Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

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Hi Bruce,

Thanks Bruce i understand that.

But can't i run free-surfer with all these parameters (size, spacing and orientation) ?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 8:22:38 PM Subject: Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

Hi Ritesh

your best bet is to run everything normally, then convert the output to whatever format/orientation/voxel size you want

cheers Bruce On Thu, 10 May 2018, Ritesh Mahajan wrote:

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Thank you Bruse. Actually i converted the input into RAI orientation using mri_convert --out_orientation and gave RAI input the free-surfer through recon-all. The results are not generated.

My goal is to run free-surfer with RAI orientation and result should be in RAI. I also want the output of free-surfer with dimensions as 128*128*128 and spacing as 2,2,2 mm.

Can you tell whether this can be done using free-surfer?

Thanks, Ritesh Mahajan

----- Original Message ----- From: "Ritesh Mahajan" ritesh.mahajan@ripl.ricoh.com To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 10, 2018 1:44:40 PM Subject: run recon all with forced orientation, spacing and dimension

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Hello Team,

As i know free-surfer generates the output with following:

1. Dimensions : 256*256*256
2. Spacing : 1, 1,1 mm
3. Orientation : LIA

Is there any way to run free-surfer with user specified orientation, spacing and dimension ?

Thanks, Ritesh Mahajan

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