You would be better off resampling the existing CIFTI data to the fsaverage4 surface rather than redoing the projection and smoothing in the volume. Instructions for getting to fsaverage are available here:
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFA Q-9.HowdoImapdatabetweenFreeSurferandHCP? Also I would recommend starting from the ICA+FIX cleaned data, not the minimally preprocessed data. If you must smooth the data, you can do that with wb_command -cifti-smoothing before following the above steps. Peace, Matt. From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lana Ruck <lr...@umail.iu.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, December 27, 2017 at 4:41 PM To: <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] bbregister error -- Human Connectome Project Data 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/fsaver > age4/surf/lh.white > MRISread(/N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_a > ll/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/fsaver > age4/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/REST1L >> R_register.dat >> tmp >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.26127 >> Log file is >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1L >> R_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/REST1L >> R_register.dat >> >> $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ >> Linux c5.karst.uits.iu.edu <http://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.bb >> register.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.bb >> register.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.bb >> register.26127/template.nii... >> fslregister --s 101915 --mov >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.26127/template.nii --reg >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.26127/reg.init.dat --niters 1 --maxangle 90 --tmp >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.26127/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov >> >> Log file is >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.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.bb >> register.26127/template.nii --reg >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.26127/reg.init.dat --niters 1 --maxangle 90 --tmp >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.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 <http://c5.karst.uits.iu.edu> >> Linux c5.karst.uits.iu.edu <http://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/REST1L >> R_register.dat >> tmp >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.26239 >> Log file is >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1L >> R_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/REST1L >> R_register.dat >> >> $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ >> Linux c5.karst.uits.iu.edu <http://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.bb >> register.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.bb >> register.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.bb >> register.26239/template.nii... >> spmregister --s 101915 --mov >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.26239/template.nii --reg >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.26239/reg.init.dat --tmp >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.26239/spmregister >> Log file is >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.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.bb >> register.26239/template.nii --reg >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.26239/reg.init.dat --tmp >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bb >> register.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/REST1L >> R_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/REST1L >> R_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 >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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