There is a structural extended package that has the FreeSurfer folders. 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: Thursday, December 28, 2017 at 12:56 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] bbregister error -- Human Connectome Project Data 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 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/REST1 >>> LR.img --src_type analyze --reg >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1 >>> LR_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/REST1 >>> LR.img >>> srctype = analyze >>> srcreg = >>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1 >>> LR_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/fsav >>> erage4/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/fsav >>> erage4/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/REST >>>> 1LR_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/REST >>>> 1LR_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/REST >>>> 1LR_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. >>>> 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 <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/REST >>>> 1LR_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/REST >>>> 1LR_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/REST >>>> 1LR_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. >>>> 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/rfMR >>>> I_REST1_LR.nii.gz --regheader --reg >>>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST >>>> 1LR_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/rfMR >>>> I_REST1_LR.nii.gz >>>> reg file >>>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST >>>> 1LR_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 >> 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