[Freesurfer] Call for Papers: Connectomics in NeuroImaging Workshop at MICCAI 2018, Granada (Spain)

2018-04-30 Thread Islem Rekik
External Email - Use Caution Hello Colleagues, The attached call for full-length papers flyer provides information about the 2nd International Workshop on Connectomics in NeuroImaging (*CNI 2018*), which will be held in parallel with the 21st International Conference on Medical

Re: [Freesurfer] problem using mri_vol2label for subcortical regions

2018-04-30 Thread Bruce Fischl
Hi Lucia 8 is cerebellar cortex - how could you sample it to the neocortical surface? I'm not sure I understand what you are trying to do. Bruce On Mon, 30 Apr 2018, Lucia Billeci wrote: External Email - Use Caution Dear Freesurfer Experts, I want to use mri_vol2label to

[Freesurfer] problem using mri_vol2label for subcortical regions

2018-04-30 Thread Lucia Billeci
External Email - Use Caution Dear Freesurfer Experts, I want to use mri_vol2label to obtain labels for subcortical regions. I tried the following command: mri_vol2label --c $SUBJECTS_DIR/fsaverage/mri/aseg.mgz --id 8 --l ./tests_label/8.label However I get the same vertex

[Freesurfer] Combining -3T and -mprage flags

2018-04-30 Thread King, Daniel (Research Student)
External Email - Use Caution Hi Freesurfer community, I am currently running Freesurfer 6.0 and have run a number of 3T MPRAGEs through recon-all. I have also run these with the -mprage and -3T flags to compare outputs. I have therefore ended up with four runs of the same test

Re: [Freesurfer] FSGD design for multi-centre study

2018-04-30 Thread C.P.E. Rollins
External Email - Use Caution I thought that I could not remove the class since this would mean that the contrast positive and negative values would no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12

Re: [Freesurfer] orig.mgz versus T1.mgz

2018-04-30 Thread Bruce Fischl
Hi Colleen it depends on what you want to do. The T1.mgz probably isn't the correct volume to use in any case. The orig.mgz is close to the raw data (e.g. it has a skull in it and has not been bias corrected). If you want a skull-stripped, bias-corrected version you could use either the

[Freesurfer] orig.mgz versus T1.mgz

2018-04-30 Thread C.P.E. Rollins
External Email - Use Caution Dear Freesurfer developers, A collaborator shared with me Freesurfer outputs, but I would like to some analyses requiring the scans in NIFTI format. I understand mri_convert should do the trick for this, though I was wondering whether I should use