[Freesurfer] DOSS Question
External Email - Use Caution Dear FreeSurfer Experts, I have been having trouble with performing DOSS analyses with mri_glmfit. One of the groups in my sample is too small to be performed with DODS, but when I try to call the DOSS option in mri_glmfit, it returns the same error, saying that DODS is not possible with this sample. I even tried defining the design matrix manually using --X, but it returns the same error. mri_glmfit --glmdir lh.rate.CI.paired-diff.thickness.DOSS --y mgh/rates/lh.thickness-rate.stack.fwhm10.mgh --fsgd FSGD/CI_baselines/paired-diff-demean-CI.fsgd doss --surf fsaverage lh --C Contrasts/BMICorrelationCI_DOSS.mtx gdfRead(): reading FSGD/CI_baselines/paired-diff-demean-CI.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 BMIatBaseline -1.49788e-08 3.57667 1 AgeAtFirstTP -5.62933e-08 3.40434 Class Size and Means of each Continuous Variable 1 MaleNormal 26 -0.5852 0.2393 2 MaleCI 2 0.8115 2.2778 3 FemaleNormal 38 0.2564 -0.2749 4 FemaleCI 6 0.6414 -0.0556 ERROR: Class MaleCI has 2 members. With 2 variables and using DODS, you need at least 3 members If anyone has any ideas on how to go about this, that would be greatly appreciated. Thank you. William ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Demeaning for Longitudinal Analyses
External Email - Use Caution Dear FreeSurfer experts, I am currently running longitudinal analyses using the paired analysis tutorial for two time points. There are two tests I am trying to run: 1. Calculating significant changes in volume between the two time points, controlling for age and gender. 2. Correlating BMI with change in volume between the two time points, controlling for age and gender. For (1), would it be necessary to demean age for a one-sample longitudinal analysis? And for (2), would I need to demean both BMI and age? Thank you for your help. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hippocampal Suubfields Segmentation Violation
External Email - Use Caution Dear FreeSurfer experts, I am trying to compute hippocampal subfields with https://secure-web.cisco.com/1f2QJwnqjis6w0KTpz2gk4AyWSMQmrO3JmYGqPPbxpD5JmmDwbJUxZvvKKZq6qt2Y3hoFg8_CcTB_QmP5hdXEqByKvJoyiipEKvwvEhB1aLd1_SovZI6F7-sjY9ZMjQxIGngrN1ZEtMTF9y2YNZbAr0nNvcskDaNW803jSZ1y3CFGTbRdm8MnVa6zDdc-DRz-982-ay8UM0Nv5zKpFqHzvNzFn0X-R-xuf3nNYTxWe2mSo_3dRDrKI_abtuVjWSmZJNlJ3R8JwY2gsSF5XqaT4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala. I have tried this with multiple subjects multiple times but the following error persists. Any help would be greatly appreciated. Thank you. -- Fitting mesh to image data took 959.4679 seconds Transforming points Transforming points Wrote image to file image.mgz Constructing image-to-world transform from header information (asmr1.mgz) Constructing image-to-world transform from header information (/Users/rajilab/Documents/CHS_IMAGING_DATA/97-2002/03638/FS/tmp/hippoSF_T1_v21_left/imageDump.mgz) Wrote image to file asmr2.mgz This file does not contain MRI parameters Caught unexpected exception of unknown type. Segmentation violation detected at Mon Mar 22 21:39:10 2021 Configuration: Crash Decoding : Disabled Current Visual : Quartz Default Encoding : ISO-8859-1 MATLAB Architecture: maci64 MATLAB Root: /Applications/freesurfer/7.1.1/MCRv84 MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Darwin 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64 Processor ID : x86 Family 6 Model 85 Stepping 4, GenuineIntel Software OpenGL: 0 Virtual Machine: Java 1.7.0_55-b13 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : Quartz Fault Count: 1 Abnormal termination: Segmentation violation Register State (from fault): RAX = 0003 RBX = 00010a71e080 RCX = 7fea4a20 RDX = 71207180 RSP = 7fea4a20 RBP = 7fff2030195e RSI = 7000 RDI = 7fff203031f9 R8 = 4a9295e0 R9 = 71207180 R10 = 7fff202f0002 R11 = 7fea4a2d9e60 R12 = 71207498 R13 = R14 = 000124484d9b R15 = 0060 RIP = 71207498 RFL = 712071e0 CS = 00012431b27b FS = 712071c0 GS = 0001 Stack Trace (from fault): [ 0] 0x00010c970e64 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00028260 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+0052 [ 1] 0x00010c974a2a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00043562 _ZN2fl4test17terminate_handledEv+0906 [ 2] 0x00010c974477 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwfl.dylib+00042103 _ZN2fl4diag13terminate_logEPKcPK17__darwin_ucontext+0119 [ 3] 0x00012405eb7a /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00387962 _Z32mnRunPathDependentInitializationv+3146 [ 4] 0x00012405ee58 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00388696 _Z32mnRunPathDependentInitializationv+3880 [ 5] 0x00012405c733 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwmcr.dylib+00378675 mnFatalSignalHandler+0275 [ 6] 0x7fff2051cd7d /usr/lib/system/libsystem_platform.dylib+00015741 _sigtramp+0029 [ 7] 0x + [ 8] 0x00012431b27b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01782395 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+00010667 [ 9] 0x000124274a17 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01100311 _Z15inRunFinalizers7opcodesPS_Pi+0119 [ 10] 0x00012431929d /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01774237 _Z10inRunMfileiPP11mxArray_tagiS1_P6Mfh_mpP15inWorkSpace_tag+2509 [ 11] 0x000124edec55 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_dispatcher.dylib+00400469 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+0645 [ 12] 0x0001242bc48b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01393803 _Z23inEvalPcodeHeaderToWordP15_memory_contextiPP11mxArray_tagP12_pcodeheaderP6Mfh_mpj+0219 [ 13] 0x00012426ef4b /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01077067 _Z25in_local_call_with_setjmpIN5boost3_bi6bind_tIvPFvP15_memory_contextPiPP11mxArray_tagP12_pcodeheaderjENS1_5list5INS1_5valueIS4_EENS0_3argILi1EEENSG_ILi2EEENSE_ISA_EENSE_IiEEEN6mlutil14cmddistributor17inExecutionStatusET_S5_S8_b+0171 [ 14] 0x00012426a221 /Applications/freesurfer/7.1.1/MCRv84/bin/maci64/libmwm_interpreter.dylib+01057313
[Freesurfer] Regressing out gender
External Email - Use Caution Hello, I am currently attempting a paired t-test of subjects between two time points, regressing out the effects of age and gender. I am currently running the paired analysis tutorial, and have done the step of computing the differences between pairs using mris_preproc --paired-diff. However, I am having trouble with the FSGD and contrast files. Currently, this is my FSGD file: GroupDescriptorFile 1 Class M Class F Variables Age Input subject1pair M 80 Input subject2pair F 82 ... I am not sure how to make the contrast file for this, I would like to answer the question of " does the mean paired difference differ from 0, regressing out the effect of age and gender?" Any assistance would be greatly appreciated. William ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Vertex by Vertex Analysis
External Email - Use Caution Hello, I would like to perform a group difference analysis with gray-white matter contrast between healthy controls and patients, covarying for the cortical thickness at each vertex throughout the entire brain surface. How would we go about doing this? Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Longitudinal Gray/white Contrast Measure
External Email - Use Caution Dear FreeSurfer experts, I am currently running a longitudinal analysis in FreeSurfer v5.3 to look at changes in volume and gray/white contrast. I ran all the processing steps and used this command below to look at results for volume: long_mris_slopes --qdec ./qdec/qdec.table.dat --meas volume --hemi lh --do-label --do-rate --time years --qcache fsaverage --sd $SUBJECTS_DIR We also would like to look at change in gray-white matter intensity ratio over time (between 2 timepoints) as well, but there is no separate measure defined for it. I was wondering what we can do to calculate this. Thank you. William ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Raw Data for Clusters
External Email - Use Caution Dear FreeSurfer Experts, I am running Qdec 1.4 and I want to extract raw data (in this case, volume) from the significant clusters after Monte-Carlo simulation. In this particular case, the summary file shows 5 significant clusters after correction: # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ # CreationTime 2018/10/16-23:28:21-GMT # cmdline mri_surfcluster --in /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/sig.mgh --csd /Users/user/MyInstall/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm18/abs/th13/mc-z.csd --mask /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/mask.mgh --cwsig /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.cluster.mgh --vwsig /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.vertex.mgh --sum /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.cluster.summary --ocn /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.ocn.mgh --oannot /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.ocn.annot --csdpdf /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.pdf.dat --annot aparc --cwpvalthresh 0.05 --o /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.masked.mgh --surf white # cwd /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only # sysname Darwin # hostname N-Volunteer-iMac.local # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # annot aparc # SUBJECTS_DIR /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only # SearchSpace_mm2 64328 # SearchSpace_vtx 149926 # Bonferroni 0 # Minimum Threshold 1.3 # Maximum Threshold infinity # Threshold Signabs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold0 mm^2 # CSD thresh 1.30 # CSD nreps1 # CSD simtype null-z # CSD contrast NA # CSD confint 90.00 # Overall max 2.06685 at vertex 34785 # Overall min -4.82491 at vertex 356 # NClusters 5 # Total Cortical Surface Area 64328 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWP CWPLowCWPHi NVtxs Annot 1 -4.825 356 2272.51 60.8 -9.4 -1.7 0.00010 0.0 0.00020 3745 superiortemporal 2 -4.419 146292 2658.98 19.8 52.0 -5.7 0.00010 0.0 0.00020 3104 rostralmiddlefrontal 3 -4.267 138330 1525.99 35.6 35.27.0 0.00460 0.00370 0.00550 1936 rostralmiddlefrontal 4 -3.304 140353 1712.65 34.9 -30.2 56.6 0.00220 0.00160 0.00280 3540 postcentral 5 -3.050 28351 1096.87 19.6 -34.8 -8.7 0.04530 0.04260 0.04800 1687 parahippocampal -- However, when I run the command to extract the raw data from these clusters using this line: mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0 The terminal window outputs this: rh-Diff-SZ-HC-Intercept-volume user$ mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0 sysname Darwin hostname N-Volunteer-iMac.local machine x86_64 user user UseRobust 0 Loading mc-z.abs.th13.sig.cluster.mgh Loading y.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 4 segmentations Computing statistics for each segmentation 0-4 68496849.000 1-2 54765476.000 2-1 16871687.000 Reporting on 3 segmentations Computing spatial average of each frame 0 1 2 Writing to mc-z.abs.th13.cluster.ocn.dat mri_segstats done - So I get a .dat file that only has 3 columns, which does not match up to the 5 that I originally observed after the correction. If you could let me know what the problem is that would be greatly appreciated. Thank you. William ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
