Re: [Freesurfer] Projecting subcortical ROI to the cortical surface

You can convert the ROI into a label (mri_vol2label), then "paint" the label onto the nearest cortex using mri_label2label with the --paint option. dmax controls the maximum distance, so you'll need to set that pretty large. You can then load the label onto the surface to see where it landed.

Re: [Freesurfer] Projecting subcortical ROI to the cortical surface

Hi Ryan do you have diffusion data? You could use tracula and find the cortical ROI(s) that are most likely the end points of that bit of white matter. cheers Bruce On Wed, 15 May 2019, Nillo, Ryan Michael R wrote: External Email - Use Caution Hi Bruce, We want to study

Re: [Freesurfer] Projecting subcortical ROI to the cortical surface

External Email - Use Caution Hi Bruce, We want to study whether or not presence of periventricular heterotopias affect the thickness, volume, or surface area of the nearest cortical ROI. Since the condition we are studying is caused by failure of neurons to migrate to the corte

Re: [Freesurfer] Projecting subcortical ROI to the cortical surface

Hi Ryan I don't think projection of that kind of ROI is well-posed. Different parts of it are probably closest to wildly different parts of cortex. What are you trying to acheive? cheers Bruce On Wed, 15 May 2019, Nillo, Ryan Michael R wrote: External Email - Use Caution   

Re: [Freesurfer] Obtaining stats for a custom label

what do you mean when you say you "load it on FreeSurfer"? Do you mean FreeView? Please send command lines, and also please post to the list. On 5/15/19 5:38 PM, Nillo, Ryan Michael R wrote: > > External Email - Use Caution > > When I run tkregisterfv --mov subject/surf/rh.custom.nii --re

Re: [Freesurfer] Spatial smoothing kernel in fsfast

External Email - Use Caution Thanks. On Wed, 15 May 2019 at 16:42, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Right, with -fwhm 0, it will not smooth the data. > > On 5/14/19 2:21 PM, Zhi Li wrote: > > > > External Email - Use Caution > > > > Yes. Smoothin

Re: [Freesurfer] Issue with vol2surf

It is just mri_vol2surf like you have using the --regheader On 5/15/19 4:53 PM, Martin Juneja wrote: > > External Email - Use Caution > > Thanks Doug, sure I will try that. > Would you mind sharing the command line to sample ROIs onto MNI > surface (after running recon-all on MNI template

Re: [Freesurfer] Issue with vol2surf

External Email - Use Caution Thanks Doug, sure I will try that. Would you mind sharing the command line to sample ROIs onto MNI surface (after running recon-all on MNI template)? On Wed, May 15, 2019 at 1:32 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > I would ru

Re: [Freesurfer] Control Points to Include Hyperintensity in WM Surface

Instead of putting control points, you should edit the wm.mgz. BTW, it looks like some of the control points were not fully in white matter, which can be problematic. On 5/14/19 2:27 PM, Rachel Hoel wrote: > > External Email - Use Caution > > Dear Freesurfer Developers, > > We're still s

Re: [Freesurfer] Spatial smoothing kernel in fsfast

Right, with -fwhm 0, it will not smooth the data. On 5/14/19 2:21 PM, Zhi Li wrote: > > External Email - Use Caution > > Yes. Smoothing in the volume may smooth across sulci and other tissue > types. I would like to use ICA-AROMA to denoise the data, especially > remove the head motion c

Re: [Freesurfer] Voxel to Surface Coordinates

sorry, what is an ICBM152 surface map? On 5/15/19 8:34 AM, Song, Da-Yea wrote: > External Email - Use Caution > > I apologize for the confusion. > > We are doing a ROI based analysis with our EEG data that have been > transformed onto a ICBM152 surface map. Using an atlas that we have >

Re: [Freesurfer] Issue with vol2surf

I would run recon-all on the MNI152, then sample the ROIs onto the MNI152 surface, then transfer them to fsaverage using mris_apply_reg or mri_surf2surf. On 5/15/19 1:46 PM, Martin Juneja wrote: > > External Email - Use Caution > > Hi FS experts, > > I am interested in displaying my ROI:

Re: [Freesurfer] Thalamus segmentation {Disarmed}

External Email - Use Caution Dear Zheng, The reticular nucleus is in the atlas and we use it to fit it to the image, but its segmentation is not always reliable and that’s why we don’t provide it (nor its volume). Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow

[Freesurfer] Download a sample dataset Failed

External Email - Use Caution Dear Professors, I began my study of FreeSurfer few days ago. So happy to learn and enjoy data analyses using FreeSurfer. Now, a problem happened when I wanna download a sample dataset which can be used to become familiar with the LME Matlab tools.

Re: [Freesurfer] Computing measures like area for a custom surface

External Email - Use Caution Dear Douglas, dear Bruce, thanks a lot for your fast and helpful replies, they solved my problem. For the record: to get the area of my custom surface, I used: mri_surf2surf --s tim --sval-area graymid --hemi lh --trgval lh.area.graymid --trg_

Re: [Freesurfer] Voxel to Surface Coordinates

External Email - Use Caution I apologize for the confusion. We are doing a ROI based analysis with our EEG data that have been transformed onto a ICBM152 surface map. Using an atlas that we have incorporated into our FreeSurfer pipeline, we are trying to convert our ROIs from t

[Freesurfer] Thalamus segmentation {Disarmed}

External Email - Use Caution Dear Experts, When I used the recent FS version for thalamus segmentation, I have segmented it sucessfully. However, in the .txt file, there are no the volume of lateraldorsal and reticular nuclei. Is there any error in my processing steps? I don't k

[Freesurfer] A Question Regarding Smoothing a Surface

External Email - Use Caution Dear experts, I have a parcellation scheme (an annotation file). Now I wanna smooth the map for better visualization. The command "mri_surf2surf" can do it ,but it doesn't recognize .annot. Now I wonder how to do it. I would appreciate it if u could