Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Multi-band slice timing correction
by Wang, Ruosi 07 Sep '16

07 Sep '16

Dear Freesurfer developers: I'm seeking out ways for performing multi-band slice timing correction with freesurfer 5.3. I've searched the mailing list, and noticed that there might be a couple of ways for doing this. But, I still have some conerns for different ways, and please see below for my questions: 1) using new version of stc.fsl and slicedelay I tried to download these files from a link provided in an emai loop <http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg43359.html> of the mailing archive, but failed to do so. Could you please share the updated downloading link to these files. In addition, what kinds of information shall I provide? The slice order and number of SMS slice groups? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/stc.fslftp://… 2) using freesurfer 6 for preprocessing Since freesurfer 6 is still in beta version, can I use the proproc-sess of fs6 for data preprocessing only and switch to fs 5.3 afterwards for all the other anlaysis? Is there any downside for this, in comparison with just using the new version of stc.fsl and sliceday? In addition, for the input file so of -sliceorder, shall it be the slice number ordered by time? And for the input file of -ngroups, shall it be the number of slices that are colloected at the same time? Thank you so much, it is deeply appreciated. Best, Ruosi -- Ruosi Wang Graduate Student Vision Lab in Psychology Department Harvard University William James Hall, 7 floor 33 Kirkland Street Cambridge, MA 02138

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Converting RAW data to ANALYZE format
by Maryam Kouchakidivkolaei 07 Sep '16

07 Sep '16

Dear experts: I have bunch of files in RAW format, how can I convert them to NIFTI or ANALYZE format? Any help would be appreciated. Thanks, Maryam

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qdec: Generate Stats Data tables {Disarmed}
by C.Anastasopoulos＠lumc.nl 07 Sep '16

07 Sep '16

Hello, I am facing a problem similar to what others in the community have reported: when trying to "Generate Stats Data tables" in qdec, I get following error: SUBJECTS_DIR is '/home/ubuntubeast/Documents/freesurfer_subj_dir' mkdir -p /home/ubuntubeast/Documents/freesurfer_subj_dir/qdec/stats_tables/ ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x287ec5a0): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: mkdir -p /home/ubuntubeast/Documents/freesurfer_subj_dir/qdec/stats_tables/ Stack trace: Uncaught exception: command failed: mkdir -p /home/ubuntubeast/Documents/freesurfer_subj_dir/qdec/stats_tables/ while executing "vtkTemp2 GenerateStatsDataTables" I tried using the command asegstats2table --common-segs --meas volume --e /home/ubuntubeast/Documents/freesurfer_subj_dir/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 001 002 003 004 which gave NO errors. Do you have any suggestions? I am using .csh and freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on a Ubuntu 14.04 Thank you in advance, Constantin

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Matrix is ill-conditioned (mri_glmfit)
by Rodriguez-Thompson, Anais 07 Sep '16

07 Sep '16

Hi FreeSurfer experts, When running mri_glmfit I am getting the error "matrix is ill-conditioned or badly scaled, condno=10182.4" My fsgd file is attached to this email. My command is: mri_glmfit --y /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/144_GDD_Thickness_RBC_Folate/lh_thickness_map.mgh --fsgd /cluster/roffman/users/fsgd/GDD/144_GDD_CT_Covary_RBC_Folate_linear.fsgd --surf fsaverage lh --fwhm 4.6 --C /cluster/roffman/users/fsgd/OneGroupOneCovariateRegressOut2Covariates.mtx --glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/144_GDD_Thickness_RBC_Folate/LH_CT_Covary_RBC_Folate_Nuis_Gender_Age_linear The design matrix is: 1.000 2.981 -0.403 -1.054; 1.000 3.033 2.219 -1.054; 1.000 3.051 0.239 0.943; 1.000 3.033 0.150 0.943; 1.000 2.901 -0.586 -1.054; 1.000 3.036 -0.834 -1.054; 1.000 2.945 -0.482 -1.054; 1.000 2.977 1.055 0.943; 1.000 2.936 -0.627 0.943; 1.000 2.990 0.586 -1.054; 1.000 2.943 -0.479 0.943; 1.000 2.912 -0.530 0.943; 1.000 2.879 0.777 -1.054; 1.000 2.958 -0.630 0.943; 1.000 2.929 -0.520 0.943; 1.000 2.962 0.140 0.943; 1.000 3.071 2.194 0.943; 1.000 3.017 0.619 -1.054; 1.000 2.992 -0.314 -1.054; 1.000 3.021 -0.579 0.943; 1.000 3.041 -0.467 0.943; 1.000 2.963 0.930 0.943; 1.000 3.017 0.729 0.943; 1.000 3.027 -0.314 0.943; 1.000 3.097 0.680 -1.054; 1.000 2.985 1.091 0.943; 1.000 3.034 -1.562 -1.054; 1.000 3.039 -0.370 0.943; 1.000 2.954 -0.191 0.943; 1.000 3.045 -0.907 -1.054; 1.000 3.004 -0.492 0.943; 1.000 3.049 -1.468 0.943; 1.000 2.951 1.006 -1.054; 1.000 2.975 0.135 -1.054; 1.000 3.057 0.489 0.943; 1.000 3.017 0.474 -1.054; 1.000 2.976 -0.168 0.943; 1.000 2.989 1.993 0.943; 1.000 3.056 0.859 0.943; 1.000 2.953 -1.124 -1.054; 1.000 3.018 -1.172 -1.054; 1.000 2.928 -0.194 -1.054; 1.000 2.922 -0.546 -1.054; 1.000 2.857 -0.171 -1.054; 1.000 2.968 -0.120 -1.054; 1.000 2.925 1.784 0.943; 1.000 2.992 -0.874 0.943; 1.000 2.798 -1.058 -1.054; 1.000 3.007 -0.268 -1.054; 1.000 2.975 -0.237 0.943; 1.000 2.992 -0.449 -1.054; 1.000 3.123 -0.558 -1.054; 1.000 3.013 -0.181 -1.054; 1.000 2.993 1.096 -1.054; 1.000 2.961 1.605 0.943; 1.000 2.907 -0.749 -1.054; 1.000 2.897 -0.693 -1.054; 1.000 2.964 0.013 -1.054; 1.000 2.927 1.315 -1.054; 1.000 3.022 -0.752 -1.054; 1.000 2.943 -0.637 0.943; 1.000 2.999 -0.467 -1.054; 1.000 3.012 0.535 -1.054; 1.000 2.984 1.766 -1.054; 1.000 2.975 -0.553 -1.054; 1.000 3.030 -0.650 0.943; 1.000 2.902 -1.048 -1.054; 1.000 2.954 -0.502 -1.054; 1.000 3.031 -0.749 -1.054; 1.000 3.051 -0.510 0.943; 1.000 3.033 -0.074 0.943; 1.000 3.090 0.856 0.943; 1.000 2.961 0.894 -1.054; 1.000 3.056 0.239 -1.054; 1.000 2.990 2.484 0.943; 1.000 2.999 -1.218 -1.054; 1.000 3.014 -0.311 0.943; 1.000 3.064 -0.512 0.943; 1.000 2.894 -1.178 -1.054; 1.000 2.944 -1.539 0.943; 1.000 2.926 -1.542 0.943; 1.000 3.051 -0.897 -1.054; 1.000 2.995 -1.532 -1.054; 1.000 2.997 0.048 -1.054; 1.000 2.980 -0.214 0.943; 1.000 3.006 -0.275 -1.054; 1.000 2.930 0.912 -1.054; 1.000 2.857 -1.364 0.943; 1.000 3.023 -0.013 0.943; 1.000 3.048 0.158 0.943; 1.000 2.953 1.292 0.943; 1.000 2.922 1.065 0.943; 1.000 3.009 -1.552 0.943; 1.000 2.946 -0.296 0.943; 1.000 3.031 2.072 -1.054; 1.000 2.910 2.671 0.943; 1.000 2.971 -0.405 -1.054; 1.000 2.976 0.043 -1.054; 1.000 3.007 -0.339 0.943; 1.000 3.030 -0.232 0.943; 1.000 2.972 -0.018 0.943; 1.000 2.924 -0.693 0.943; 1.000 3.003 0.301 -1.054; 1.000 3.034 0.374 -1.054; 1.000 3.070 -0.551 -1.054; 1.000 2.943 2.365 0.943; 1.000 3.035 -0.979 -1.054; 1.000 2.926 -1.575 0.943; 1.000 2.954 -0.390 -1.054; 1.000 2.966 0.777 -1.054; 1.000 2.992 0.102 0.943; 1.000 2.887 -0.005 0.943; 1.000 3.136 -1.330 -1.054; 1.000 2.941 -0.813 0.943; 1.000 2.953 -0.816 -1.054; 1.000 2.914 -0.997 -1.054; 1.000 3.039 2.365 0.943; 1.000 3.009 -0.441 -1.054; 1.000 3.066 -1.127 0.943; 1.000 2.985 -0.441 -1.054; 1.000 2.874 0.910 0.943; 1.000 2.989 0.326 0.943; 1.000 2.985 0.777 -1.054; 1.000 3.021 0.797 0.943; 1.000 3.015 -0.227 0.943; 1.000 2.972 -0.191 0.943; 1.000 3.017 -0.500 0.943; 1.000 2.914 2.553 -1.054; 1.000 3.096 -0.265 -1.054; 1.000 3.073 1.052 -1.054; 1.000 3.020 -0.765 0.943; 1.000 3.146 1.078 0.943; 1.000 2.917 -0.609 0.943; 1.000 2.974 -0.326 0.943; 1.000 2.909 0.889 0.943; 1.000 3.108 -1.236 0.943; 1.000 3.073 -0.224 -1.054; 1.000 3.033 -0.625 0.943; 1.000 2.970 1.949 0.943; 1.000 3.008 2.214 0.943; 1.000 2.981 0.787 0.943; 1.000 3.102 -0.966 -1.054; 1.000 2.930 0.512 0.943; 1.000 2.934 -1.547 0.943; Do you know what is going on and how I can fix it? Thank you for your help! Anais Rodriguez-Thompson Clinical Research Coordinator Brain Genomics Laboratory Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617) 643-3215

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Qdec Error: Couldn't open qcache file
by Jana Dinges 07 Sep '16

07 Sep '16

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qdec problem
by wanghaibao 07 Sep '16

07 Sep '16

Hi, Douglas thank you for your reply. yes, the number in the text box cannot be changed, including threshold and False Discovery Rate in display. and also when i Save the picture of Display in File menu, the name cannot be input into the text box. Can you not just change the number in the text box? On 09/06/2016 12:49 PM, wanghaibao wrote: > Hello,*Douglas* > I used the freesurfer 5.3 in fedora 20,there is a question in my > reseach,may be not a question! > When i view the results of analysis in the qdec window,why did i > cannot change the value of the Threshold,such as min(which had been > seted with the value of 2) ,in the same way,the max is 5?If i want to > change the value of them,how can i do it? what wrong with it and how > to solve it? > thank you in advance > haibao wang > sep-6, 2016

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mri_glmfit --pvr Assistance
by Timothy Hendrickson 07 Sep '16

07 Sep '16

FreeSurfer Experts, I have a data set which comprises one group and the co-variate IQ. I would like to correlate this data set with the dependent measure LGI. I originally performed this in QDEC, however I read elsewhere that a vertex-by-vertex correlation cannot be done in QDEC. Further, I read that it must be done via command line with mri_glmfit and the --pvr flag. I am confused as to what sort of file I should input into the --pvr flag (do I run a separate analysis?, etc). Any advice would be extremely helpful. Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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recon-all error
by Liu Y 07 Sep '16

07 Sep '16

Dear Freesurfer Developers, After updating my op to Ubunto from 14 to 16.04, and re-installing the Freesurfer, when I run recon-all, it ended with an error message: /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux yw-HP-Z240-Tower-Workstation 4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s A2090_1 exited with ERRORS at ke 7.9.2016 10.20.05 +0300 I have searched the list and could not find answer, need your help. Best regards, Yawu 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Ubuntu 16.04 LTS 3) recon-all.log: see attached

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Extracting aseg.stats data
by Tamara Tavares 07 Sep '16

07 Sep '16

Hello, I am trying to extract the volumes from the aseg file of multiple subjects using the command: asegstats2table --subjects C9F03_1 C9F03_2 C9F07_1 --meas volume --tablefile aseg_stats_test.txt I keep getting the following error: SUBJECTS_DIR : home/bmiadmin/Tamara/FreeSurfer_GENFI/analysis/output Parsing the .stats files ERROR: The stats file home/bmiadmin/Tamara/FreeSurfer_GENFI/analysis/output/C9F03_1/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files I have set my subject directory to where all my output files are located and the subjects/stats folder does contain a aseg.stats file. I have attached a aseg.stats file. Thank you in advance for your help! Tamara

2 1

extract thickness values from clusters
by Clara Kühn 07 Sep '16

07 Sep '16

Dear Freesurfer Experts, I did a longitudinal 2 stage model and now I would like to extract the thickness and area values from significant clusters that survived the Monte Carlo correction. As I understood from the various e-mails in the archives expressing the same request there is a file "something.y.ocn.dat" where those thickness values are supposedly stored for each cluster and each subject. However, this file included "the average value of each subject in each cluster" (as it states in the group comparison tutorial), meaning the -log10(pvalue). I would like to show that the significant difference between two groups is driven by a certain group and to do that I want to display the thickness and area values of each cluster in bar graphs. What could I do to receive these values? Cheers, Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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