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30083 discussions

help for calculating the correlation
by tange_neuro 19 Aug '19

19 Aug '19

External Email - Use Caution Hi all, I am deeply confused and terribly needed some help, and I failed to find the answer in the Freesurfer website. I had two patient groups F and R. To analysis the correlation between active time and cortical thickness, I tried two different methods A and B (A, treating patients in different group F and R as shown in attached figure A; B, treating all patients as one group FR as shown in attached figure B), and got distinctly different results. So, my questions: 1、Which one is actually correct for calculating the correlation between active time and thickness, and what does the other one mean? 2、Does "--cache 3 abs --cwp 0.999" means that the result is only corrected with vertex level P < 0.001, and no cluster level correction is conducted? I am looking forward to getting your help. Sincerely yours, Ge Tan

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autorecon3 with T2_min parameter
by Marco Aqil 19 Aug '19

19 Aug '19

External Email - Use Caution ?Hi, When calling recon-all autorecon3, with the -T2pial flag, and a -T2_min value specified via expert options file, I noticed that this parameter is passed to the first call of mris_make_surfaces, which looks, for example, as follows: ---------------- #@# Make Pial Surf lh Mon Aug 19 13:43:02 CEST 2019 <scripts folder path> mris_make_surfaces -save-res -save-target -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs -T2_min 35 sub-006 lh ---------------- However, the second call of mris_make_surfaces, which relies on T2 data to refine the pial, does not receive the T2_min parameter, and looks as follows: --------------- #@# Refine Pial Surfs w/ T2/FLAIR Mon Aug 19 14:02:23 CEST 2019 <other T2 pial steps> mris_make_surfaces -save-res -save-target -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 sub-006 lh --------------- Is this the expected behavior, or should the T2_min be passed to the second call as well? In case it is needed, I am using freesurfer-dev, version obtained on july 11th. Thank you very much. Best, Marco?

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question about qdec
by 310913949 19 Aug '19

19 Aug '19

External Email - Use Caution Hi FS Experts, I meet some problem when I use QDEC for Group analysis. When I click Generate Stats Data Tables, it report the errors as follows: dec/gender.levels Female Male done. Reading discrete factor levels from config file /usr/local/freesurfer/subjects/qdec/diagnosis.levels TLE extra_TLE done. Data table /usr/local/freesurfer/subjects/qdec/qdec.table.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_01' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_03' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_04' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_06' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_11' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_12' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_14' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_47' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_55' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_05' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_16' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_18' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_20' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_23' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_24' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_40' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_75' in SUBJECTS_DIR Input table: /usr/local/freesurfer/subjects/qdec/qdec.table.dat Subj#, SubjID, Data... 1 PT1_01 Female 23.000000 TLE 2 PT1_03 Male 38.000000 TLE 3 PT1_04 Male 26.000000 TLE 4 PT1_06 Female 45.000000 TLE 5 PT1_11 Female 20.000000 TLE 6 PT1_12 Male 23.000000 TLE 7 PT1_14 Female 39.000000 TLE 8 PT1_47 Female 30.000000 TLE 9 PT1_55 Female 22.000000 TLE 10 PT1_05 Male 42.000000 extra_TLE 11 PT1_16 Female 34.000000 extra_TLE 12 PT1_18 Male 30.000000 extra_TLE 13 PT1_20 Male 40.000000 extra_TLE 14 PT1_23 Male 30.000000 extra_TLE 15 PT1_24 Female 29.000000 extra_TLE 16 PT1_40 Male 30.000000 extra_TLE 17 PT1_75 Female 24.000000 extra_TLE 1 gender discrete 2 1 Female 2 Male 2 age continuous 0 3 diagnosis discrete 2 1 TLE 2 extra_TLE Continuous Factors: Mean: StdDev: ------------------- ----- ------- age 30.882 7.631 Number of subjects: 17 Number of factors: 3 (2 discrete, 1 continuous) Number of classes: 4 Number of regressors: 8 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/usr/local/freesurfer/subjects' mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ ---------------------------------------------------------- asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects PT1_01 PT1_03 PT1_04 PT1_06 PT1_11 PT1_12 PT1_14 PT1_47 PT1_55 PT1_05 PT1_16 PT1_18 PT1_20 PT1_23 PT1_24 PT1_40 PT1_75 File "/usr/local/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax I have read some answer in the freesurfer mailing list, but I still don't know how to deal with it. Could you please give me some suggestion? Thanks, Kan

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volume data from part of the brain
by Hang Zeng 19 Aug '19

19 Aug '19

External Email - Use Caution Hi Freesurfers, when I collected the fMRI data, I set the slices to cover part of the brain (only cover the occipital and the temporal lobe). The anatomy scan was of course whole brain. After analysing the data with the pipeline (preproc mkanalysis selxavg3), I overlaid the results on the surf, it looked so weird. So I analysed the data using spm, and used bbregister to register the functional volume to the anatomical data (which also looked weird). The result looked different but doesn't make sense. Because I should see the activations on the occipital and the temporal lobe surf, but instead it appeared on the upper part of the brain surf. I guess this is because of the registration? So how to analyse the data in this situation and how to view the results? Thanks! Zoe

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The R-fMRI Course V3.0 Is Released
by YAN Chao-Gan 18 Aug '19

18 Aug '19

External Email - Use Caution Dear Colleagues, We are pleased to announce the release of The R-fMRI Course V3.0 ( http://rfmri.org/Course) The R-fMRI Course V3.0 is a major update since V2.1. The R-fMRI Course V3.0 systematically introduces the principles of resting-state fMRI (R-fMRI), current research, methodological issues, computational platform and its applications to brain disorders. More importantly, The R-fMRI Course V3.0 explains the data processing details for DPABI/DPABISurf/DPARSF, including data conversion, data preprocessing, temporal dynamic analysis, quality control, statistical analysis and results viewing. A key point of The R-fMRI Course V3.0 is the video course for 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. DPABISurf is designed to make surface-based data analysis require minimum manual operations and almost no programming/scripting experience. We anticipate The R-fMRI Course V3.0 will guide users to be skilled at how to use this open-source toolbox. The R-fMRI Course V3.0 English Version (http://rfmri.org/Course) (Mostly recorded at The R-fMRI Workshop, July 30~31, 2019) 1. Resting-State fMRI: Current Research, Methodological Issues and Computational Platform 2. Resting-State fMRI: Applications to Brain Disorders 3. The REST-meta-MDD Project: towards a Neuroimaging Biomarker of Major Depressive Disorder 4. Data Processing of Resting-State fMRI: DPARSF 5. The R-fMRI Maps Project 6. Surface-Based Brain Imaging Analysis and DPABISurf 7. DPABI Animal Data Processing 8. Temporal Dynamic Analysis 9. DPABI: Quality Control, Statistical Analysis and Results Viewing 10. DPABISurf: A Surface-Based Resting-State fMRI Data Analysis Toolbox 11. Output structure of DPARSF 12. Output structure of DPABISurf 13. Verification of Reproducibility of R-fMRI Metrics and Reproducible Network Underpinnings of Rumination 14. DPABI: Utilities 15. DPABISurf Advanced: More about FreeSurfer The R-fMRI Course was firstly released on July 15, 2009. During the past 10 years, the course was kept updating, and received 291,425 views. We hope this major update will further help advancing R-fMRI methodology and its application to clinical translational studies. 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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apart.a2009s naming convention: from "_and_" to "&"
by Jyrki Ahveninen 17 Aug '19

17 Aug '19

Hi guys, I (and probably others) have noticed the aparc.a2009s label naming convention has changed in recons starting from 6.0. “_and_” has become “&”, such as in lh.G&S_subcentral. It is fixable, but it may become a bit confusing for those who use fsaverage vs. individually segmented labels in a study that uses the different versions of 6.0 and beyond (e.g., those interested in using the subpmillmeter recon option). And & is also a special character, too. It is completely fixable, of course, but I just thought to bring this up, because it might cause confusion in some users. (For me, it was just a “why the xxxx does not my mris_divide_parcellation splittable” moment.) Thankfully, Jyrki

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FreeSurfer 6 vertex-wise cortical volume computation details?
by Tim Schäfer 17 Aug '19

17 Aug '19

External Email - Use Caution Dear FreeSurfer experts, can anybody refer me to a publication that explains in detail how vertex-wise cortical volume (the data in <subject>/surf/?h.volume) is computed in FreeSurfer 6? My understanding is the following: * area is computed as 1/3 the area of all triangles meeting at that vertex. * thickness is the shortest distance from the vertex (at white surface) to any vertex on pial, then the other way around from that pial vertex, divided by two. * volume is area * thickness Is that true, and where can I read up on it? Thanks, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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spatial scale bar question
by Nasiriavanaki, Zahra 16 Aug '19

16 Aug '19

Dear Freesurfers Hi I am trying to add a spatial scale bar to my cortical maps in tksurfer. However, as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks when you zoom in the brain. I couldn't find a scale bar option in Freeview neither. I appreciate if you could let me know how to get a scale bar. Thanks Mona

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Conversions between MNI152, MNI305 & surface
by Lauri Tuominen 15 Aug '19

15 Aug '19

External Email - Use Caution Hello! I keep having 2 somewhat related problems: 1. How to convert a single coordinate from MNI305 to surface. Previosly Doug suggested to try the example 8b in https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems. However, that one is about moving a coordinate from 152 to 305. I would like to know how to show that MNI305 coordinate on a surface so I could eyeball it with tksurfer. Maybe one of the examples on that page is the one I am looking for but I don’t understand which one it could be. 2. How to transform a volume between MNI152 & MNI305 spaces. I tried: a) mri_vol2vol --targ ${my_volume_in_MNI305} --inv --mov $FSL_DIR/data/standard/MNI152lin_T1_2mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --o I_hope_this_volume_is_in_MNI152 b) mri_vol2vol --mov ${my_volume_in_MNI305} --MNI152reg --o I_really_hope_this_volume_is_in_MNI152 Neither of these methods seem to work. a-method moves the image too much anteriorly, and the b-method posteriorly. Thank you in advance, any help will be greatly appreciated! Thank you so much! Lauri

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mris_convert segmentation fault on R hemisphere aparc.a2009s only?
by Damion V Demeter 15 Aug '19

15 Aug '19

External Email - Use Caution I am having an issue processing some of my subjects through the HCP pipeline and have no idea what this error means. If anyone could help out, I'd appreciate it! Here is all the info: 1. Some (not all) of my subjects are getting a segmentation fault error during the post-freesurfer step of the HCP pipeline. Previous subjects were fully processed fine without error (over 100 of them) and are from the same group (all scanner and acquisition settings identical). Here is the segmentation fault error line: FreeSurfer2CaretConvertAndRegisterNonlinear.sh: line 294: 46979 Segmentation fault mris_convert --annot "$FreeSurferFolder"/label/"$hemisphere"h."$Map".annot "$FreeSurferFolder"/surf/"$hemisphere"h.white "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere"."$Map".native.label.gii 2. I have narrowed down this error further and have found that it only happens on the right hemisphere aparc.a2009s file. I have manually run the command above for the left and right hemisphere files separately as a test, and the L hemisphere files complete without fail. The R hemisphere, however, always gets this segmentation fault. This only occurs on certain subjects, but all the files this command is using look good and error free. All previous steps appeared to finish without fail and all expected files were written and can be opened (I'm 99% sure...I might have missed something). I am at a complete loss at how to troubleshoot this further or fix this error. Does anyone have any ideas or solutions? Thank you!

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