no worries. That is a pretty short TR and a pretty long TE for a typical T1-weighted scan. Do you know what kind of scan it was? That is, the name of the sequence (e.g. FLASH, MPRAGE, SPGR, etc...)

cheers Bruce

On Tue, 27 Feb 2018, adriancarl.steiner@uzh.ch wrote:

Hi Bruce Thank you very much for your swift response. Our image was  T1-weighted, with a resolution of 240 x 240 x 160 and a field intensity of 3 Tesla. The Sequence was TR/TE 10.66/6.04 ms. I have attached the recon-all.log file to this mail. Sorry for  not having supplied the required information the first time, as I said it is my first try with freesurfer.

Cheers

Adrian

-----freesurfer-bounces@nmr.mgh.harvard.edu schrieb: -----An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Von: Bruce Fischl Gesendet von: freesurfer-bounces@nmr.mgh.harvard.edu Datum: 27.02.2018 16:05 Kopie: Fedele Tommaso Tommaso.Fedele@usz.ch Betreff: Re: [Freesurfer] Quality issues when running recon-all

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

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