[Freesurfer] Problems with segmentation

Hi freesurfers After checking recon-all -autorecon-all processing, I realized that a part of the duramadre has been not fully removed (please see attached file). Can anyone help me how to solve this please. Best regards. -- Leo Kay. <>___ Freesurfer m

[Freesurfer] Philips DICOM format problem

Hi All I'm new in freesurfer. I have a question regards Philips DICOM format. I tried to convert from dicom to .mgz using mri_convert but i get the following error message: MRIresample(): error inverting matrix; determinant is nan, matrix is: -0.000 -0.000 nan nan; 0.000 0.000 nan

[Freesurfer] recon-all

Hi I have been trying to import my data and create a subject directory using the following command: recon-all -i -s replacing with the path where my T1 structural nifti is allocated, and -s with the name of the subject (susu), which is supposed to be the name of the directory too. But a

[Freesurfer] [Fressurfer] fMRI and anatomical T1

Hi all Can anyone help me overlaying fMRI activations from fsl on a anatomical T1 volume in freesurfer. Is there any previous format conversion to do before? Thanks in advance best regards, -- Leo Kay. ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

[Freesurfer] Fwd: fMRI and anatomical T1 overlaid

anatomical T1 To: leonardo kay Cc: freesurfer@nmr.mgh.harvard.edu There is a tutorial on this on our wiki. Basically, you need to run reg-feat2anat to get a registration file, then run tksurfer passing it the registration file and the stat volume as the overlay. doug leonardo kay wrote:

[Freesurfer] (no subject)

Hi all Do anyone have experience doing parcellations using AXIAL T2 FLAIR acquisitions? What sequence do you recomend most for parcellation/labelling under freesurfer? Best regards, -- Leo Kay. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.ed

[Freesurfer] Cortical Thickness

Hi Freesurfer experts. Do anyone know how to measure the cortical thickness of an specific brain area? I have been using mris_anatomical_stats but it only outputs the brain cortical thickness of the requested hemisphere. Best regards. -- Leo Kay. ___

[Freesurfer] Creating a ROI mask

Hi freesurfer 's Can anyone help me how to create a ROI mask. I have read the Cortical Thickness of a Volume-defined ROI tutorial but it doesn't specify how to generate that ROI.nii file. How many points are needed? What brain image must be used as a reference? Any help will be greatly appreciated

[Freesurfer] Subject information

Hi all Is there someway (command line) to get direct information on each subject acquisition parameters? Best regards. -- Leo Kay. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] make_average_subject error

Hi all Could anyone help me with this error: MRISreadAnnotationIntoArray: vertex index out of range: 1499028058 i=5A595959, in_array_size=133467 annot file: /home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot This appeared after trying to average my subject data. It says