Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

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Re Re: Extracting aseg.stats data
by Tamara Tavares 08 Sep '16

08 Sep '16

That seemed to work, thank you! Tamara

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Re: [Freesurfer] White matter surface don't change after editing
by Cong 08 Sep '16

08 Sep '16

Hi dear all I attach a new picture to illustrate this problem. I erased some voxels in wm.mgz and rerun. The lh.orig(blue line) looks well, but lh.white(yellow line) don’t along the white surface in some area. Could anyone give me some advice? Thanks very much. Best wishes Cong Chen >> Date: Sun, 4 Sep 2016 15:15:42 +0800 >> From: Cong <3110103623(a)zju.edu.cn> >> Subject: [Freesurfer] White matter surface don't change after editing >> >> Dear freesurfer team? >> I have some MRI images from a GE scanner, it seems that images? quality is poor because grey matter is bright in so much area and these grey matter is included in wm.mgz. So I deleted wrong voxels in wm.mgz by freeview and rerun through command ? recon-all -autorecon2-wm -autorecon3 -subjid subjname?. But ?h.white (yellow line) don?t change after rerunning as you can see in the attached picture. Is this problem caused by deleting too many voxels and how to fix it? Thanks very much. >> >> Regards >> Cong Chen

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extract JUST pial surface for brain-printing purposes - what can I skip?
by djpeters＠u.washington.edu 08 Sep '16

08 Sep '16

Hi Freesurfer list, Say I was interested ONLY in extracting the pial surface for the purpose of getting a 3D print of a brain. Are there any time-intensive steps that can I safely exclude from the recon-all pipeline? For example, if I exclude the CARegister step ( -nocareg ), will I still get a good pial surface? Thanks so much, -Dan

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design matrix palm
by maaike rive 08 Sep '16

08 Sep '16

Hi all, I was adviced to use PALM for permutation of non-orthogonal surface data. However, I have some questions regarding the design matrix en contrast files to be used in PALM, but somehow I cannot subscribe to the FSL mailing list, and I was hoping one of the freesurfer users could help me out. I have a complex design and I would like to test for interactions as well for subgroups; in addition, I have several covariates. If I use the following collumns: A1 B1 A2 B2 cov1 cov2 cov3 I assumed I can at least test for the effects of A vs B (1 - 1 1 -1 0 0 0) and 1 vs 2 (1 1 -1 -1 0 0 0) and interactions (1 -1 -1 1 0 0 0). Q1: Is it true that I cannot compare subgroups, because columns denoted zero will be handeled as being a covariate? i.e. the contrast 1 -1 0 0 0 0 0 is inappropriate and I would have to build a new design matrix (A1 B1 cov1 cov2 cov3)? This is what I was told previously when using randomise for DTI data, but I'm not sure PALM works the same way. Q2: What I also understood from randomise is that you have to define both 1 -1 and -1 1; there is no option for a 2tailed t-test or F test. Is that correct and does it also apply to PALM? Thanks, Maaike

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qdec problem
by wanghaibao 07 Sep '16

07 Sep '16

Hi,Douglas maybe, you are right. i have tried most of new versions, as follows, but the problem still has. I don't know whether Fedora (3.14-288,fc20.x86_64) 20 (Heisenbug) match with these versions. thank you very much. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 freesurfer-Linux-centos6_x86_64-dev Sounds like the GUI is doing strange things. What platform are you running on? What version of FS? Can you try it on a different type of computer? On 09/07/2016 08:20 AM, wanghaibao wrote: > 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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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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Freesurfer September 2016