Data with 1mm voxel size

[Armin Allahverdy]

Hi all

Can we use FreeSurfer pipeline of HCP for T1w and T2w images with 1mm voxel size? Because HCP data are originally in size of 0.7 mm voxel size.  

[Glasser, Matthew]

Yes, though accuracy in thin heavily myelinated cortex is reduced a bit.

 

You should change the input templates for PreFreeSurfer to 1mm instead of 0.7mm.

Matt.

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[Armin Allahverdy]

Thanks for your response, but I meant the freesurfer part, specifically the high-resolution white surface placement, where we must up-sample the 1mm resolution images to 0.7 mm resolution?

Can we skip this up-sampling step? If yes, how can we do?

Thanks in advance,

Armin

[Glasser, Matthew]

There is no mandatory upsampling step.

[Armin Allahverdy]

I used following code to run freesurfer step without using up sampling to 0.7 mm, 
export HCPPIPEDIR=/home/all9kt/CINEPS2/CINEPS2Pipeline_N
. /home/all9kt/CINEPS2/CINEPS2Pipeline_N/Examples/Scripts/SetUpHCPPipeline.sh
export SUBJECTS_dIR=/home/all9kt/CINEPS2/studyfolder

export HCPPIPEDIR_Global=/home/all9kt/CINEPS2/CINEPS2Pipeline_N/global/scripts
export HCPPIPEDIR_Templates=/home/all9kt/CINEPS2/CINEPS2Pipeline_N/global/templates
export CARET7DIR=/home/all9kt/workbench/bin_linux64
source ${HCPPIPEDIR}/Examples/Scripts/SetUpHCPPipeline.sh
#SUBJECTS_dIR="/home/all9kt/CINEPS2/studyfolder"
SUBJECT_ID="sub-130"  # Change this to your subject ID

SUBJECT_Id="sub-130k1mm"


${HCPPIPEDIR}/FreeSurfer/FreeSurferPipeline.sh \
--subjectDIR="${SUBJECTS_dIR}" \
--subject="${SUBJECT_Id}" \
--t1="${SUBJECTS_dIR}/${SUBJECT_ID}/T1w/T1w_acpc_dc_restore.nii.gz" \
--conf2hires=FALSE \
--t2="${SUBJECTS_dIR}/${SUBJECT_ID}/T1w/T2w_acpc_dc_restore.nii.gz" \
--t1brain="${SUBJECTS_dIR}/${SUBJECT_ID}/T1w/T1w_acpc_dc_restore_brain.nii.gz"

but I faced to this Error:

~/CINEPS2/studyfolder/sub-130k1mm/mri ~
Mon Jun 17 15:28:00 EDT 2024:FreeSurferPipeline.sh: While running '/home/all9kt/CINEPS2/CINEPS2Pipeline_N/FreeSurfer/FreeSurferPipeline.sh --subjectDIR=/home/all9kt/CINEPS2/studyfolder --subject=sub-130k1mm --t1=/home/all9kt/CINEPS2/studyfolder/sub-130/T1w/T1w_acpc_dc_restore.nii.gz --conf2hires=FALSE --t2=/home/all9kt/CINEPS2/studyfolder/sub-130/T1w/T2w_acpc_dc_restore.nii.gz --t1brain=/home/all9kt/CINEPS2/studyfolder/sub-130/T1w/T1w_acpc_dc_restore_brain.nii.gz':

Mon Jun 17 15:28:00 EDT 2024:FreeSurferPipeline.sh: ERROR: Expected t2w_input_file: rawavg.T2.prenorm.mgz DOES NOT EXISTMon Jun 17 15:28:00 EDT 2024:FreeSurferPipeline.sh: ABORTING 

how can I solve this error?

I have to say when conf2hires is true, I wont face this issue.

Thanks in advance

Armin

[Glasser, Matthew]

Perhaps conf2hires is required to make the pipeline run currently.  I don’t think it is harmful on the 1mm data.