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DPABISurf V1.1 Is Released
by YAN Chao-Gan 25 Jul '19

25 Jul '19

External Email - Use Caution Dear Colleagues, We are pleased to announce the release of DPABISurf V1.1! DPABISurf is a surface-based resting-state fMRI data analysis toolbox evolved from DPABI/DPARSF, as easy-to-use as DPABI/DPARSF. DPABISurf is based on fMRIPprep 1.4.1 (Esteban et al., 2018)(RRID:SCR_016216), and based on FreeSurfer 6.0.1 (Dale et al., 1999)(RRID:SCR_001847), ANTs 2.2.0 (Avants et al., 2008)(RRID:SCR_004757), FSL 5.0.9 (Jenkinson et al., 2002)(RRID:SCR_002823), AFNI 20160207 (Cox, 1996)(RRID:SCR_005927), SPM12 (Ashburner, 2012)(RRID:SCR_007037), PALM alpha112 (Winkler et al., 2016), GNU Parallel (Tange, 2011), MATLAB (The MathWorks Inc., Natick, MA, US) (RRID:SCR_001622), Docker (https://docker.com) (RRID:SCR_016445), and DPABI V4.1 (Yan et al., 2016)(RRID:SCR_010501). DPABISurf provides user-friendly graphical user interface (GUI) for pipeline surface-based preprocessing, statistical analyses and results viewing, while requires no programming/scripting skills from the users. <http://www.rfmri.org/dpabi> The DPABISurf pipeline first converts the user specified data into BIDS format (Gorgolewski et al., 2016), and then calls fMRIPprep 1.4.1 docker to preprocess the structural and functional MRI data, which integrates FreeSurfer, ANTs, FSL and AFNI. With fMRIPprep, the data is processed into FreeSurfer fsaverage5 surface space and MNI volume space. DPABISurf further performs nuisance covariates regression (including ICA-AROMA) on the surface-based data (volume-based data is processed as well), and then calculate the commonly used R-fMRI metrics: amplitude of low frequency fluctuation (ALFF) (Zang et al., 2007), fractional ALFF (Zou et al., 2008), regional homogeneity (Zang et al., 2004), degree centrality (Zuo and Xing, 2014), and seed-based functional connectivity. DPABISurf also performs surface-based smoothing by calling FreeSurfer’s mri_surf2surf command. These processed metrics then enters surfaced-based statistical analyses within DPABISurf, which could perform surfaced-based permutation test with TFCE by integrating PALM. Finally, the corrected results could be viewed by the convenient surface viewer DPABISurf_VIEW, which is derived from spm_mesh_render.m. <http://www.rfmri.org/dpabi> DPABISurf is designed to make surface-based data analysis require minimum manual operations and almost no programming/scripting experience. We anticipate this open-source toolbox will assist novices and expert users alike and continue to support advancing R-fMRI methodology and its application to clinical translational studies. DPABISurf is open-source and distributed under GNU/GPL, available with DPABI at http://www.rfmri.org/dpabi. It supports Windows 10 Pro, MacOS and Linux operating systems. You can run it with or without MATLAB. 1. With MATLAB. 1.1. Please go to http://www.rfmri.org/dpabi to download DPABI. 1.2. Add with subfolders for DPABI in MATLAB's path setting. 1.3. Input 'dpabi' and then follow the instructions of the "Install" Button on DPABISurf. 2. Without MATLAB. 2.1. Install Docker. 2.2. Terminal: docker pull cgyan/dpabi 2.3. Terminal: docker run -d --rm -v /My/FreeSurferLicense/Path/license.txt:/opt/freesurfer/license.txt -v /My/Data/Path:/data -p 5925:5925 cgyan/dpabi x11vnc -forever -shared -usepw -create -rfbport 5925 /My/FreeSurferLicense/Path/license.txt: Where you stored the FreeSurferLicense got from https://surfer.nmr.mgh.harvard.edu/registration.html. /My/Data/Path: This is where you stored your data. In Docker, the path is /data. 2.4. Open VNC Viewer, connect to localhost:5925, the password is 'dpabi'. 2.5. In the terminal within the VNC Viewer, input "bash", and then input: /opt/DPABI/DPABI_StandAlone/run_DPABI_StandAlone.sh ${MCRPath} Now please enjoy the StandAlone version of DPABISurf with GUI! If you don't want to run with GUI, you can also call the compiled version of DPABISurf_run. E.g., docker run -it --rm -v /My/FreeSurferLicense/Path/license.txt:/opt/freesurfer/license.txt -v /My/Data/Path:/data cgyan/dpabi /bin/bash /opt/DPABI/DPABI_StandAlone/run_DPABISurf_run_StandAlone.sh ${MCRPath} /data/DPABISurf_Cfg.mat New features of DPABISurf_V1.1_190725 (download at http://rfmri.org/dpabi) 1. New module for Surface-Based Temporal Dynamic Analysis (DPABI_TDA_Surf) was added. Dynamic regional indices (ALFF, fALFF, ReHo, Degree Centrality and Global Signal Correlation) and dynamic functional connectivity could be automatically calculated by one click through DPABI_TDA_Surf (with DPABISurf preprocessed data). The statistics maps (CV, Mean and SD) of the dynamic regional indices would also be generated by DPABI_TDA_Surf. A neuroimaging index which measures the concordance of the dynamic regional indices is incorporated into DPABI_TDA_Surf. Please see more details at: Yan, C.-G., Yang, Z., Colcombe, S.J., Zuo, X.-N., Milham, M.P., 2017. Concordance among indices of intrinsic brain function: insights from inter-individual variation and temporal dynamics. Sci Bull 62, 1572-1584. 2. The calculation of degree centrality now considers a vertex's correlation to both left and right hemispheres. 3. Standardization considers bilateral hemispheres. 4. Smooth function after Standardization was added. 5. If ICA-AROMA was chosen, no head motion realign parameters would be regressed out. 6. Fixed compatibility issues with old matlab versions. 7. The default surface-based smoothing kernel changed to 6mm instead of 10mm. 8. The DPABISurf results organizing function was added to the R-fMRI Maps Project. 9. Output an excel table for the volume of subcortical structures (calculated by freesurfer): {WorkingDir}/Results/AnatVolu/Anat_Segment_Volume.tsv. 10. DPABISurf_VIEW, the surface-based viewer now has a function to yoke between different viewers. 11. Docker updated basing on fMRIPrep 1.4.1. Besides pull from docker hub, the docker file can be also downloaded form here <ftp://ftpdownload:FTPDownload@lab.rfmri.org/sharing/DPABI/Docker/dpabi41docker.tar.gz> . 12. Besides the stand alone version of DPABI (with GUI), the compiled version of DPABISurf_run was also added to docker. Users can run DPABISurf_run with scripting. E.g., docker run -it --rm -v /My/FreeSurferLicense/Path/license.txt:/opt/freesurfer/license.txt -v /My/Data/Path:/data cgyan/dpabi /bin/bash /opt/DPABI/DPABI_StandAlone/run_DPABISurf_run_StandAlone.sh ${MCRPath} /data/DPABISurf_Cfg.mat Tips for Linux or Mac O: please start matlab from terminal in order to reach docker in DPABI (e.g., Linux: matlab; Mac: open /Applications/MATLAB_R2018a.app/). References: - Ashburner, J. (2012). SPM: a history. *Neuroimage*, 62(2), 791-800, doi:10.1016/j.neuroimage.2011.10.025. - Avants, B.B., Epstein, C.L., Grossman, M., Gee, J.C. (2008). Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. *Med Image Anal*, 12(1), 26-41, doi:10.1016/j.media.2007.06.004. - Cox, R.W. (1996). AFNI: software for analysis and visualization of functional magnetic resonance neuroimages. *Comput Biomed Res*, 29(3), 162-173. - Dale, A.M., Fischl, B., Sereno, M.I. (1999). Cortical surface-based analysis. I. Segmentation and surface reconstruction. *Neuroimage*, 9(2), 179-194, doi:10.1006/nimg.1998.0395. - Esteban, O., Markiewicz, C.J., Blair, R.W., Moodie, C.A., Isik, A.I., Erramuzpe, A., Kent, J.D., Goncalves, M., DuPre, E., Snyder, M., Oya, H., Ghosh, S.S., Wright, J., Durnez, J., Poldrack, R.A., Gorgolewski, K.J. (2018). fMRIPrep: a robust preprocessing pipeline for functional MRI. *Nat Methods*, doi:10.1038/s41592-018-0235-4. - Gorgolewski, K.J., Auer, T., Calhoun, V.D., Craddock, R.C., Das, S., Duff, E.P., Flandin, G., Ghosh, S.S., Glatard, T., Halchenko, Y.O., Handwerker, D.A., Hanke, M., Keator, D., Li, X., Michael, Z., Maumet, C., Nichols, B.N., Nichols, T.E., Pellman, J., Poline, J.B., Rokem, A., Schaefer, G., Sochat, V., Triplett, W., Turner, J.A., Varoquaux, G., Poldrack, R.A. (2016). The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. *Sci Data*, 3, 160044, doi:10.1038/sdata.2016.44. - Jenkinson, M., Bannister, P., Brady, M., Smith, S. (2002). Improved optimization for the robust and accurate linear registration and motion correction of brain images. *Neuroimage*, 17(2), 825-841. - Tange, O. (2011). Gnu parallel-the command-line power tool. *The USENIX Magazine*, 36(1), 42-47. - Winkler, A.M., Ridgway, G.R., Douaud, G., Nichols, T.E., Smith, S.M. (2016). Faster permutation inference in brain imaging. *Neuroimage*, 141, 502-516, doi:10.1016/j.neuroimage.2016.05.068. - Yan, C.G., Wang, X.D., Zuo, X.N., Zang, Y.F. (2016). DPABI: Data Processing & Analysis for (Resting-State) Brain Imaging. *Neuroinformatics*, 14(3), 339-351, doi:10.1007/s12021-016-9299-4. - Zang, Y., Jiang, T., Lu, Y., He, Y., Tian, L. (2004). Regional homogeneity approach to fMRI data analysis. *Neuroimage*, 22(1), 394-400, doi:http://dx.doi.org/10.1016/j.neuroimage.2003.12.030. - Zang, Y.F., He, Y., Zhu, C.Z., Cao, Q.J., Sui, M.Q., Liang, M., Tian, L.X., Jiang, T.Z., Wang, Y.F. (2007). Altered baseline brain activity in children with ADHD revealed by resting-state functional MRI. *Brain Dev*, 29(2), 83-91, doi:10.1016/j.braindev.2006.07.002. - Zou, Q.-H., Zhu, C.-Z., Yang, Y., Zuo, X.-N., Long, X.-Y., Cao, Q.-J., Wang, Y.-F., Zang, Y.-F. (2008). An improved approach to detection of amplitude of low-frequency fluctuation (ALFF) for resting-state fMRI: Fractional ALFF. *Journal of Neuroscience Methods*, 172(1), 137-141, doi: http://dx.doi.org/10.1016/j.jneumeth.2008.04.012. - Zuo, X.-N., Xing, X.-X. (2014). Test-retest reliabilities of resting-state FMRI measurements in human brain functional connectomics: A systems neuroscience perspective. *Neuroscience & Biobehavioral Reviews*, 45, 100-118, doi:http://dx.doi.org/10.1016/j.neubiorev.2014.05.009. Best, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Principal Investigator Director, International Big-Data Center for Depression Research Deputy Director, Magnetic Resonance Imaging Research Center Institute of Psychology, Chinese Academy of Sciences 16 Lincui Road, Chaoyang District, Beijing 100101, China - Initiator <http://rfmri.org/DPARSF>DPABI <http://rfmri.org/DPABI> <http://rfmri.org/DPARSF>, <http://dpabi.org>DPARSF <http://rfmri.org/DPARSF>, PRN <http://rfmri.org/PRN> and The R-fMRI Network <http://rfmri.org> (RFMRI.ORG <http://rfmri.org/>) http://rfmri.org/yan http://scholar.google.com/citations?user=lJQ9B58AAAAJ

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T1 orientation prior to running recon-all
by Abid Qureshi 24 Jul '19

24 Jul '19

External Email - Use Caution Dear Freesurfer, Does my T1 MPRAGE need to be in a particular orientation prior to running recon-all? Meaning should I use mri_convert to change to RAS orientation to avoid any L/R confusion with the output measures. For instance, mri_info says the orientation: MPRAGE = LPS orig.mgz = LIA T1.mgz = LIA I'm confused because if you bring up an image in freeview, say the T1.mgz, it uses the RAS coordinate system. Thanks, Abid

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Multiple overlays onto surface
by Alshelh, Zeynab 24 Jul '19

24 Jul '19

Hi Freesurfers, Is it possible to view two overlays on one surface image using TkSurfer? One of the surface overlays is binary while the other isn't. I have been able to load them both onto TkSurfer but I can only view one at a time. Kind regards, ---- Zeynab Alshelh, PhD | Postdoctoral Research Fellow Pain and Neuroinflammation Imaging Laboratory Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129 +1 (617) 794 6838 zalshelh(a)mgh.harvard.edu | www.nmr.mgh.harvard.edu

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(no subject)
by fsbuild 24 Jul '19

24 Jul '19

External Email - Use Caution Hello Sebastian, Please download the zip archive from the following link, https://drive.google.com/file/d/1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR/view?usp=… Then expand and read the README.patch file and follow the instructions.  When you are done, you should be able to launch freeview by double clicking on the icon of the application bundle in the Finder. - R. On Jul 24, 2019, at 05:51, Cassel, Sebastian /DZNE <Sebastian.Cassel(a)dzne.de> wrote:Dear all, based on this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-Ap… there any update for this?I have a MacBookPro with MacOs Mojave (10.14.3) and I'm facing the same issue with FreeSurfer 6.0.0 stable. Start FreeView via launch pad is failing during loading a volume, starting it via terminal works perfectly fine. BestSebastian         External Email - Use Caution        _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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WG: Update FreeView on MacOs
by Cassel, Sebastian /DZNE 24 Jul '19

24 Jul '19

Dear all, based on this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051591.htm l Is there any update for this? I have a MacBookPro with MacOs Mojave (10.14.3) and I'm facing the same issue with FreeSurfer 6.0.0 stable. Start FreeView via launch pad is failing during loading a volume, starting it via terminal works perfectly fine. Best Sebastian External Email - Use Caution

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Question about mris_pmake in the latest version of Freesurfer
by Zhi Li 23 Jul '19

23 Jul '19

External Email - Use Caution Dear Freesurfer experts, Now I would like to calculate the distance between two vertices. However, when I tried "mris_pmake --subject fsaverage --hemi lh --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:46986,endVertex:162197 ", it echoed "unrecognized option '--surface0'". I found similar questions in previous mailing list that in the latest version of Freesufer, it would echo "unrecognized options 'XXX'" even these flags are listed in the introduction of mris_pmake. But I did not found ways to solve this problem. Looking forward to your kind suggestions. Many thanks and best wishes, Lizhi

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Resending question about Freesurfer LME analysis
by Bronwyn Overs 23 Jul '19

23 Jul '19

External Email - Use Caution Dear Freesurfer Mailing list, I didn't receive any respondes to my below query so I'm re-sending in the hope that someone can assist. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Bronwyn Overs" <b.overs(a)neura.edu.au> To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Tuesday, July 16, 2019 11:27:48 AM Subject: Fwd: Question about Freesurfer LME analysis Dear Freesurfer Mailing list, I have run a mass-univariate spatiotemporal model using 'lme_mass_fit_EMinit' and then applied an FDR correction across both hemispheres (syntax provided below). On completion I realised that m ost of the corrected p-values for my main and interaction effects were well above the alpha of 0.05. The corrected p-value thresholds in log base 10 format are included in the attached figure and summarised below. Summary of p-value thresholds in attached images: Figure Key Log10P P Figure 1 A1 -1.193 0.064 A2 -0.695 0.202 B1 -0.969 0.107 B2 -0.243 0.571 C1 -0.195 0.638 C2 -0.001 0.998 Figure 2 A -2.663 0.002 B -1.295 0.051 I have no idea why this has happened and would greatly appreciate any insight you can provide. I would also note that the same issue occurred in a model where we exclude all subjects with only a single time-point. However, it did not occur when we included only Caucasians in our analysis and excluded the two dummy coded ethnicity covariates. This leads me to think its something to do with the complexity of the model, but I cannot understand why the error is only occurring when we correct for multiple comparisons. I have provided the details of sample and methods below. Sample Our sample includes 112 controls subjects, and 106 at-risk subjects (individuals with a first degree relative of BD but not personal history of BD). All subjects are aged between 12 and 30 years. 153 or these subjects have 2 time-points (77 control, 76 at-risk), while the remaining 65 individuals have only 1 MRI time-point. We also have mixed ethnicites - 165 Caucasians, 23 Asians, and 30 mixed (Asians-Caucasians). Analysis Design The QDEC file contains the following 6 variables: 1. Y (years between scans) 2. A (baseline age) 3. G (group, 1=case, 0=control) 4. S (sex, 1=female, 0=male) 5. E1 (Ethnicity 1, 1=asian, 0=other) 6. E2 (Ethnicity 1, 1=mixed-asian-caucasian, 0=other) Design matrix: [ones(length(M),1) M M(:,1).*M(:,3)] i.e. main effects for each of the qdec variables + an interaction term for years X group DVs: Cortical thickness, area and volume Model: Mass-univariate spatiotemporal model using 'lme_mass_fit_EMinit' CODE: % Read in surface files [Y,mri] = fs_read_Y(mgh); % Read in qdec file Qdec = fReadQdec(qdec); % Remove fsid from qdec Qdec = rmQdecCol(Qdec,1); % Store col 1 (fsid-base) in sID variable sID = Qdec(2:end,1); % Remove col 1 (fsid-base) from Qdec array Qdec = rmQdecCol(Qdec,1); % Convert Qdec to numeric matrix M M = Qdec2num(Qdec); % Sort data and evaluate design matrix [M,Y,ni] = sortData(M,1,Y,sID); X = eval([ones(length(M),1) M M(:,1).*M(:,3)]) % Compute vertex-wise temporal covariance estimates. [Th0, Re] = lme_mass_fit_EMinit(X,[1],Y,ni,cortex,3); %Segmentation and model fitting. [Rgs, RgMeans, stats] = fit(Th0, Re, [1], sphere, cortex, X, Y, ni); %Check surfaces. surfcomp(Th0, RgMeans, sphere, fig1, fig2) Correction for multiple comparisons: FDR across both hemispheres CODE: P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ]; G = [ F_lhstats.sgn(lhcortex) F_rhstats.sgn(rhcortex) ]; [detvtx, sided_pval, pth] = lme_mass_FDR2(P,G,[],0.05,0); pcor = -log10(pth); thrlh(r,2) = {pcor}; thrrh(r,2) = {pcor}; [~,dc] = size(detvtx); dvtx(r,2) = {dc}; Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

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Combining white/pial surfaces created during separate runs of autorecon2
by Emily Smith 22 Jul '19

22 Jul '19

External Email - Use Caution Hello Freesurfer support team, I am trying to create accurate white/pial surfaces, however, due to signal drop-out, Freesurfer is consistently underestimating the pial surface -- a problem which I am only able to fix using control points. Unfortunately, while adding cps does push the pial surface outward, it creates inaccurate/biased white surfaces which would skew thickness estimates (etc.). As such, I would like to use the white surface generated using the command *recon-all -autorecon2 -subjid <subjid> -mprage -hires* (created before cp incorporation) and the pial surface generated using the command *recon-all -autorecon2-cp -subjid <subjid> -mprage -hires* (created after cp incorporation) to run the last step of recon-all autorecon3. Which files should I copy over? So far I have tried copying the files noted below from the pre-cp directory into the post-cp directory and tried running autorecon3 with no success. Thanks in advance. ********************************************************************************************************************************************** TRIAL #1: *Copied these files from pre-cp directory to post-cp directory:* ?h.white.preaparc ?h.white.preaparc.H ?h.white.preaparc.K *Got this error message:* #@# Jacobian white lh Thu Jul 18 17:49:33 EDT 2019 /home/smithe16/freesurfer/subjects/April_29_2019_0100_combined/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn't match ../surf/lh.white.preaparc No such file or directory mrisReadTriangleFile failed. No such file or directory mris_jacobian: could not read target surface ../surf/lh.sphere.reg No such file or directory Linux cynthia 4.4.0-145-generic #171-Ubuntu SMP Tue Mar 26 12:43:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s April_29_2019_0100_combined exited with ERRORS at Thu Jul 18 17:49:35 EDT 2019 ********************************************************************************************************************************************** TRIAL #2: *Copied these files from pre-cp directory to post-cp directory:* ?h.white.preaparc ?h.white.preaparc.H ?h.white.preaparc.K ?h.inflated ?h.inflated.H ?h.inflated.K ?h.smoothwm ?h.sphere *Got this error message:* 1 Reading lh.sulc MRISreadNewCurvature: incompatible vertex number in file ../surf/lh.sulc No such file or directory MRISregister: could not read curvature file 'lh.sulc' No such file or directory Linux cynthia 4.4.0-145-generic #171-Ubuntu SMP Tue Mar 26 12:43:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s April_29_2019_0100_combined_2 exited with ERRORS at Fri Jul 19 12:43:09 EDT 2019

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mri_robust_template always fails in fmriprep when aligning multiple T1 images (Return code: -9)
by Frederick, Blaise B. 22 Jul '19

22 Jul '19

Dear Freesurfer experts, I’m running into a problem with mri_robust_template when trying to align multiple T1 images (this is with Freesurfer 6.0.1). I’m using fmriprep 1.4.1 to preprocess subjects from the OASIS3 dataset (or at least, attempting to). Each subject has 5-7 T1 scans over 3-4 time points, and one of the first steps in fmriprep’s pipeline is to align them all using mri_robust_template. However, the registration is failing every time with the return code -9. I can’t seem to find any indication of what that return code means, so I don’t know what to try to fix. Does anybody have any idea what “Return code: -9” means? Thanks, Blaise RuntimeError: Command: mri_robust_template --satit --fixtp --mov /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30005_ses-d0581_run-02_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30005_ses-d1274_run-01_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30005_ses-d1274_run-02_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30005_ses-d2377_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30005_ses-d2384_T1w_ras_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30005_ses-d3453_T1w_ras_corrected.nii.gz --inittp 1 --iscale --noit --template sub-OAS30005_ses-d0581_run-01_T1w_template.nii.gz --subsample 200 --lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp3.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp4.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp5.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp6.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp7.lta Standard output: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ --satit: Will estimate SAT iteratively! --fixtp: Will map everything to init TP! --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30005_ses-d0581_run-02_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30005_ses-d1274_run-01_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30005_ses-d1274_run-02_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30005_ses-d2377_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30005_ses-d2384_T1w_ras_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30005_ses-d3453_T1w_ras_corrected.nii.gz as movable/source volume. Total: 7 input volumes --inittp: Using TP 1 as target for initialization --iscale: Enableing intensity scaling! --noit: Will output only first template (no iterations)! --template: Using sub-OAS30005_ses-d0581_run-01_T1w_template.nii.gz as template output volume. --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30005_ses-d0581_run-02_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30005_ses-d0581_run-02_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30005_ses-d1274_run-01_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30005_ses-d1274_run-01_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30005_ses-d1274_run-02_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30005_ses-d1274_run-02_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30005_ses-d2377_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30005_ses-d2377_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30005_ses-d2384_T1w_ras_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30005_ses-d2384_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30005_ses-d3453_T1w_ras_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30005_ses-d3453_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30005_ses-d0581_run-02_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz ) [init] ========================= TP 4 to TP 1 ============================== Register TP 4 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30005_ses-d1274_run-02_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz ) [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30005_ses-d1274_run-01_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz ) [init] ========================= TP 5 to TP 1 ============================== Register TP 5 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30005_ses-d2377_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30005_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30005_ses-d0581_run-01_T1w_corrected.nii.gz ) -- Original : (1, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (1, 1, 1)mm and (177, 256, 256) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter: - Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter: - Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter: -- Original : (1, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (1, 1, 1)mm and (177, 256, 256) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) Standard error: Return code: -9 ------------------------------------------------------- Blaise Frederick Associate Professor of Psychiatry/Biophysicist Harvard Medical School/McLean Hospital bbfrederick(a)mclean.harvard.edu http://www.nirs-fmri.net

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freesurfer stopped
by Adomas Bunevicius 22 Jul '19

22 Jul '19

External Email - Use Caution Dear Freesurfer developers, I was working with training dataset and received, but unfortunately Freesurfer stopped: Last 4 lines: ......... "no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234" Log file attached. Thank you,Adam

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