanks and happy holidays! Linda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu