As a work-around to the above issue, I did the registrations directly in FSL using FLIRT, and then converted the resultant fsl reg.mat files to freesurfer reg.dat files (using tkregister2; they all look fine). Now, all I need is to project these rfMRI data to fsaverage4, and I thought mri_vol2surf was the right way to do this.

Unfortunately, I am now having the same directory issue with mri_vol2surf (new error log below), where it can't find /surf/lh.white for my subject. The HCP pre-processed data has already been through recon-all, so there are several *white*surf* files to choose from for each subject, but they are not in the directory specified by default in MRISread (subjid/surf/).

I thought I could fix this by specifying the right target subject (--trgsubject fsaverage4, which I have manually copied, along with the other $FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message boards), or specifying the right directory (I've tried the --surf command with both the fsaverage4 path, and to multiple [subject]?h.white paths, but it just appends them to the non-existent default path--see below). Thus, regardless of what I specify, I keep getting the same error related to a default search in subjid/surf/.

Is there a way to point MRISread to the correct surf files, without re-doing recon-all or moving the pre-processed surfaces to a "surf" folder for all 40 subjects?

Lana

[lruck@c5 LH_all]$ mri_vol2surf --mov /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR.img --src_type analyze --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat --hemi lh --fwhm 6 --trgsubject fsaverage4 --surf /N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white --out /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/
srcvol = /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR.img
srctype = analyze
srcreg = /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat
srcregold = 0
srcwarp unspecified
surf = /N/dc2/scratch/lruck/LEH_all/fsaverage4/surf/lh.white
hemi = lh
trgsubject = fsaverage4
surfreg = sphere.reg
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
analyzeRead() roi_scale 0.000000000
Done loading volume
INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0.
Input reg is register.dat
-------- original matrix -----------
0.96607 0.00120 0.00047 -0.78994;
0.01685 0.96915 -0.00899 2.16005;
-0.00580 -0.00642 0.98726 -0.56166;
0.00000 0.00000 0.00000 1.00000;
-------- original matrix -----------
INFO: smoothing volume at fwhm = 6 mm (std = 2.54797)
Reading surface /N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white
MRISread(/N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white): could not open file
No such file or directory
mri_vol2surf: could not read surface /N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white
No such file or directory

Lana Ruck, M.A.

Associate Instructor, Department of Anthropology

Graduate Scholars Fellow, Cognitive Science Program

Indiana University, Bloomington

Student Building 166
lruck@umail.iu.edu

On Wed, Dec 27, 2017 at 1:43 PM, Lana Ruck <lruck@umail.iu.edu> wrote:

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