Okay so if I am going to try and run this option, recon-all must also be done on the structural scans. I have the pre-processed structurals, and I understand from y'all's 2013 paper <http://linkinghub.elsevier.com/retrieve/pii/S1053811913005053> that they have already been through all of the steps in recon-all. First--is it correct that all steps (1-31) have been done on the data? Second, as with my original question, it seems that the HCP directories are quite different than the defaults that would be created by a standard Freesurfer recon-all run. Assuming that Freesurfer scripts will look for recon-all files in directories not present in the HCP data as downloaded, (for example, subjid/mri/... and subj/surf/... are not valid paths in the pre-processed data), would it just be better to get the un-processed structurals and re-run all of the recon-all steps myself?
I guess I'm just wondering what the value of the pre-processed data is if it is re-organized as to be un-readable by Freesurfer defaults. 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 7:02 PM, Matt Glasser <m...@ma-tea.com> wrote: > I wouldn’t 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+User >> s+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/10 >> 1915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR.img --src_type analyze >> --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_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/rfMR >> I_REST1_LR/ >> srcvol = /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_REST1_LR/REST1LR.img >> srctype = analyze >> srcreg = /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >> I_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/101915/MNINonLinear/Results/rfMR >>> I_REST1_LR/rfMRI_REST1_LR.nii.gz --regheader --reg >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMR >>> I_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 >> freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.e >> du/mailman/listinfo/freesurfer The information in this e-mail is >> intended only for the person to whom it is addressed. If you believe this >> e-mail was sent to you in error and the e-mail contains patient >> information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error but does not contain patient information, please contact the >> sender and properly dispose of the e-mail. >> >> _______________________________________________ >> 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. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > _______________________________________________ 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. If you believe this > e-mail was sent to you in error and the e-mail contains patient > information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error but does not contain patient information, please contact the sender > and properly dispose of the e-mail. > > _______________________________________________ > 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. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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