[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 https:

[Freesurfer] template to dicoms

ously 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

[Freesurfer] vertices out of range after mris_label2annot

Hi experts, I have a bunch of custom-made labels (from the ConnectomeMapper software) that I want to put into a single annotation file. Therefore, I create a color-lookup table and use mris_label2annot as follows: mris_label2annot --s fsaveragec --h lh --ctab lh_laus500_clut_new.txt --a laus500_f

[Freesurfer] manual parcellation

I'd be happy 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 o

Re: [Freesurfer] ico4 parcellation and mri_segstats

ct) that do 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, >> Outpu

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

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,

[Freesurfer] BOLD vol2surf dimension mismatch

e 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

[Freesurfer] ico4 parcellation and mri_segstats

me reason. Am I 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 ___

Re: [Freesurfer] label shape with mris_divide_parcellation

on. > > cheers > Bruce > > > On Thu, 19 Apr 2012, 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.

[Freesurfer] label shape with mris_divide_parcellation

ay 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 ___ Frees

[Freesurfer] custom making an overlay

ation, 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! -- L

[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 wo

Re: [Freesurfer] label transformation to MNI space

hinal label define 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 f

Re: [Freesurfer] label transformation to MNI space

cmd: > 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 apa

[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 in