1. Yes, that's reasonable. You can use .nii.gz and the output extension and it will automatically gzip compress it.

2. No, I don't think so. 3. The only real way to check is visual inspection.

cheers Bruce On Tue, 26 Jul 2011, Antonella Kis wrote:

Hi Bruce,

I will graetly appreciate if you can help me with the following questiosn:

1).I am not sure what you mean by type of acquisition but going back to my last question, the only thing I know is that my MRI data contains more sequences/series (3DAx_T1, 3DSag_T1, Ax_Flair, Ax_PD, Ax_T2, BOLD, DTI_15, DTI_32). I converted my dicom files from 3DAx_T1 to a NIFTI format and I wonder why the size of this file is so big (38 MB) while same type of  files from other subjects but converted by somebody else before me, are only around 4.5 MB. Is 38 MB a regular NIFTI size to be used in Freesurfer or will take a long time for data preprocessing?

2). In the aparc.stats data if the number of vertices is increasing from a region to another the cortical thickness should also increase?

3). How I can check to make sure my segmentations  aparc+aseg, cortical parcellation  and their labelling are correct?

Thank you very much. Antonella

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From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 22, 2011 3:47 PM Subject: Re: [Freesurfer] Pre-processing issues

Hi Antonella

do you know what the type of acquisition is? That name isn't enough to know for sure, but it might be.

And yes, you can run more than 1 recon at a time assuming you have enough ram on your machine. It won't go faster of course unless you have multiple cpus

cheers Bruce On Fri, 22 Jul 2011, Antonella Kis wrote:

...

Dear Bruce,

I have two more questions for today, please: 1). Just to be sure that  I understood correct: for my  cortical thickness studies and also for a group studies analysis I will use only the data from the 3DAx_T1series which was converted to a .nii.gz file. Is this right?

2). If I want to shortness the pre-processing time while running the recon-all for my subjects, can I run recon-all for three subjects  by opening three terminals in the same time? Running more subjects in the same time will induce more errors for a manual correction or the results will be the same with the one while running each subject individual/only one terminal at the time.

Thank you and have a great weekend. Antonella

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