Yes, this is ok. This was a bit of a hack that someone introduced into recon-all a number of years ago, and we have not gotten around to fixing it.

On 2/8/2022 7:25 PM, Harriet Dempsey-Jones wrote:

External Email - Use Caution

Hi there,

I am using AFNI to process some epi data. As part of this analysis, I am creating anatomical surfaces on which to project my data using recon-all in Freesurfer.

My pre-processing in AFNI indicated that best alignment of my epi to anatomical image is achieved using a combination of affine and non-linear warping (3dQwarp in AFNI). So I was hoping to use this warped anatomical image from my experimental data to create a surface from with recon-all.

I just tried to set this to run, and it errored and failed (see bottom of email)

The gist appears to be that when it was completing the mri_convert stage it errored because the anatomical nifti image I had fed it, was not 256 FOV. It appears to be larger because I had to add some space to the image to rotate it during alignment.

The error suggests using the flag -cw256 with recon-all, but I cannot find any documentation about how this works or what it does. I searched the forum archives as well, which came up with 60k hits, but none of them seemed to contain -cw256 when I control+f looking for it.

Could someone let me know a bit more about this flag and whether it is ok to use for my purposes?

I have included my recon-all code too for reference purposes. Please also let me know if there is anything glaringly wrong there, I am very new to fMRI analysis.

Thank you for any help you might be able to give me!

ERROR

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mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 4078 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/orig.mgz...

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ERROR! FOV=273.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible.

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Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s P00_FG exited with ERRORS at Tue Feb  8 22:13:53 AEST 2022

MY CODE

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#!bin/tcsh

# Freesurfer start-up module load freesurfer

# Set up vars set subj_init = FG set subj_num = P00 set subj = {$subj_num}_{$subj_init}

set recon_use = (-all) # set recon_use = (-autorecon1)

set anat = /scratch/inode/uqhdemp1/Fingertip_maps/{$subj}/{$subj}.results/{$subj_init}_uniden_avg_wholebrain_unpad_warped_3dQ.nii

set base_dir = /scratch/inode/

set subj = {$subj_num}_{$subj_init} set expert_file = 1b_FS_expertfile

## 1. Freesurfer recon all recon-all $recon_use -s $subj -hires -i $anat -sd $base_dir/Surfaces -openmp 12 -expert $base_dir/Parent_scripts/Surfaces/$expert_file

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