Re: [Freesurfer] How to load specific color label for rois

Hi Manish, what is it that you want to display. If a segmentation (volume), then you can create a color table similar to $FREESURFER_HOME/FreeSurferColorLUT.txt. For a parcellation, the colors are imbeded in the annotation file, and you'd have to generate a new annotation file (mris_annotation2

Re: [Freesurfer] Repost: Error with annot file

Hi Antonella, the argument to --annot has to be an annotation file (something.annot). mri_glmfit-sim should generate an annot file. If you are running mri_surfcluster to get ocn.mgh, it will also generate an annot file. doug On 8/27/12 8:31 PM, Antonella Kis wrote: Hi, I am trying to run th

[Freesurfer] Repost: Error with annot file

Hi, I am trying to run the mri_label2vol but I am getting the following error. I am not sure which annot file I should use for my QDEC clusters. I tried to use my annot file from mri_glmfit-sim but it didn't work. I was running: mri_label2vol --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESU

Re: [Freesurfer] tracula-snowleopard updates

Hi, Yes, they do, just overwrite the ones in freesurfer/bin. Nick On Mon, 2012-08-27 at 09:45 -0700, Cat Chong wrote: > Hello Experts, > > > Just a quick question: Do the Tracula updates(dmri_mergepaths, etc) > for snow_leopard replace the 'old' ones in freesurfer's "bin" > directory? > che

Re: [Freesurfer] Control points and errors

Hello Bruce, By creating new errors after adding cp, it usually leaves out a large portion of cortex (and its white matter) that was originally correctly identified in the first attempt. I have tried to add cp in areas that are not in partial volume voxels. The version command says I am using: $I

[Freesurfer] tracula-snowleopard updates

Hello Experts, Just a quick question: Do the Tracula updates(dmri_mergepaths, etc) for snow_leopard replace the  'old' ones  in freesurfer's "bin" directory? cheers, Cat ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.har

[Freesurfer] How to load specific color label for rois

Hi Freesurfer's, How can I load color labels for specific for display purposes? Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] creating a gca file from .mgz files

Hi Jefff you can give mri_ca_normalize a flag to tell it to use a manual segmentation instead of the gca. Try -seg . Then the gca name won't matter - it should ignore it. You could use label2label I guess, although if it's accurate across brains then you probably don't need it and can just bu

[Freesurfer] Error with annot file

Hi, I am trying to run the mri_label2vol but I am getting the following error. I am not sure which annot file I should use for my QDEC clusters. I tried to use my annot file from mri_glmfit-sim but it didn't work. I was running: mri_label2vol --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURF

Re: [Freesurfer] creating a gca file from .mgz files

Hello, Okay, but from looking at the recon-all pipeline it looks like to generate the norm.mgz file the .gca atlas is needed first. If I create the seg_edited.mgz file from my manually labelled file can I use that in rebuild_gca_atlas.csh to generate the .gca atlas? This would incorporate the m

Re: [Freesurfer] REPOST: How to Convert QDEC clusters to standard MNI_152_T1 space

Hi Doug, Thank you very much for your reply and help. If I am not doing cluster by cluster how I can know which cluster is which   when I overlay the file onto MNI152? Is the following correct I am not sure how to input (using which option) my sig.mgh from QDEC: mri_label2vol   --temp

[Freesurfer] Command line to get BA stats with the thresholds

Hi! Is there a command line to obtain the BA values with the recommended thresholds from all subjects at once? Thank you, Andreia Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fre

Re: [Freesurfer] REPOST: How to Convert QDEC clusters to standard MNI_152_T1 space

You should use mri_label2vol. If you want to do it label by label, then you need to convert the cluster annotation (the .annot file) into labels with mri_annotation2label. Or you can feed the annotation directly into mri_label2vol to create a segmentation volume. You don't need to specify a s

[Freesurfer] REPOST: How to Convert QDEC clusters to standard MNI_152_T1 space

Hi,  I want to overlay  my QDEC clusters on the connectivity maps in FSL  on the MNI ( this is the template I use for my connectivity maps). I am not sure how I can mention the label of my clusters, the uncorrected clusters. Should I use the sig.mgh as subject id, my clusters were obtain