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