Structural MRI is a broad topic. Can you be more specific about what type of features? All the tools you mentioned can be used for structural MRI analysis. I would also add MRTrix if you're interested in diffusion and tractography.

Thomas Welton Thanks for your response, i am trying to extract Grey Matter, White Matter and CSF

If you mean to calculate the volume of each region, with FSL, you can use FAST to segment white, grey and CSF. Then you can use fslmaths to threshold and fslstats to calculate the volume of each. There are equivalents in the other packages you mentioned.

Thomas Welton Thank you

Generally Freesurfer is considered one of the gold standard tools for sMRI analysis (structural segmentation, gray matter thickness etc.)

Hi, Oyetunde

I agree with Rangaprakash and Thomas, all of them they mentioned will work for your sMRI project.

Here, I also would like to recommend another toolbox for sMRI analysis, CAT (use it with SPM, http://www.neuro.uni-jena.de/cat/). Using CAT, you can do gray/white matter, CSF segmentation, as well as cortical reconstruction like Free Surfer. CAT may be easier for you to run.

Enjoy,

Shun

Hi,

I don't know whether today my answer is useful to you or not.

• I searched a lot to find good software to analyze sMRI. Among all of the tools, I found out the CAT12 (a toolbox of SPM12) is one of the best software for segmenting and analyzing structural MR images with excellent accuracy (I agree with Shun Yao). In addition to high accuracy, it also has a high segmentation speed, which helps you save time.
• After CAT12, I recommend you using FSL and Freesurfer. ُSimilarly they could be used for structural analysis.
• As well as I suggest you using brainsuite (http://www.brainsuite.org/).

Hope to find this useful,

Mahshad