Hello, 

I am currently starting a project with the minimally pre-processed rfMRI from the Human Connectome Project, but I need to do some additional processing first. This includes smoothing at 6mm FWHM and projection onto the fsaverage4 surface. I have smoothed the pre-processed rfMRI data using mri_convert (and have also converted the provided brain-extracted anatomical), but I am having issues registering the smoothed rfMRI volumes, and I understand that I need these register.dat files for mri_vol2surf. 

I have tried bbregister --init-fsl; bbregister --init-spm; and manual registration using tkregister2. All of them give me the same error--I think it is a path error looking for a subject-specific brain mask (see detailed console errors below). 

After reading through others' problems with bbregister, I made sure I am running the updated versions of bb- and fsl-register, below:
fslregister,v 1.40 2016/02/12 21:43:15 zkaufman
bbregister,v 1.75 2016/05/10 20:02:28 greve
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
I also made sure these files had the edits recommended to others, so I don't think this is an previously-addressed issue.

That // in all my errors suggests to me that this is a path problem with my HCP data? I am new to FreeSurfer, but I would think that the HCP-pre-determined path organization should be compatible with FSL and FreeSurfer, since their pipelines use both. Is this a compatibility issue with FreeSurfer 6.0? 

Anyways, I would prefer to use bbregister --init-fsl, but do not know how to point it to the right directory for a brainmask. There is no information provided in any of the --help menus or Wiki pages regarding how to specify brain masks for registration, and the HCP pre-processed data provides multiple 'mask.nii.gz' files that I suppose are not being recognized by bbregister (perhaps because they are not .mgz? I tried converting one to mgz and also got an error from mghWrite). Either way, I have 4 rfMRI runs per subject and over 40 subjects to process, so any advice on this error would be greatly appreciated. 

Thanks in advance!
Lana Ruck
                                                                            
 
Console errors (bolded and underlined) for bbregister --init-fsl,  bbregister --init-spm, and tkregister2: 

[lruck@c5 MNINonLinear]$ bbregister --mov ./Results/rfMRI_REST1_LR/REST1LR.img --bold --s 101915 --init-fsl --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat
tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127
Log file is /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat.log
Wed Dec 27 12:51:51 EST 2017

setenv SUBJECTS_DIR /N/dc2/scratch/lruck/LH_all/
cd /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear
/N/soft/rhel6/freesurfer/6.0.0/freesurfer/bin/bbregister --mov ./Results/rfMRI_REST1_LR/REST1LR.img --bold --s 101915 --init-fsl --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat

$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
Linux c5.karst.uits.iu.edu 2.6.32-696.16.1.el6.x86_64 #1 SMP Sun Oct 8 09:45:56 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /N/soft/rhel6/freesurfer/6.0.0/freesurfer
mri_convert ./Results/rfMRI_REST1_LR/REST1LR.img /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii
mri_convert.bin ./Results/rfMRI_REST1_LR/REST1LR.img /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./Results/rfMRI_REST1_LR/REST1LR.img...
  analyzeRead() roi_scale   0.000000000
TR=720.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii...
fslregister --s 101915 --mov /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/reg.init.dat --niters 1 --maxangle 90 --tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov

Log file is /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/reg.init.dat.fslregister.log

Wed Dec 27 12:51:52 EST 2017
--s 101915 --mov /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/reg.init.dat --niters 1 --maxangle 90 --tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov
$Id: fslregister,v 1.40 2016/02/12 21:43:15 zkaufman Exp $
c5.karst.uits.iu.edu
Linux c5.karst.uits.iu.edu 2.6.32-696.16.1.el6.x86_64 #1 SMP Sun Oct 8 09:45:56 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
ERROR: cannot find /N/dc2/scratch/lruck/LH_all//101915/mri/brainmask


[lruck@c5 MNINonLinear]$ bbregister --mov ./Results/rfMRI_REST1_LR/REST1LR.img --bold --s 101915 --init-spm --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat
tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239
Log file is /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat.log
Wed Dec 27 12:54:14 EST 2017

setenv SUBJECTS_DIR /N/dc2/scratch/lruck/LH_all/
cd /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear
/N/soft/rhel6/freesurfer/6.0.0/freesurfer/bin/bbregister --mov ./Results/rfMRI_REST1_LR/REST1LR.img --bold --s 101915 --init-spm --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat

$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
Linux c5.karst.uits.iu.edu 2.6.32-696.16.1.el6.x86_64 #1 SMP Sun Oct 8 09:45:56 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /N/soft/rhel6/freesurfer/6.0.0/freesurfer
mri_convert ./Results/rfMRI_REST1_LR/REST1LR.img /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/template.nii
mri_convert.bin ./Results/rfMRI_REST1_LR/REST1LR.img /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/template.nii 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./Results/rfMRI_REST1_LR/REST1LR.img...
  analyzeRead() roi_scale   0.000000000
TR=720.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/template.nii...
spmregister --s 101915 --mov /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/template.nii --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/reg.init.dat --tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/spmregister
Log file is /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/spmregister.log
Wed Dec 27 12:54:14 EST 2017
--s 101915 --mov /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/template.nii --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/reg.init.dat --tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/spmregister
$Id: spmregister,v 1.46 2016/02/16 17:17:20 zkaufman Exp $
matlab matlab
fmt nii
UseSPMGetSpace 1
ERROR: /N/dc2/scratch/lruck/LH_all//101915/mri/brainmask.mgz not found in either COR or MGZ formats


[lruck@c5 MNINonLinear]$ tkregister2 --mov /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz --regheader --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat --surf
tkregister_tcl /N/soft/rhel6/freesurfer/6.0.0/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz
reg file       /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat
LoadVol        1
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: could not find orig as either mgz or COR
/N/dc2/scratch/lruck/LH_all//subject-unknown/mri/orig