Re: [Freesurfer] CORRECTING DEFECT 1 problem

Hi Ruwan have you looked at the data? Can you tell us what the acquisition parameters are or send us a 3-plane image of the norm.mgz with the lh.orig.nofix and rh.orig.nofix surfaces? The big defects are usually a symptom of something else cheers Bruce On Mon, 22 Apr 2019, Pradeepa Ruwan w

Re: [Freesurfer] Freeview update error

External Email - Use Caution Hello FreeSurfer community, I believe I have installed both freetype and freetype-devel now. I now get a new error, that is similar, but may have a slightly different solution: Freeview:symbol lookup error: /usr/local/freesurfer/bin/../lib/qt/lib/libQ

[Freesurfer] thresholded cluster output data

External Email - Use Caution Hi Everyone, I'm new to freesurfer, and I was wondering if there is a way to output clusterwise threshold from Freeview (or any other tool) to illustrate cluster size, location, and significance? I understand that mri_glmfit-sim outputs cluster data

[Freesurfer] mri_vol2surf error

External Email - Use Caution Hello FS users, I am having a problem with mri_vol2surf. I want to project subcortical voxels onto the cortical surface. I found out that I can do this with the mri_vol2surf command. I am following the example given on the documentation, but I am ge

Re: [Freesurfer] mri_surf2surf help

External Email - Use Caution I am still having an issue with the command. This is what I am running: (MRI_DIR is the subj/mri, and SURF_DIR is the subj/surf directory) tkregister2 --mov /rawavg.mgz --targ /orig.mgz --reg /register.native.dat --noedit --regheader mri_surf2surf --

[Freesurfer] freeview and complex values

Hi Surfers, I am trying to use freeview to present retinotopy mapping in subcortical regions. I need to show complex (real and imag) values generated by a retinotopy analysis in a 'color wheel' format (similar to what tksurfer does). Any hint? _ Shahin Nas

Re: [Freesurfer] freeview and complex values

Hi Shahin, Freeview does not support color wheel colormap yet. We will add that option very soon. Best, Ruopeng On 4/22/19 2:52 PM, sha...@nmr.mgh.harvard.edu wrote: > Hi Surfers, > I am trying to use freeview to present retinotopy mapping in > subcortical regions. I need to show complex (r

Re: [Freesurfer] Freeview update error

External Email - Use Caution Hi Kelly, you can try yum install qt5-qtbase-gui qt5-qtwebkit qt5-qtwebkit-devel And if it still doesn't work, you can try yum install harfbuzz On Mon, Apr 22, 2019 at 9:05 AM Kelly Vaughn wrote: > External Email - Use Caution > > Hello Fr

[Freesurfer] Projecting a subcortical label to the surface

External Email - Use Caution Hello FreeSurfer users, I have a subcortical segmentation that I want to project to the nearest cortical vertex. Would I use the mri_vol2surf command to accomplish this, or do I need to convert the segmentation into a label, then project the label to

[Freesurfer] where to find label values of Hippocampus Segmentation v6.0

External Email - Use Caution Hello Freesurfer developers, this is just a quick question: where/with what function can I get all the label values that are included in lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz I want to replace the HIP l