Nifty is a format that a lot of people use (including us) but it is not needed for our processing. Pick *one* file in your dicom series and pass it to recon-all:

recon-all -i <path to 1 dicom file> -s <subject ID you create> -sdir <path to the dir that will contain all outputs> -all

cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of saman fouladi
Sent: Wednesday, October 21, 2020 11:57 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] please help me

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Thank you for your response

I have 60 subject MRI that each contains 174 dcm file. and i want predict age of these subjects. in step one i want extract morphology features and in step2 create a deep learning model that predict age.

According to what I said, what should I do?

If I have to use recon-all with what code can I do this? And what is the use of nifty?

On Wednesday, October 21, 2020, 1:06:50 AM GMT+3:30, Fischl, Bruce <bfischl@mgh.harvard.edu> wrote:

Hi Saman

Recon-all will give you a comprehensive assessment of most macroscopically visible structures in the brain. You don’t have to convert to nifty first – just point recon-all at a single slice in the proper dicom series (for your 3D T1-weighted scan), and it will spend a few hours doing stuff

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of saman fouladi
Sent: Tuesday, October 20, 2020 4:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] please help me

External Email - Use Caution

I want to process MRI images to extract Morphology features.

I convert my dcm file to nii format by mri-convert command and then I used FSL software and BET(Best extraction Tool).

Next I do not know what to do to extract morphological features?

My other question is what is the difference between recon-all and use FEAT( in FSL software)? What are the uses of each?

Thank you

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