I wouldn¹t trust resting state data that have not been properly denoised. You should only need the structural and FIX cleaned packages for what you are doing. The link that I put below explains how to get HCP data onto the fsaverage4 surface. You will need FreeSurfer and Connectome Workbench for this.
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 5:55 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] bbregister error -- Human Connectome Project Data Matt, Thanks for the quick reply! I'll check out that Wiki document and the 2016 Nature paper first. The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is because I would like to use the iterative parcellation algorithm from the Liu Lab @Harvard (as described in Wang, D. et al. 2015: Parcellating Cortical Functional Networks in Individuals. Nat. Neurosci; http://nmr.mgh.harvard.edu/bid/DownLoad.html), but I am unsure if the ICA-FIX data are appropriate for this. I know that the minimally pre-processed rfMRI data just need to be smoothed and projected to fsaverage4 for the MATLAB algorithm to work, but I didn't see a clear way to get the ICA-FIX data in the right format, as per the specifications provided by the Lui Lab. I am also not using a local machine to do the processing (I am using my Uni's supercomputing infrastructure), so I don't know if I can get connectome workbench installed in order to pre-process CIFTI data. That's why I am working with standard formats (the supercomputer has freesurfer, fsl, etc.). Assuming I can get cnm-wb installed by admins on the supercomputer, and that I can use it to get the ICA-FIX data appropriately formatted for parcellation with MATLAB, do you suggest I download the extended packages, or will the compact ones have everything I need? Lana 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 6:26 PM, Matt Glasser <m...@ma-tea.com> wrote: > 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#HCPUsersFAQ- > 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/REST1L >> R.img --src_type analyze --reg >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1L >> R_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/REST1L >> R.img >> srctype = analyze >> srcreg = >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1L >> R_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/fsave >> rage4/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/fsave >> rage4/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/REST1 >>> LR_register.dat >>> tmp >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.26127 >>> Log file is >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1 >>> LR_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/REST1 >>> LR_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.b >>> bregister.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.b >>> bregister.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.b >>> bregister.26127/template.nii... >>> fslregister --s 101915 --mov >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.26127/template.nii --reg >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.26127/reg.init.dat --niters 1 --maxangle 90 --tmp >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.26127/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov >>> >>> Log file is >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.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.b >>> bregister.26127/template.nii --reg >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.26127/reg.init.dat --niters 1 --maxangle 90 --tmp >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.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/REST1 >>> LR_register.dat >>> tmp >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.26239 >>> Log file is >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1 >>> LR_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/REST1 >>> LR_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.b >>> bregister.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.b >>> bregister.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.b >>> bregister.26239/template.nii... >>> spmregister --s 101915 --mov >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.26239/template.nii --reg >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.26239/reg.init.dat --tmp >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.26239/spmregister >>> Log file is >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.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.b >>> bregister.26239/template.nii --reg >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.26239/reg.init.dat --tmp >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.b >>> bregister.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/REST1 >>> LR_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/REST1 >>> LR_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 > freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinf > o/freesurfer The information in this e-mail is intended only for the person to > whom it is addressed. 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