Freesurfer

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30132 discussions

Re: [Freesurfer] longitudinal TRACULA -prep error
by Yendiki, Anastasia 01 Oct '18

01 Oct '18

Hi Carissa – Don’t set variables to “None” in the config file. Just remove those lines from the config file altogether – that’s the same as not having any inputs for them. Hope this helps, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Carissa Nicole Weis <cnweis(a)uwm.edu<mailto:cnweis@uwm.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, September 27, 2018 at 4:28 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] longitudinal TRACULA -prep error External Email - Use Caution Hello, I’m running into an error in the longitudinal TRACULA pipeline that I’m not sure how to resolve. I saw this error in the message board but there was no resolution to the problem so I thought I’d ask again. I’ve successfully run the recon-all longitudinal pipeline and am trying to run the trac-all –prep step with a longitudinal configuration file. Here’s the error, it happens for both time points listed in my configuration file: #@# Image corrections Thu Sep 27 12:59:31 CDT 2018 mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1... crypt_gkey = *CyXds2s6sOqQ Starting DICOMRead2() dcmfile = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 dcmdir = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI Ref Series No = 6 Found 2666 files, checking for dicoms Found 2660 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 38 nslices = 70 ndcmfiles = 2660 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=10000.00, TE=57.70, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz... crypt_gkey = *CyXds2s6sOqQ mri_probedicom --i /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 > /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dcminfo.dat cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals flip4fsl /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz x -y z /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvecs /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvals /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals eddy_correct /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz 0 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0000 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0001 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0002 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0003 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0004 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0005 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0006 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0007 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0008 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0009 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0010 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0011 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0012 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0013 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0014 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0015 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0016 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0017 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0018 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0019 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0020 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0021 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0022 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0023 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0024 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0025 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0026 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0027 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0028 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0029 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0030 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0031 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0032 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0033 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0034 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0035 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0036 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0037 mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.norot xfmrot /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.ecclog /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.norot /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_eddy.nii.gz mri_convert / /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/b0mag.nii.gz mri_convert / /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/b0mag.nii.gz corRead(): can't open file /COR-.info $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /... crypt_gkey = *CyXds2s6sOqQ Linux vis-1.mortimer 2.6.32-754.3.5.el6.x86_64 #1 SMP Tue Aug 14 20:46:41 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Sep 27 13:41:04 CDT 2018 #------------------------------------- /sharedapps/LS/psych_imaging/freesurfer/5.3.0_9.19.18/bin/trac-preproc #------------------------------------- #@# Inter-subject registration (base template) Thu Sep 27 13:41:05 CDT 2018 cp /bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/mni2anatorig.mat /bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/anatorig2mni.mat /bigraid-03/LS/Data/istar/freesurfer/106/dmri/xfms cp: cannot stat `/bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/mni2anatorig.mat': No such file or directory cp: cannot stat `/bigraid-03/LS/Data/istar/freesurfer/106_day2.fs.long.106/dmri/xfms/anatorig2mni.mat': No such file or directory Linux vis-1.mortimer 2.6.32-754.3.5.el6.x86_64 #1 SMP Tue Aug 14 20:46:41 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Sep 27 13:41:05 CDT 2018 Here’s the contents of my configuration file: setenv SUBJECTS_DIR /bigraid-03/LS/Data/istar/Freesurfer setsubjlist= ( 106_day2.fs 106_6mo.fs ) set baselist = ( 106 106 ) set runlist = (1 2) set dcmlist = ( /bigraid-03/LS/RawData/iSTAR/106_day2/106_day2/p*/e*/DTI_all/DTI/*.1 /bigraid-03/LS/RawData/iSTAR/106_6mo /106_6mo/p*/e*/DTI_all/DTI/*.1 ) set bvecfile = /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt set bvalfile = /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt set dob0 = 1 set b0mlist = None set b0plist = None set echospacing=None set doeddy =1 set dorotbvecs =1 set thrbet = 0.5 set doregflt =0 set doregbbr =1 set doregmni =1 set mnitemp= $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz set dogregcvs = 0 set cvstemp =cvs_avg35 set cvstempdir = $FREESURFER_HOME/subjects set usemaskanat =1 set pathlist = (lh.unc_AS rh.unc_AS fmajor_PP fminor_PP lh.ccg_PP rh.ccg_PP lh.cab_PP rh.cab_PP ) set ncpts = (5 5 7 5 5 5 4 4) set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt set nstick =2 set nburnin =200 set nsample = 7500 set nkeep = 5 set reinit =0 Thanks so much for your help! Carissa Carissa N. Weis, B.S. Graduate Student Affective Neuroscience Laboratory University of Wisconsin-Milwaukee cnweis(a)uwm.edu<mailto:cnweis@uwm.edu>

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Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
by Matthew Grecsek 01 Oct '18

01 Oct '18

External Email - Use Caution If you are referring to the T1 raw images, no they appear normal and the standard Freesurfer pipeline generates correct volumes. If you are referring to the DTI raw images off the scanner, they also don't appear to have brain parts missing, although some appear more noisy and pixelated than others. This is a mTBI subject with no other anatomical brain anomalies scanned with a Siemens 3T. ------------------------------------------------ Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700 Do the raw images look like that too? From: <freesurfer-boun...(a)nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu>>> on behalf of Matthew Grecsek <m...(a)grecsek.com<mailto:m...@grecsek.com <m...(a)grecsek.com>>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>> Date: Wednesday, September 19, 2018 at 4:07 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>>> Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault External Email - Use Caution Yes, a part of the brain appears missing. See attached screenshot. I did not use a configuration file, I simply accepted all defaults and kicked off the process with -s and -i flags. ------------------------------------------------ Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700 Hi Matt – It looks like some sort of registration issue. When you display the FA map (dmri/dtifit_FA) and structural segmentation in diffusion space (label/diff/aparc+aseg), do they look fine? Is there any part of the brain that is cut off from any of the images? Also, can you attach your config file? Thanks! a.y

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error glm-fit-sim
by Caroline Beelen 01 Oct '18

01 Oct '18

External Email - Use Caution Dear FS, I followed the group analysis page for glm analysis and it worked fine until the final step. I'm using version 5.3. After performing glm-fit-sim it says "glm-fit done" (for all files), but when trying to open these it says: "Reading colortable from annotation file... Colortable with 1 entries read (originally none) Colortable with 1 entries read (originally none) CTABisentryvalid: index -1 was 00B Resource temporarily unavailable CTABisentryvalid: index -1 was 00B Resource temporarily unavailable Resource temporarily unavailable" (etc..) It opens, but nothing is visible and I have the feeling it cannot open color files?? MRI glmfit gives positive clusters for some values. I therefore used the abs sign for glm-fit-sim. What might be wrong? Thanks. Caroline

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freeview problem on Linux RHEL 7-4 libGLU.so.1
by Avner Meoded 01 Oct '18

01 Oct '18

Hello all, I installed the latest version for Linux I get this message when trying to run an example: "freeview.bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory" I installed the missing library and now it is in /usr/local/fsl/bin/FSLeyes/libGLU.so.1 any idea ho to solve this problem Thanks avner

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cannot stat volumesAmygdala.txt
by John Papatriantafyllou 30 Sep '18

30 Sep '18

External Email - Use Caution dear Freesurfers, after processing hippocampal subfields i cannot get amygdala stats. Instead i get the following massage *cannot stat volumesAmygdala.txt* Any suggestions? John PS i run freesurfer under neurodebian system on pc with windows 10

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Re: [Freesurfer] amygdala segmentation atlas influence
by Iglesias Gonzalez, Eugenio 30 Sep '18

30 Sep '18

External Email - Use Caution Dear Raj, A few years ago, we published a paper on how Monte Carlo sampling could be used to quantify this. Unfortunately, the method was incredibly slow and difficult to tune, and the performance gain was tiny, so we never put it in FreeSurfer. But this is a direction I’m still interested in, and which I’m planning to revisit in the future. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Emily K Clarke <ekc23(a)duke.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 26 September 2018 at 15:15 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Cc: "Dr Rajendra Morey, M.D." <rajendra.morey(a)duke.edu> Subject: [Freesurfer] amygdala segmentation atlas influence External Email - Use Caution Hello all, I have run the amygdala segmentation in my datasets to obtain volumes of nuclei. I am aware from the fswiki that the volumes should be interpreted with caution because of the reliance on the atlas. When running FS, is there a way to get some metric about how much the segmentation relied on the atlas relative information from the T1 being segmented. If this metric is not available to the user, is some version of it calculated by the software and therefore available internally. Thanks in advance for your help! raj

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Re: [Freesurfer] ERROR: dimension mismatch between X and
by Backhausen, Lea 29 Sep '18

29 Sep '18

External Email - Use Caution Thank you so much for your help - it's working now. ---------------------------------------- Lea Backhausen Wissenschaftliche Hilfskraft Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de _____________________________________________________________________________________ Date: Thu, 27 Sep 2018 15:24:01 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] ERROR: dimension mismatch between X and contrast To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <09411cf0-185b-26c6-9ad0-479edb2d6e2c(a)mgh.harvard.edu> Content-Type: text/plain; charset="Windows-1252" You have 3 groups and 2 covariates, so you will have 3*(2+1)=9 regressors, in this order ADHD-offset COM-offset TD-offset ADHD-Age COM-Age TD-AGE ADHC-IQ COM-IQ TD-IQ You will need to have a single value for each regressor in your contrast matrix, meaning that you should have 9 values. You have 10 values, thus the error. On 09/27/2018 09:39 AM, Backhausen, Lea wrote: > > ????????External Email - Use Caution > > Dear FreeSurfer experts, > > I get this error message when running group analysis on cortical > thickness using glmfit: > ERROR: dimension mismatch between X and contrast > Contrasts/ADHD_COM_TD_age_IQ.mtx X has 9 cols, C has 10 cols > > Please find attached the FSGD file, the contrast file and the terminal > output below. > > I want to do ANCOVA with three groups (ADHD, COM and TD) controlling > for the effects of age and IQ. > So I assume the regressors would be ADHD COM TD age IQ and my contras > matrix 1 -1 0 0 0 1 0 -1 0 0 according to information from these two > tutorials: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V and > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V. > > Can anybody help me out? Where am I wrong? Why does glmfit assume X > has 9 cols? > > Any help would be much appreciated, thank you in advance! > > Best > Lea > > > Terminal Output: > mri_glmfit --y rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd > FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx > --surf fsaverage rh --cortex --glmdir > rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir > gdfRead(): reading FSGD/ADHD_COM_TD_orig_age_IQ.fsgd > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > Continuous Variable Means (all subjects) > 0 Age 13.6015 1.73148 > 1 IQ 107.288 11.1649 > Class Means of each Continuous Variable > 1 ADHD? 13.7193 104.3478 > 2 COM? 12.8657 105.3929 > 3 TD? 14.0119 112.3784 > INFO: gd2mtx_method is dods > Reading source surface > /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ > SUBJECTS/fsaverage/surf/rh.white > Number of vertices 163842 > Number of faces??? 327680 > Total area???????? 65020.839844 > AvgVtxArea?????? 0.396851 > AvgVtxDist?????? 0.717994 > StdVtxDist?????? 0.193566 > > $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd > /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ > SUBJECTS cmdline mri_glmfit.bin --y > rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd > FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx > --surf fsaverage rh --cortex --glmdir > rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir > sysname? Darwin > hostname edr06188.dip.tu-dresden.de > machine? x86_64 > user???? Lea > FixVertexAreaFlag = 1 > UseMaskWithSmoothing???? 1 > OneSampleGroupMean 0 > y > /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ > SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh > logyflag 0 > usedti? 0 > FSGD FSGD/ADHD_COM_TD_orig_age_IQ.fsgd labelmask > /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ > SUBJECTS/fsaverage/label/rh.cortex.label > maskinv 0 > glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > Creating output directory > rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir > Loading y from > /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/ > SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh > ?? ... done reading. > INFO: gd2mtx_method is dods > Saving design matrix to > rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/Xg.dat > Computing normalized matrix > Normalized matrix condition is 1027 > Matrix condition is 4.07619e+06 > Found 149926 points in label. > Pruning voxels by thr: 1.175494e-38 > Found 149926 voxels in mask > Saving mask to rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/mask.mgh > Reshaping mriglm->mask... > search space = 74490.844410 > ERROR: dimension mismatch between X and contrast > Contrasts/ADHD_COM_TD_age_IQ.mtx?????? X has 9 cols, C has 10 cols > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 6 Date: Thu, 27 Sep 2018 15:38:38 +0000 From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Best way to update Freeview To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4CBE100D-0B0E-4B8D-B21B-4520523B668D(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Arkadiy, this should be fixed now. best, Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Maksimovskiy, Arkadiy" <AMAKSIMOVSKIY(a)mclean.harvard.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, September 26, 2018 at 6:01 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Best way to update Freeview Hi everyone, I was able to download Freeview- the link now works. However I am having an issue with starting this version. bash-3.2$ export FREESURFER_HOME=/Applications/freesurfer_6.0/ bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer_6.0/ FSFAST_HOME /Applications/freesurfer_6.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Volumes/DrEmetBrown/ MNI_DIR /Applications/freesurfer_6.0/mni bash-3.2$ freeview dyld: Library not loaded: @rpath/QtWidgets.framework/Versions/5/QtWidgets Referenced from: /Applications/freesurfer_6.0//Freeview.app/Contents/MacOS/Freeview Reason: image not found Abort I am running a Mac OS HighSierra (10.13.6). It seems that people had similar issues in the past, but not quiet like this one. I would love to hear any tips on how to fix it. Thanks, arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Re: [Freesurfer] tksurfer-sess frame time course question
by ylab 29 Sep '18

29 Sep '18

External Email - Use Caution Dear Doug, Thank you very much for your response. >> (1) why did I get Frame (0-8) for my data that should have 12 frames? > When you use -rmprestim, it subtracts the mean of the prestim baseline > AND removes the prestim time points (-4 -2 and 0) so you only end up > with 9 frames. I see. This makes perfect sense. >> (2) how can I visualize contrasts created with -setwdelay? > Your visualization command is correct. I don’t understand why you are > seeing the same image for each frame. Can you load them separately and > see if they are different? I tried to load them separately, but still got the same images. tksurfer-sess -df sessdirfile -s YY03 -analysis YY.sm5.lh -contrast w1_all_null -map sig tksurfer-sess -df sessdirfile -s YY03 -analysis YY.sm5.lh -contrast w5_all_null -map sig I also loaded /YY03/bold/YY.sm5.lh/w1_all_null/sig.nii.gz, and /YY03/bold/YY.sm5.lh/w5_all_null/sig.nii.gz, using GUI on FreeView, still got the same images. Then, I created new contrasts without -rmprestim mkcontrast-sess -analysis YY.sm5.lh -contrast w1b_all_null -a 1 -a 2 -a 3 -a 4 -a 5 -a 6 -a 7 -a 8 -c 0 -setwdelay [1 0 0 0 0 0 0 0 0 0 0 0] mkcontrast-sess -analysis YY.sm5.lh -contrast w5b_all_null -a 1 -a 2 -a 3 -a 4 -a 5 -a 6 -a 7 -a 8 -c 0 -setwdelay [0 0 0 0 1 0 0 0 0 0 0 0] Without -rmprestim, I was able to see different maps. So it looks like when I used -rmprestim, I failed to create different sig.nii.gz files for the different contrasts. Now, I can continue my analyses without -rmprestim. But I have one follow up question. (3) when I used -rmprestim with mkcontrast-sess, is it correct to assume that the statistical results produced by selxavg3-sess were based on the data with the prestimulus activation subtracted? With -rmprestim, sig.nii.gz had 9 frames. I am confused because, the data I visualized with freesurfer version 5 by clicking the activated areas had 12 frames. I am wondering where did the first three frames came from in those plots. Thank you in advance. Shogo

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Re recon -all
by Miguel Ángel Rivas Fernández 28 Sep '18

28 Sep '18

External Email - Use Caution Hi Freesurfer devs, I tried to re run the recon -all after put some control points in the brainmask and I get the following error: pcpb3846:~ lab1-rmn$ recon -all -autorecon2-cp -autorecon3 -4025 cp_before -bash: recon: command not found What could be the problem? The Freesurfer version that I am using at this moment is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Thanks in advance, Best, -- *Miguel Ángel Rivas Fernández*

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Clarification about .annot file format
by paul mccarthy 28 Sep '18

28 Sep '18

External Email - Use Caution Howdy, There is a discussion regarding the .annot file format over at the nibabel github repository, regarding the interpretation of the flag/alpha value: https://github.com/nipy/nibabel/issues/649 If one wishes to create an .annot file with colours that have a transparency value, how should it be stored in the file? By piecing together the information from the freesurfer code [1,2], and Graham Wideman's helpful notes [3], I came to the conclusion that alpha values should be stored as 1-the actual value. But it would be great to get some clarification on this from somebody who knows more than me Thanks very much, Paul McCarthy [1] https://github.com/freesurfer/freesurfer/blob/dev/matlab/read_annotation.m [2] https://github.com/freesurfer/freesurfer/blob/dev/matlab/write_annotation.m [3] https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles#Annota…

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