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