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Thank you so much!

On Dec 7, 2021, at 12:06 PM, Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu wrote:

Hi Fateme, Infant Freesurfer takes a single input image so there is no rawavg file created at the beginning of the pipeline. You should be able to replace rawavg in your command with the original image that you used as an input. Lilla

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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fateme Haghpanah fateme@cs.toronto.edu Sent: Wednesday, December 1, 2021 9:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] InfantFS - resampling asset to native space

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Dear FreeSurfer Developers,

We are using InfantFS and noticed that after running recon-all ("infant_recon_all --newborn --s ${SUBJ}”) , the voxel size changes to 1*1*1. I know that using "mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz” we can convert the aseg output of adult FreeSurfer to native space. Is there any similar command to do so for infants?

I wanted to try this one, however there is no rawavg.mgz file in the mri folder of infant subjects.

Thanks in advance, Fateme

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