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/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/10 >> 1915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat >> tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_REST1_LR/tmp.bbregister.26127 >> Log file is /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_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/rfMR >> I_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/rfMR >> I_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/rfMR >> I_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/rfMR >> I_REST1_LR/tmp.bbregister.26127/template.nii... >> fslregister --s 101915 --mov /N/dc2/scratch/lruck/LH_all/10 >> 1915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii >> --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_REST1_LR/tmp.bbregister.26127/reg.init.dat --niters 1 --maxangle 90 >> --tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_REST1_LR/tmp.bbregister.26127/fslregister --dof 6 --fsvol >> brainmask.mgz --nobetmov >> >> Log file is /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_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/10 >> 1915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii >> --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_REST1_LR/tmp.bbregister.26127/reg.init.dat --niters 1 --maxangle 90 >> --tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_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/10 >> 1915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat >> tmp /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_REST1_LR/tmp.bbregister.26239 >> Log file is /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_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/rfMR >> I_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/rfMR >> I_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/rfMR >> I_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/rfMR >> I_REST1_LR/tmp.bbregister.26239/template.nii... >> spmregister --s 101915 --mov /N/dc2/scratch/lruck/LH_all/10 >> 1915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/template.nii >> --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_REST1_LR/tmp.bbregister.26239/reg.init.dat --tmp >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_REST1_LR/tmp.bbregister.26239/spmregister >> Log file is /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_REST1_LR/tmp.bbregister.26239/spmregister.log >> Wed Dec 27 12:54:14 EST 2017 >> --s 101915 --mov /N/dc2/scratch/lruck/LH_all/10 >> 1915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26239/template.nii >> --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_REST1_LR/tmp.bbregister.26239/reg.init.dat --tmp >> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_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/10 >> 1915/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz >> --regheader --reg /N/dc2/scratch/lruck/LH_all/10 >> 1915/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/10 >> 1915/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz >> reg file /N/dc2/scratch/lruck/LH_all/1 >> 01915/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* >> >> >> > _______________________________________________ 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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