Freesurfer

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30064 discussions

glmfit: matrix error
by Wang, Xin 12 Sep '17

12 Sep '17

Hello, FreeSurfer group, When I ran glmfit I got the following error massage. I standardize ages but the problem remains. Any other suggestions? Alternatively, is there any way to by-pass this design checking step? Thank you very much. Xin -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh_group_currPTSD_AgeGenderSiteFACT_adult.fwhm10.fsaverage.mgh --fsgd group_currPTSD_AgeGenderSiteFACT_adult.fsgd dods --glmdir RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh --surf fsaverage/ lh --C group_currPTSD_AgeGenderSiteFACT_adult.mtx 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.330000 (col 38), Max=18.703472 (col 62) The scale is much different between columns 38 and 62, you may want to normalize by subtracting the mean and dividing by the standard deviation. ERROR: cannot find RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh/fwhm.dat

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Q re: cluster commands
by Omar Al-Louzi 12 Sep '17

12 Sep '17

Hi freesurfer team, I'm hoping to ask two questions: 1. We are using the mri_volcluster command to find manually delineated clusters in a volume. In the output file, the command outputs Talairach coordinates for each cluster (TalX, TalY, TalZ). What do these coordinates exactly correspond to in terms of voxels? (i.e. do they reference the central voxel of each cluster, the first voxel detected, or something else) 2. Are there any freesurfer command(s) that can measure the minimum distance between two clusters in the same volume, or measure the minimum distance between one cluster in one volume( let's call it reference cluster) and multiple clusters in a second volume, granted that both volumes are in the same space and registered to each other (in other words, generate minimum distance measurements between all the clusters in the second volume and the reference cluster in the first volume). My apologies if these questions are basic or have been asked before, but I haven't come across an answer on freesurfer forums or help files. Best, Omar _____ Omar Al-Louzi, MD PGY-3 Neurology resident Massachusetts General Hospital Brigham and Women's hospital

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(no subject)
by José Gómez-Feria Ferreiro 12 Sep '17

12 Sep '17

Dear Freesurfer, Is it possible to keep on the supporting list but without receiving emails from other people? My email account is getting stuck with so many emails. Thanks, Jose

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group analysis on thickness/mask
by Xianwei Che 12 Sep '17

12 Sep '17

Dear experts, I am going to run a group analysis on thickness but limit the results to certain regions, say prefrontal cortex. l did find this thread but failed to make it work on my data ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html) I know I could extract the signal of the ROI but also interested in this way. Here are my questions: 1. mri_binarize should be working on the average data or the single data in each participant. If it should be on individual data, what the loop should be (if I have a text file SUBJECTS listing the participants). 2. How the --match is used. I --helped the mri_binarize but did not get it. Is it for specifying the ROI by number, say the number of PFC? 3. If I could finish the mask creation and merge to label; do I have to undergo the data concatenating stage (i.e. preproc, surf2surf) or directly move to glm. I saw another thread skipping these stages but it's on volume data ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html) Thank you so much! *-------------* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia

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PetSurfer GTM: gtmstats2table
by Elijah Mak 12 Sep '17

12 Sep '17

Hi Doug, Would it be possible to use the gtmstats2table command to extract GTM values from other parellations? Thanks! Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities Research Group University of Cambridge, Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

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lobes volume (WM and GM)
by Gonzalo Rojas Costa 12 Sep '17

12 Sep '17

Hi: I need the complete WM volume for each lobe... not only the WM up to 5mm beneath the lobes (default value) or 20 mm... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oAAAAJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta

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lobes volume (WM and GM)
by Gonzalo Rojas Costa 12 Sep '17

12 Sep '17

Hi: I created the following script (for freesurfer 5.3.0) to compute the lobes volume (including GM and WM). mri_annotation2label --subject pac --hemi rh --lobesStrict lobulos --seg lobulos --stat lobulos mri_annotation2label --subject pac --hemi lh --lobesStrict lobulos --seg lobulos --stat lobulos mris_anatomical_stats -a lobulos -f pac.lobulos.rh pac rh mris_anatomical_stats -a lobulos -f pac.lobulos.lh pac lh mri_aparc2aseg --s pac --labelwm --hypo-as-wm --rip-unknown --volmask --o $SUBJECTS_DIR/pac/mri/lobulitos.mgz --annot lobulos --wmparc-dmax 20 mri_segstats --seg $SUBJECTS_DIR/pac/mri/lobulitos.mgz --ctab /usr/local/freesurfer/LobulesColorLUT.txt --excludeid 0 --sum $i.lobulo.aseg.sum --id 1001 1004 1005 1006 2001 2004 2005 2006 3001 3004 3005 3006 4001 4004 4005 4006 251 252 253 254 255 But, I didn't got the complete WM volume for each lobe (frontal lobe for example... see red arrow in attached image)... why ?... Any solution ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oAAAAJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta

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QDEC FDR for left and right hemispheres
by Huang, Caleb (NIH/NINDS) [F] 12 Sep '17

12 Sep '17

Hello, When I run FDR on QDEC, I get different p-values for the left and right hemispheres. Is it appropriate to use just one threshold for the sake of consistency? Also, as an unrelated question, is there a way to display the thresholds as p-values rather than log(p)? -Caleb

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side effects launching recon-all from matlab system(cmd) call
by Giuseppe Cabras 12 Sep '17

12 Sep '17

Dear freesurfer developers, I call recon-all -all from a matlab script using a system(cmd) which is (apparently) correctly executed, as shown in the recon-all.log (matlab_* attached), i.e.: /usr/local/freesurfer/bin/recon-all -all -cw256 -3T -multistrip -clean-bm -i /home/MRIdata/PUD/31148_MRI_sMRI_400614.nii -s /home/gc/study/recon-all/400614dclass and apparently it run without errors as you can see in the matlab_recon-all.log file, but I get (systematically) a wrong TalAviQA: 0.00000 while, if I run the above bash command directly I get a correct: TalAviQA: 0.97713 as shown in the bash_recon-all.log (attached). I guessed that something wrong happened in talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig and the error traced in talairach_avi.log (matlab_* and bash_* attached). In fact matlab_talairach_avi.log is shorter and all imgreg_4dfp end sections are missing which imply that TalAviQA can not be extracted by awk and mritotal transform is performed instead. But really I don't understand why this happens and whether similar issues affects other recon-all subtask using matlab. I double checked this on two linux sistems and with fs version 6.0 and 5.3 ... same results. Thanks in advance for any help, cheers, -- Giuseppe Cabras, PhD - Department of Mathematics, Computer Science and Physics InterUniversity Center for Behavioral Neurosciences University of Udine - via delle Scienze, 206 - 33100 UDINE

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FS6.0 on RHEL7 FIPS enabled - ERROR: crypt() returned null with 4-line file
by Sean T. Ma 12 Sep '17

12 Sep '17

Hi FS experts, I ran into a crypt() error while running the `recon-all` on a test brain with Freesurfer 6.0 installed. The server is an FIPS enabled RHEL7. In the `recon-all.log`, the error happened after the `mri_convert.bin` execution: ERROR: crypt() returned null with 4-line file I have attached a snippet below as well as the recon-all.log. Has anyone encountered this error before? I'm suspecting the issue might be due to the enabling of FIPS on RHEL7. I'm having similar OpenSSL prolembs in FSL/FSLeyes. Your input is appreciated! Best, Sean mri_convert /nfs/fmri/Analysis/FSinputs/test/t1spgr_156sl.nii /nfs/fmri/Analysis/FSresults/test/mri/orig/001.mgz mri_convert.bin /nfs/fmri/Analysis/FSinputs/test/t1spgr_156sl.nii /nfs/fmri/Analysis/FSresults/test/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /nfs/fmri/Analysis/FSinputs/test/t1spgr_156sl.nii... ERROR: crypt() returned null with 4-line file Linux madcbrain.umms.med.umich.edu 3.10.0-693.el7.x86_64 #1 SMP Thu Jul 6 19:56:57 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s test exited with ERRORS at Wed Sep 6 12:01:48 EDT 2017

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