Freesurfer October 2018

freesurfer@nmr.mgh.harvard.edu

113 participants
156 discussions

autorecon1 with skull stripped image
by Rosalia Dacosta Aguayo 18 Oct '18

18 Oct '18

External Email - Use Caution Dear Free Surfer's team, I have a doubt. I have a sample of patients in which I already have done the skull stripping using specific options with bet, so the skull stripping has been successful. I wonder if I could feed autorecon1 with the skull stripped image instead of the T1 image with skull. Thank you very much for your time, Rosalia

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Adding longitudinal time points to clean dataset {Disarmed}
by Molly Prigge 17 Oct '18

17 Oct '18

External Email - Use Caution Hello Freesurfer experts, We have a large longitudinal dataset (n=~200) of up to 4 time points per participant. All images were processed using Freesurfer v6.0 and have already undergone QA, and editing the cross, Base or long where needed. We are finishing up collection of a 5th time point and will begin collecting a 6th time point next year (average interscan interval 2.5 years). We are running the new scans through the same Freesurfer v6.0 and same workstation as the previous time points. Is it appropriate to use the Bases already created with Times 1-4 for the 5th and 6th timepoint long file creation? We are hoping to avoid losing all the QA editing already done on the Base and long files from Times 1-4 and not have to redo all QA on Times 1-5 long files when time 6 is complete. We appreciate any guidance. Thanks! Molly --------------------------- Molly DuBray Prigge, PhD Research Associate Department of Pediatrics molly.prigge at hsc.utah.edu MRI Study Phone: 801.585.9061

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Raw Data for Clusters
by WON JONG CHWA 17 Oct '18

17 Oct '18

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 Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 1.300000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # 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 TalZ CWP CWPLow CWPHi NVtxs Annot 1 -4.825 356 2272.51 60.8 -9.4 -1.7 0.00010 0.00000 0.00020 3745 superiortemporal 2 -4.419 146292 2658.98 19.8 52.0 -5.7 0.00010 0.00000 0.00020 3104 rostralmiddlefrontal 3 -4.267 138330 1525.99 35.6 35.2 7.0 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 6849 6849.000 1 -2 5476 5476.000 2 -1 1687 1687.000 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

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Using a .asc file as overlay in freeview/tksurfer
by Worker, Amanda 17 Oct '18

17 Oct '18

External Email - Use Caution Hello, I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck. As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command: % mris_convert -c lh.thickness lh.white lh.thickness.asc I am trying to overlay this onto lh.pial for one subject, however I cannot load the file and I get the following error message: % mri_read(): couldn't determine type of file /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc surfer: couldn't load /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc. If you were trying to load a functional volume, make sure you selected the right registration method, and if necessary, that the registration file exists. If you were trying to load a volume-encoded value file, make sure it has the same number of values as this surface does vertices (128970). sclv_read_from_volume: error in FunD_New Interestingly, I can load the file as a curvature file, but then can't play around with the threshold. Do you have any idea what I'm doing wrong? Any help would be appreciated! Thanks, Amanda

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license format error
by Georg Schramm 17 Oct '18

17 Oct '18

External Email - Use Caution Dear FreeSurfer Developers, I have a installed freesurfer (6.0.0-centos6_x86_64) on 2 of our linux servers. One the first server: platform: ubuntu 16.04 uname -a: Linux fermi 4.4.0-133-generic #159-Ubuntu SMP Fri Aug 10 07:31:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux It runs fine. On the second server: platform: CentOS 7.4.1708 uname -a: Linux r23g36 3.10.0-862.11.6.el7.x86_64 #1 SMP Tue Aug 14 21:49:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux I get the following license format error when running recon-all: -------------------------------------------------------------------------- GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15 ... -------------------------------------------------------------------------- The license files are new (downloaded this week) and exactly the same on both servers (I compared the hexdumps). I also checked that I have read permissions to the license file in $FREESURFER_HOME on the 2nd server. Do you have any idea what could go wrong on the 2nd server? Bests, Georg

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create label from cluster obtained with mri_glm-fit-sim
by Ting Li 16 Oct '18

16 Oct '18

External Email - Use Caution Dear Freesurfer Experts, I really need your attention and help. Thanks a lot. We want to create label through the mri_glm-fit-sim cluster results. We have found the same topic in 2013 and tried the method you have provided. However, it doesn’t work. If you think it is not the right way, could you give me an example to do it right. I really appreciate your great help. Thanks a lot. Here is my code: mri_annotation2label --subject F999 --hemi lh --annotation cache.th20.neg.sig.ocn.annot --labelbase lh.test_label Here is my error information: subject = F999 annotation = cache.th20.neg.sig.ocn.annot hemi = lh labelbase = lh.test_label surface = white Reading surface /media/set2iscsi/ting/origin_gz_data/F999/surf/lh.white Loading annotations from /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot could not read annot file /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot No such file or directory INFO: could not load from /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot, trying /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot could not read annot file /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot No such file or directory ERROR: MRISreadAnnotation() failed This is the annot files in my directory F999: ls F999/label/*.annot F999/label/cache.th20.neg.sig.ocn.annot F999/label/lh.BA_exvivo.annot F999/label/rh.aparc.DKTatlas.annot F999/label/lh.aparc.a2009s.annot F999/label/lh.BA_exvivo.thresh.annot F999/label/rh.BA_exvivo.annot F999/label/lh.aparc.annot F999/label/rh.aparc.a2009s.annot F999/label/rh.BA_exvivo.thresh.annot F999/label/lh.aparc.DKTatlas.annot F999/label/rh.aparc.annot

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FreeSurfer Errors (2)
by Sparsh Jain 16 Oct '18

16 Oct '18

External Email - Use Caution Hey! I sent two responses on Friday. The second response was bigger than 1 MB so it awaited moderator approval. I don't know if you received it eventually. Following up to that mail, my reconstruction on the subject with 176 images crashed after about 32 hours of execution with the error 'could not read label' and 'too many symbolic links' in fsaverage. I have attached the entire command line output. Please help me understand what I'm doing wrong ! Thanks Sparsh

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fsfast preproc-sess: viewing preproc surface outputs
by Jacob Matthews 16 Oct '18

16 Oct '18

External Email - Use Caution Hi FS Team, We are running our first fsfast pipeline, and starting with a single subject to test everything. We successfully ran preproc-sess with the following command: preproc-sess -s 11987_20180731 -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -sliceorder odd -fsd bold We wanted to check the outputs. It was clear how to view most intermediate outputs, but we didn't know how to view the surface space outputs: fmcpr.odd.sm5.fsaverage.rh.nii.gz fmcpr.odd.sm5.fsaverage.lh.nii.gz Loading them into freeview as surfaces fails. We thought perhaps they needed to be loaded on top of an fsaverage surface, but didn't know where to start this process. Thanks, Jacob Matthews MRI Specialist Rotman Research Institute Baycrest Hospital 416-785-2500 ext. 3322

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Midline errors
by Maxime Perron 16 Oct '18

16 Oct '18

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qdec analysis with more than 2 covariates
by vittal korann 16 Oct '18

16 Oct '18

External Email - Use Caution Hi Doug, Recently I started working on freesurfer for volume based analysis. For QDEC, I need to include more than 2 variables. For example if I include patients who hail from different places like statutory town, census town and rural. In present scenario, can I include all three as covariates. Here is the error that qdec showing while running GLM: "ERROR: Subject 2 seems to have a mismatched number of discrete factors (expected 4, found 1)" "Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white ERROR: no contrasts specified." "Error in Analyze: command fai;ed mri_glmfit --y /usr/local/freesurfer/subjects/qdec/qdecAnalys/y.mgh --fsgd /usr/local/freesurfer/subjects/qdec/qdecAnalys/qdec.fsgd dods -glmdir /usr/local/freesurfer/subjects/qdec/qdecAnalys/ -surf fsaverage lh -label /usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label" Could you help us out in this regard. Would appreciate any help!! Korann

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Freesurfer October 2018