Hi Adrian
it's impossible for us to diagnose without more information. What was the acquisition (field strength, resolution, sequence type, etc...) and at least send us the contents of the recon-all.log file.
cheers Bruce On Tue, 27 Feb 2018, adriancarl.steiner@uzh.ch wrote:
Dear Freesurfer community,
I am at my first experience with Freesurfer. Following the tutorial, I ran Freesurfer on MR images for my Master Thesis.
When running Freesurfer's 'recon-all' command on a Mac Pro to process a .nii MRI file, I was able to complete all calculations in approximately 10 hours as estimated, and obtained a message that all operations were completed without Errors or bugs.
However, the image I was able to retrieve from the lh.pial file seems to be of greatly inferior quality compared to the ones we obtained from a test run using tutorial data. Attached to this mail, you will find screenshots of the MR and the lh.pial output from Freesurfer.
This is the code I entered into Terminal to set up recon-all:
export FREESURFER_HOME=/Volumes/LaCie/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
mri_convert -c -oc 0 0 0 /Volumes/LACIE-SHARE/Adrian/Patient data .nii/IA/IA_MRpre .nii/T1_3D_TFE_DBS.nii /Volumes/LaCie/freesurfer/buckner_data/tutorial_subjs/multimodal/fmri/fbirn-101/template.nii
S_NAME=IA
DATA_PATH=/Volumes/LaCie/freesurfer/buckner_data/tutorial_subjs/multimodal/fmri/fbirn-101/template. nii
recon-all -i $DATA_PATH -subject $S_NAME -all
Given the good quality of the MR, I expected a better quality in the Freesurfer Output. Could you please help me understand how I can improve my results?
Thank you in advance for your Support
Adrian Steiner