Specify a file format for the output (eg, C01.mgz)

On 4/24/18 3:17 PM, Abdullah Ishaque wrote:

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Hi,

Thank you for the prompt response.

I used the following command:

mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol from the previous step) --out C01 --regheader C01 --hemi lh --projfrac 0.5

This created two files called COR-.info and COR001. I tried loaded the COR001 file into freeview and tksurfer, but I keep the error "MRISalloc(8229512, 76): could allocated faces \ cannot allocate memory

Am I making a mistake somewhere?

Thanks,

On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve <dgreve@mgh.harvard.edu> wrote:

That all looks correct. For the registration, just use --regheader C01

On 4/24/18 11:12 AM, Abdullah Ishaque wrote:

Hi,

It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps.

I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject, sample them from the mid-cortical level to create cortical myelin surface maps, and perform vertexwise and ROI based analyses.

Here's what I've done so far:

1. recon-all for all the subjects

2. Used bbregister to register the native T2 scans to the conformed T1 scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl --reg register.dat --t2 (my understanding here is that this generates the .dat file that has the transformation to register the T2 image to the conformed orig.mgz file from subject C01)

3. Applied the register.dat file to the native T2 using mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers the T2 to the orig.mgz file in the conformed space)

The next step for me is to perform mri_vol2surf. My question here is, which file should I select for the --srcreg flag and what should the --trgsubject input be? Secondly, am I on the right track to complete the analysis i.e., correct file types and my understanding of the steps? Clarifications regarding these questions and any suggestions for further directions will be very helpful!

Let me know. Thanks!

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--

Abdullah Ishaque, BSc.

MD/PhD Student, Neuroscience and Mental Health Institute

Faculty of Medicine and Dentistry, University of Alberta

aishaque@ualberta.ca

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