Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

contrast matrix
by xiangbo_2010 17 Nov '12

17 Nov '12

Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes three discrete factors: factor 1 with three levels (A,B,C ); factor 2 with three levels (O,P,Q); gender (F, M), and one covariate. So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the interaction between factor 1 and factor 2 regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang

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re white matter mask
by Catherine Bois 16 Nov '12

16 Nov '12

Hi, I have a question re the screenshot attached in the present email... Several slices of the white matter mask of this scan seem to have several " holes" ie black spots like this. These parts are included in the brain mask, but the brain mask seems to be quite non-uniform in terms of "whiteness" of the brain mask. I have gone in and filled some in manually; ie done white matter edits, is this the correct way to fix this problem, or do the holes indicate some other problem? Thank you very much for your help, Regards Cathy

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Defining a region of interest
by xiangbo_2010 16 Nov '12

16 Nov '12

psylab-desktop:/media/freesurfer1/CT> tksurfer fsaverage rh inflated -annot aparc.annot -fthresh 2 -overlay lh.COMTthree.glmdir/COMTthree/sig.mgh setting fthresh to 2.0000 subject is fsaverage hemi is rh surface is inflated surfer: current subjects dir: /media/freesurfer1/CT surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /media/freesurfer1/CT checking for nofix files in 'inflated' Reading image info (/media/freesurfer1/CT/fsaverage) Reading /media/freesurfer1/CT/fsaverage/mri/orig.mgz surfer: Reading header info from /media/freesurfer1/CT/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 tkmedit: Trying to open lh.COMTthree.glmdir/COMTthree/sig.dat surfer: Interpreting overlay volume lh.COMTthree.glmdir/COMTthree/sig.mgh as encoded scalar volume. surfer: curvature read: min=-0.676989 max=0.486764 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Found embedded color table in annotation. 13916 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl Reading /usr/local/freesurfer/tktools/tkm_common.tcl Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % ----------------------------------- selected vertex 57932 out of 163842 current 40.12 -7.05 -49.24 orig 63.86 -19.65 -15.51 pial 0.00 0.00 0.00 white 64.69 -19.40 -15.31 inflated 0.00 0.00 0.00 normals 0.99 0.01 -0.16 nneighbors 6 ripflag 0 surfer: dmin=0.4857, vno=57932, x=40.1208, y=-7.0543, z=-49.2368 surfer: curv=-0.308152, fs=0.000000 surfer: val=3.228469, val2=0.000000 surfer: amp=3.228469, angle=0.000000 deg (0.000000) surfer: vertex 57932 marked (curv=-0.308152, stat=3.228469) x = (40.1, -7.1, -49.2), n = (1.0, 0.0, -0.2). ----------------------------------- selected vertex 17616 out of 163842 current 39.62 -2.00 -51.33 orig 62.97 -16.28 -16.81 pial 0.00 0.00 0.00 white 63.84 -15.82 -16.46 inflated 0.00 0.00 0.00 normals 0.98 0.05 -0.18 nneighbors 6 ripflag 0 surfer: dmin=0.3911, vno=17616, x=39.6229, y=-2.0015, z=-51.3347 surfer: curv=-0.321697, fs=0.000000 surfer: val=3.037957, val2=0.000000 surfer: amp=3.037957, angle=0.000000 deg (0.000000) surfer: vertex 17616 marked (curv=-0.321697, stat=3.037957) x = (39.6, -2.0, -51.3), n = (1.0, 0.0, -0.2). ----------------------------------- selected vertex 17616 out of 163842 current 39.62 -2.00 -51.33 orig 62.97 -16.28 -16.81 pial 0.00 0.00 0.00 white 63.84 -15.82 -16.46 inflated 0.00 0.00 0.00 normals 0.98 0.05 -0.18 nneighbors 6 ripflag 0 surfer: dmin=0.3911, vno=17616, x=39.6229, y=-2.0015, z=-51.3347 surfer: curv=-0.321697, fs=0.000000 surfer: val=3.037957, val2=0.000000 surfer: amp=3.037957, angle=0.000000 deg (0.000000) ----------------------------------- selected vertex 57937 out of 163842 current 39.67 -5.70 -51.49 orig 63.13 -18.77 -17.53 pial 0.00 0.00 0.00 white 63.95 -18.47 -17.49 inflated 0.00 0.00 0.00 normals 0.97 -0.00 -0.23 nneighbors 6 ripflag 0 surfer: dmin=0.1531, vno=57937, x=39.6731, y=-5.6965, z=-51.4914 surfer: curv=-0.157153, fs=0.000000 surfer: val=3.481167, val2=0.000000 surfer: amp=3.481167, angle=0.000000 deg (0.000000) surfer: vertex 57937 marked (curv=-0.157153, stat=3.481167) x = (39.7, -5.7, -51.5), n = (1.0, -0.0, -0.2). ----------------------------------- selected vertex 57939 out of 163842 current 39.54 -5.36 -52.05 orig 62.77 -18.73 -18.05 pial 0.00 0.00 0.00 white 63.56 -18.47 -18.09 inflated 0.00 0.00 0.00 normals 0.97 -0.01 -0.25 nneighbors 6 ripflag 0 surfer: dmin=0.2759, vno=57939, x=39.5351, y=-5.3601, z=-52.0518 surfer: curv=-0.129672, fs=0.000000 surfer: val=3.159937, val2=0.000000 surfer: amp=3.159937, angle=0.000000 deg (0.000000) surfer: vertex 57939 marked (curv=-0.129672, stat=3.159937) x = (39.5, -5.4, -52.1), n = (1.0, -0.0, -0.3). ----------------------------------- selected vertex 11634 out of 163842 current 39.74 -8.26 -51.06 orig 62.85 -20.64 -17.51 pial 0.00 0.00 0.00 white 63.51 -20.49 -17.63 inflated 0.00 0.00 0.00 normals 0.97 -0.03 -0.24 nneighbors 6 ripflag 0 surfer: dmin=0.3010, vno=11634, x=39.7392, y=-8.2621, z=-51.0574 surfer: curv=-0.097159, fs=0.000000 surfer: val=3.183451, val2=0.000000 surfer: amp=3.183451, angle=0.000000 deg (0.000000) surfer: vertex 11634 marked (curv=-0.097159, stat=3.183451) x = (39.7, -8.3, -51.1), n = (1.0, -0.0, -0.2). surfer: making path (ctrl-c to cancel)... done At 2012-11-16 22:07:16,"Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >can you respond to the list? Not sure what's going on... >Bruce > > >On Fri, 16 Nov 2012, xiangbo_2010 wrote: > >> >> Thank you for my reply, when I check the button, the points have no change. >> Before check the button, these points are white, and have no bright colors, >> Thanks! >> >> >> >> >> At 2012-11-16 21:58:28,"Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >> >sorry, not sure I understand. After you click "make closed fill boundary" >> >what happens? Before you click do you see the points hilighted on the >> >surface? >> >On Fri, 16 Nov 2012, xiangbo_2010 wrote: >> > >> >> Dear experts: >> >> I used the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial >> /Visualization?highligh >> >> t=%28ROI%29 to defining a region of interest, but when I make a series of >> >> left clicks on the surface? then click the "Make Closed Fill Boundary" i >> con >> >> in the tools window. howevre, there has no connect the points my >> >> clicked, and drawing a yellow or red line between them. I hope that have >> >> experts to help me. Thanks! >> >> >> >> >> >> >> >> Bo Xiang >> >> >> >> >> >> >> >> >> >> >> >> > > >The information in this e-mail is intended only for the person to whom it is >addressed. If you believe this e-mail was sent to you in error and the e-mail >contains patient information, please contact the Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error >but does not contain patient information, please contact the sender and properly >dispose of the e-mail.

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Defining a region of interest
by xiangbo_2010 16 Nov '12

16 Nov '12

Dear experts: I used the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization?highlight… to defining a region of interest, but when I make a series of left clicks on the surface， then click the "Make Closed Fill Boundary" icon in the tools window. howevre, there has no connect the points my clicked, and drawing a yellow or red line between them. I hope that have experts to help me. Thanks! Bo Xiang

2 1

reconall without graphics card or GPU?
by Linda Zhang 16 Nov '12

16 Nov '12

Dear all, At our university, we have the option of using a high performance computing facility to run "computing intensive" analysis, but it doesn't have a 3D graphics card or GPU. Is it advisable to run reconall at the facility and visualise the results later on another computer? Running it on my current computer is just taking too much time. Cheers, Linda

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Re: [Freesurfer] error in analyze command failed: mri_concat
by Berg, S.F. van den 16 Nov '12

16 Nov '12

Hi Doug, I run the mri_concat command with 9 subjects in the command line. for the LH thickness and volume. A segmentation fault is the problem. What do i have to do in this case? Many thanks, Stan -------- freesurfer-Linux-centos5_x86_64-dev-20110315 -------- SUBJECTS_DIR /data1/projects/ysbrand-vumc/pddatabase-freesurfer guest@somerenserver:~$ mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh ninputs = 9 Checking inputs reading MRI_FRAME structure from file... Segmentation fault guest@somerenserver:~$ mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.thickness.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/caudalmiddlefrontal_curv/y.mgh ninputs = 9 Checking inputs reading MRI_FRAME structure from file... Segmentation fault guest@somerenserver:~$

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Using Subcortical initial output, with "fixed" cortical output
by Mark Fletcher 15 Nov '12

15 Nov '12

Dear FreeSurfers, I am using a Linux computer with FS 5.1 Due to the known "feauture" in version 5.1 where "Control points may adversely affect aseg" but also may alter the " subcortical segmentation", is it acceptable to use the initial subcortical output (before adding control points) for analysis, and then use the cortical volumetric output (after control points have been added) from corrected brains? If this is acceptable, any suggestions on how to phrase this for a paper without it seeming like FreeSurfer has a bug? Sincerely, Mark

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Re: [Freesurfer] tkregister2 error on lion
by Nick Schmansky 15 Nov '12

15 Nov '12

Rito, Hi, tkregister2 works for me on lion. do tkmedit and tksurfer work? did you install XQuartz via these instructions? https://surfer.nmr.mgh.harvard.edu/fswiki/MacTksurfer Actually i dont know if it necessary for lion to install XQuartz, but that is what i am running on my lion system (because i upgraded it from snow leopard when XQuartz was required to run tksurfer). Nick > Hi All, > > I have freesurfer 5.1 installed on my laptop running Lion. When I tried to > use tkregister2, the program doesnt load up the GUI. It failed even after > installing XQuartz. > It loaded successfully in a machine running Snow Leopard. > Any suggestions on how to get around it or are there any fixes available ? > > Thanks a lot > > Ri > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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interpretation of vertexwise thickness, area, volume analysis
by Mahinda Yogarajah 14 Nov '12

14 Nov '12

Dear Experts, Given that volume is area x thickness, how would one explain significant reductions in volume in a qdec anaysis comparing patients and controls, but not significant differences in area or thickness in the same regions where volume differences are seen. All analyses use the same parameter settings. Thanks. Mahinda

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SPM complications - moving parcels into native space
by Terri Scott 14 Nov '12

14 Nov '12

Dear all, I'm new to freesurfer and I'm trying to move a set of parcels from mni space to the native space of a subject. The parcels were created in SPM but I was going to try to register them to the subject using cvs. I registered my subject to an mni template with cvs. I converted the .img parcel file to .nii.gz, and changed the voxel size and orientation to match the mni template I used for the cvs registration of my subject. I then run this: mri_vol2vol --inv-morph --noDefM3zPath --interp nearest --no-save-reg --mov ' subj_anat_vol ' --targ ' cvs_input ' --o ' in_anat_output ' --m3z ' morph_fullpath ' >> ' log_fullpath where cvs_input is my parcel. When I run it, the parcels don't register well and come out distorted/in the wrong spot/etc. The parcel volume size is very different from the 256x256x256 template, but I don't know how to handle this problem. Any help you can give is greatly appreciated! Thanks! Terri

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