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That is a lot of non-FreeSurfer code. We only support FreeSurfer code. If this is a question about FS code, then please distill it down to that.
On 5/15/2023 8:25 AM, bong516612 wrote:
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Greetings esteemed experts and professors,
I am currently conducting a study to validate my own hypothesis, utilizing recently acquired UKB neuroimaging data.
The core structure of my project is designed to replicate the work of He and Tong, generating an individualized subcortex atlas from the UKB's freesurfer output and attaching this to the cortical atlas, the Schaefer 100.
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To this end, I am conducting a pilot using data from a specific participant.
However, upon converting the freesurfer output, aparc+aseg.mgz, to nii.gz and transferring it to MNI space, it appeared to me that this file does not reside in the standard MNI space. This led me to bring forth the following question.
Here is the line of code I have written. Could there be a mistake that I have made?
$export Subject_DIR=/u6/surprise/UKB/data/sub-1001198/20227_2_0 $cd /u5/UKB_bong/data_tmp/tmp_analysis_CNDLway $applywarp --ref=$FSL_DIR/data/standard/MNI152_T1_2mm_brain.nii.gz --in=$Subject_DIR/fMRI/rfMRI.ica/filtered_func_data_clean.nii.gz --out=/u5/UKB_bong/data_tmp/tmp_analysis_CNDLway/filtered_func_data_clean_MNI.nii.gz --warp=$Subject_DIR/fMRI/rfMRI.ica/reg/example_func2standard_warp.nii.gz --interp=spline $fslmaths /u5/UKB_bong/data_tmp/tmp_analysis_CNDLway/filtered_func_data_clean_MNI.nii.gz -mas /u5/UKB_bong/data_tmp/tmp_analysis_CNDLway/MNI152_T1_2mm_brain_mask_bin.nii.gz /u5/UKB_bong/data_tmp/tmp_analysis_CNDLway/filtered_func_data_clean_MNI.nii.gz
$cd /u5/UKB_bong/data_tmp/tmp_analysis_CNDLway/ $mri_convert /u5/UKB_bong/data_tmp/sub-1001198/20263_2_0/FreeSurfer/mri/aparc+aseg.mgz aparc+aseg.nii.gz
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mri_vol2vol --mov "/u5/UKB_bong/data_tmp/tmp_analysis_CNDLway/subcor_mask.nii.gz" --targ "$FSL_DIR/data/standard/MNI152_T1_2mm_brain.nii.gz" --o "/u5/UKB_bong/data_tmp/tmp_analysis_CNDLway/subcor_mask_MNI2mm.nii.gz" --regheader --no-save-reg --nearest
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