Re: [Freesurfer] extract morphology data

External Email - Use Caution Hello, my command line is mris_preproc --s ${subject} --hemi ${hemi} --meas ${measure} --target ${fsaverage}5 --out ${measure}/${hemi}.${subject}.${fsaverage}5.sm0.mgz and my terminal output is Transfering area for sub1's lh hemisphere ... nsubject

Re: [Freesurfer] Errors running TRACULA (data attached)

Hi Keita - Instead of setting variables to "None", just delete or comment out those lines altogether. Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ksak...@yahoo.co.jp Sent: Monday, September 28, 2020 12:28 AM To: freesurfer@nmr.mgh.harv

Re: [Freesurfer] How to draw streamlines and their corresponding ROIs using freeview

Hi Zhiyuan, You can draw streamlines in freeview as way points and turn on the spline display. ROIs can be drawn as labels. Best, Ruopeng On Sep 26, 2020, at 2:46 PM, Zhiyuan Yu mailto:z...@my.fsu.edu>> wrote: External Email - Use Caution Hi, I have extracted fibers and the correspo

Re: [Freesurfer] surface/volume editing

It looks like the orig extends too far, so try editing the wm.mgz On 9/25/2020 11:51 AM, Jake Jensen wrote: External Email - Use Caution Attached are a few snapshots of the ?.orig surfaces (pink), pial (red), and wm (yellow) On Fri, Sep 25, 2020 at 7:46 AM Douglas N. Greve mailto:d

Re: [Freesurfer] vol2surf: lesion overlap across group into surfaces

You can try converting your lesion mask to a label (mri_cor2label, DONT use the the --surf option). A label is a simple text file. Then try using mri_label2label using the --paint option (you might have to play with the distance) On 9/28/2020 12:57 AM, Horn, Mitchell Jacob wrote: Thanks agai

[Freesurfer] Extraction of subject-wise values after permutation test !

External Email - Use Caution Hello everyone, I have significant group differences in volume (controls > patients) for one of the clusters (say C1) - calculated after permutation test using PALM, which gives me following outputs: *_clustere_tstat_fwep.mgz (this is significant at p

[Freesurfer] voxel wise cortical thickness and subcortical volume

External Email - Use Caution Hi, Is it possible to use Freesurfer to extract global voxel-wise cortical thickness and subcortical volume? Thank you so much! Best, Qi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mai

Re: [Freesurfer] How to draw streamlines and their corresponding ROIs using freeview {Disarmed}

External Email - Use Caution Hi Ruopeng, Thanks for your answer! My streamlines are in mat and trk file formats and I cannot load the fiber tracts as way points in Freeview. Could you please tell me why? Best, Zhiyuan Yu From: freesurfer-bo