[Freesurfer] Vertex-wise ROI extractions on the surface

Hi, How can I extract functional data (percent contrast) from an aparc ROI on the surface on a vertex-wise basis (i.e. not one value averaged across the whole ROI, but one value per vertex inside the ROI for a given contrast)? Funcroi-config/funcroi-sess/funcroi-table-sess seem to only provide

Re: [Freesurfer] Unpacking Philips scans work-around... should this work?

ive those to recon-all as input in the same way you > would dicom (with -i and do it's thing > > cheers > Bruce > On Sat, 2 Jun 2018, DeCross, Stephanie N. wrote: > >> Hi, >> >> I have scans from a Philips scanner I want to process with FreeSurfer. >&g

[Freesurfer] Unpacking Philips scans work-around... should this work?

Hi, I have scans from a Philips scanner I want to process with FreeSurfer. Previously, the scans have been downloaded in the Philips PAR/REC format and converted into niftis, and those niftis have been used as the raw inputs in other imaging pipelines. Instead of dredging up the original

[Freesurfer] Customized ColorLUT - opacity value that will make regions totally transparent?

Hi all, I’m trying to open a couple aseg.mgz labels and color code them. I thought I’d do this by making my own ColorLUT table, setting the color of my regions, and then making every other region in the table be completely transparent by fiddling with the opacity value. I can’t figure out what

[Freesurfer] Solved! Re: MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

MNI152 ROI to FreeSurfer label can you send me the label file? On 04/20/2016 10:49 AM, DeCross, Stephanie N. wrote: I /think/ it’s really a label file? I took my binarized nii.gz and ran mri_cor2label -- c NAME.nii.gz -- id 1 -- l ./newname.label and I was under the impression that this t

Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

19, 2016, at 1:18 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> wrote: are you sure the label file is really a label file? Does the same thing happen if you specify -l labelfile on the command line? On 04/18/2016 05:08 PM, DeCross, Stephanie N. wrote

Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

al output from tksurfer? Does it work in freeview? On 04/13/2016 11:20 AM, DeCross, Stephanie N. wrote: > Hi, > > I’m trying to take an ROI in MNI152 volume space and make it into a > cortical surface label, for visualization purposes. > > With my input being the lh thresholded

[Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

Hi, I’m trying to take an ROI in MNI152 volume space and make it into a cortical surface label, for visualization purposes. With my input being the lh thresholded, binarized MNI152 nii.gz label (when I visualize it, it looks as it should in fslview), I ran: mri_vol2vol -- mov -- targ

[Freesurfer] Mask out medial wall?

Hi, Is there a way to mask out the medial wall in the tksurfer command? I’m looking for a way to have the map visually look as if there’s simply no activation within the medial wall (showing a plain gray striped/curvature shown brain in that area instead), as opposed to having the medial wall

[Freesurfer] Freeview-stable4 error?

Hi, I'm trying to look at 2 connectivity files (saved in SPM) at the same time using Freeview, but how I've been doing it in the past is no longer working and I haven’t changed anything on my end. What I had been doing: 1. cd to the folder with my connectivity files and typing the shortcut

[Freesurfer] mkcontrast manual weighting?

Hi, I’m making contrasts, and my 6 conditions are as follows: #1 female approach #2 male approach #3 female withdraw #4 male withdraw #5 car approach #6 car withdraw If I want to create the contrast all-approaching-things minus fixation, I’m dealing with #1 female approach, #2 male approach,

[Freesurfer] tkmedit coronal view - y coordinate issue

Hi, In FreeSurfer 5.3, when I click around in a coronal view slice, the Talairach y coordinate changes (in both the cursor column and the mouse column). This doesn’t make sense - it’s the same coronal slice, so shouldn’t anywhere on that same plane still have the same y coordinate? When I take

Re: [Freesurfer] mkcontrast weighting a complicated double subtraction contrast

wrote: It should have given you the same thing. I'll have to look more closely when I get back from traveling next week. Please send me an email if I don't get back to you. doug On 6/19/14 10:13 PM, DeCross, Stephanie N. wrote: I’m not sure if I’m understanding correctly - wouldn’t dividing

[Freesurfer] mkcontrast weighting a complicated double subtraction contrast

Hi, I’m having trouble figuring out the correct way to weight my conditions with mkcontrast for a couple of complicated contrasts I’m making. I have six conditions: #1 female face approach #2 male face approach #3 female face withdraw #4 male face withdraw #5 car approach #6 car withdraw For a

Re: [Freesurfer] mkcontrast weighting a complicated double subtraction contrast

-aw doug On 6/19/14 3:57 PM, DeCross, Stephanie N. wrote: Hi, I’m having trouble figuring out the correct way to weight my conditions with mkcontrast for a couple of complicated contrasts I’m making. I have six conditions: #1 female face approach #2 male face approach #3 female face withdraw