Hi Marja

can you send us the actual command and screen output you ran? It should be something like:

recon-all -all -s <subject id> -i <path to input .nii.gz file>

Depending on your hardware it will take hours to finish, but it will do pretty much everything (segmentation, surface reconstruction, template registration, thickness measurement, parcellation, etc...)

 cheers
Bruce

On Thu, 26 May 2016, Marja Caverlé wrote:

Hi All,

I am new to Freesurfer and I would like to use it for a project I am working
on right now. For this project I have two patient groups of which I have
structural MRI scans and a lot of other measures. I hope to get cortical
thickness numbers from the scans and compare these with the other measures.

Anyway, I am trying to get something done in Freesurfer and it does not
really seem to work. I assume I have to do a recon-all -all, but when I try
this, I get an error saying that the flag is unrecognised. It probably is a
small error, easy to solve, but I already get stuck on it since I am totally
new to Freesurfer.

Could anyone help me out?
Some of my questions are;

- Am I correct that recon-all -all already coregisters the scans to
template?
- What will be the outcome? Will I get pictures, or a table with numbers,
and if it is a table, which area's are specified? I have a list of ROIs, but
how do I let Freesurfer know I am interested in those areas?
- Can I do recon-all -all on a folder with all my patients, or do I have to
do it one by one? (There not that much, approximately 12 scans)
- Can I do recon-all -all on .nii.gz files? The originals are DICOM, but the
problem is that there is just one large DICOM folder, which does not specify
which files are part of which scan. I have converted them to .nii.gz since I
am a bit familiar with FSL, but I do not know whether this actually works in
Freesurfer.
- Why do I get the unrecognised flag error?

I apologise for these questions, they are probably very easy to answer, but
I just don't have a clue yet.

Thank you guys.

Best,

Marja

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