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 lruck@umail.iu.edu
On Wed, Dec 27, 2017 at 7:02 PM, Matt Glasser matt@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-bounces@nmr.mgh.harvard.edu on behalf of Lana Ruck < lruck@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 lruck@umail.iu.edu
On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser matt@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-bounces@nmr.mgh.harvard.edu on behalf of Lana Ruck < lruck@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 lruck@umail.iu.edu
On Wed, Dec 27, 2017 at 1:43 PM, Lana Ruck lruck@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*
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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.