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Hello Bruce,
1) I converted the my mri data from ALS to RAI orientation through command "mri_convert --out_orientation RAI inputALS.nii outputRAI.nii" 2) Then i gave a run for free-surfer, using recon-all command. After successful run of free-surfer without any error message, still i do not see any results generated by free-surfer. Any you please help why is it so ? 3) Under results mri folder i see only orig.mgz, orig_nu.mgz and rawavg.mgz. Other results are not generated.
Please can you explain why this happening ?
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 9:50:44 PM Subject: Re: [Freesurfer] run recon all with forced orientation, spacing and dimension
because internally we expect things to be a certain way (which is why we convert the data to that format). There are also some requirements on the data that you have to meet. For example 2mm is not high enough resolution to get accurate cortical models. The acquired data has to be no bigger than about 1.5mm in any dimension.
cheers Bruce
On Thu, 10 May 2018, Ritesh Mahajan wrote:
External Email - Use CautionHi 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:
External Email - Use CautionThank 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:
- Dimensions : 256*256*256
- Spacing : 1, 1,1 mm
- Orientation : LIA
Is there any way to run free-surfer with user specified orientation, spacing and dimension ?
Thanks, Ritesh Mahajan
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