Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

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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region mask creation
by Dandil dNd 22 Jul '19

22 Jul '19

External Email - Use Caution Hi dear FS users, I have performed recon-all on my dataset, and now I want to create region masks using the lookup table. I have found the command "zero_ltgt_4dfp" to do this, but this error comes up: "zero_ltgt_4dfp: command not found". Can anyone kindly help me to solve the problem? Best Regards, DnD

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