Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

Fwd: Re: Fwd: Re: Fwd: Some problems of the brain image after recon-all
by Xiaojun.Huang 14 Dec '13

14 Dec '13

Hi Bruce, I Have sent the raw data to you and I find if it is the problem of tksurfer Installing? Can it result in the problem? How can I Fix it? Thanks, Xiaojun. -------- 原始消息 -------- 主题: Re: [Freesurfer] Fwd: Re: Fwd: Some problems of the brain image after recon-all 日期: Tue, 10 Dec 2013 08:22:36 -0500 (EST) 发件人: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 收件人: Xiaojun.Huang <lvdosha(a)gmail.com> yes, or the whole subject dir so I can diagnose what went wrong cheers Bruce On Tue, 10 Dec 2013, Xiaojun.Huang wrote: > Hi Bruce, > I wonder if I need to upload the 3d raw data to you, If you need them. > Best, > Huang. > 于 2013/12/7 0:12, Bruce Fischl 写道: >> it comes up upside down in tksurfer without pressing any buttons or >> anything? Never seen that before - if you upload the subject I'll take a >> look >> >> cheers >> Bruce >> On Fri, 6 Dec 2013, Xiaojun.Huang wrote: >> >>> hi all, >>> >>> I am processing the 3D PD patients brain now . After recon-all running, >>> the segmentations of the GM and WM is not accurate although the original >>> dat >>> a is normal. additionally, when I use the TKSurfer Tools to review the 3D >>> brain,it is rev >>> erse. >>> More informations and images as follows: >>> >>> -------- 原始消息 -------- >>> 主题: >>> Re: [Freesurfer] Fwd: Some problems of the brain image after recon-all >>> 日期: >>> Thu, 05 Dec 2013 12:45:10 +0800 >>> 发件人: >>> Xiaojun.Huang <lvdosha(a)gmail.com> >>> 收件人: >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> >>> Hi Bruce, >>> Sorry for reply late. >>> The data were provided by a hospital and the input data were 3D >>> images.Some image informations as followed(eg.PDSub_02): >>> >>> 0008,103E,Series Description=Ax 3D VBM >>> 0008,1090,Manufacturer's Model Name=SIGNA EXCITE >>> 0018,0000,Acquisition Group Length=484 >>> 0018,0020,Scanning Sequence=GR >>> 0018,0021,Sequence Variant=SS\SP\SK >>> 0018,0022,Scan Options=FAST.GEMS\EDR.GEMS\FILTERED.GEMS >>> 0018,0023,MR Acquisition Type=3D >>> 0018,0025,Angio Flag=N >>> 0018,0050,Slice Thickness=1 >>> 0018,0080,Repetition Time [TR, ms]=7.652 >>> 0018,0081,Echo Time [TE, ms]=3.312 >>> 0018,0082,Inversion Time=0 >>> 0018,0083,Number of Averages=1 >>> 0018,0084,Imaging Frequency=127.755675 >>> 0018,0085,Imaged Nucleus=1H >>> 0018,0086,Echo Number= >>> 0018,0087,Magnetic Field Strength=3 >>> 0018,0088,Spacing Between Slices=1 >>> 0018,0091,Echo Train Length=1 >>> 0018,0093,Percent Sampling=100 >>> 0018,0094,Percent Phase Field View=100 >>> 0018,0095,Pixel Bandwidth=97.6562 >>> 0018,1020,Software Version=12\LX\MR Software release.12.0.M5A.0819.a >>> 0018,1030,Protocol Name=PDD-YANGWANQUN/4 >>> 0018,1310,Acquisition Matrix=0, 256, 228, 0 >>> 0018,1312,Phase Encoding Direction=ROW >>> 0018,1314,Flip Angle=13 >>> 0018,1315,Variable Flip Angle Flag=N >>> 0028,0010,Rows=512 >>> 0028,0011,Columns=512 >>> >>> It comes up in the proper orientation in tkmedit in three orientations as >>> attachment(eg.coromaland saggital view). >>> >>> Tanks, >>> Xiaojun. >>> >>> >>> 于 2013/12/4 22:45, Bruce Fischl 写道: >>> > Hi Xiaojun >>> > >>> > we need more details in order to help you. What was your input data? > >>> What format was it in? Does it come up in the proper orientation in > >>> tkmedit? What kind of acquisition (resolution, type, etc...) did you use? >>> > >>> > cheers >>> > Bruce >>> > On Wed, 4 Dec 2013, Xiaojun.Huang wrote: >>> > >>> >> >>> >> >>> >> >>> >> -------- 原始消息 -------- >>> >> 主题: >>> >> Some problems of the brain image after recon-all >>> >> 日期: >>> >> Tue, 03 Dec 2013 21:33:41 +0800 >>> >> 发件人: >>> >> Xiaojun.Huang <lvdosha(a)gmail.com> >>> >> 收件人: >>> >> Freesurfer(a)nmr.mgh.harvard.edu >>> >> >>> >> >>> >> Hi, >>> >> >>> >> I am processing the 3D PD patients brain now . After recon-all >> >>> running, the segmentations of the GM and WM is not accurate >>> >> although the original data is normal. additionally, when I use the >> >>> TKSurfer Tools to review the 3D brain,it is reverse. (eg. >>> >> PDSub_02 in the attach files) >>> >> >>> >> It is the first time for me to use Freesurfer.I'm sorry for the >> >>> trouble I'm giving you.And looking forward your reply. >>> >> >>> >> Thanks, >>> >> Xiaojun >>> >> >>> >> 2013.12.3 >>> >> >>> >> >>> >> >>> >> >>> >> >>> > >>> > >>> > 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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import from caret
by Colin Reveley 14 Dec '13

14 Dec '13

Hi - If one has a surface that is aligned to a volume in CARET, is it possible (or rather, is there a general procedure) to export the volume and the surface into freesurfer? The volume in CARET won't be conformed. It's header will define the origin such that CARET interprets a specific voxel/coordinate as the anterior commisure. The surface will be aligned to the volume in the sense that it's co-ordinates are with respect to that anterior commisure definition. What I need to do is run mri_convert -c to conform the volume, and then convert the surface to freesurfer format in such a way that it's now aligned to the conformed volume in freesurfer. Then I'd do some stuff (refine the surface) in freesurfer, and export the surface back to CARET. That's the general issue. Details include: the surface will need to be transformed so that it appears to freesurfer to be 1mm data, and the volume will have it's header changed so that it claims 1mm voxels (the data is higher resolution than 1mm). The problem can be considered as finding the inverse of Van Essen's Freesurfer to F99 pipeline. Or, "Surefit to Freesurfer" is a better way to look at it. The surfaces are *white and *pial though. It's some scaling, translating, conforming and format conversions. Other stuff is not a worry. connectome workbench, FS, CARET, FSL, MATLAB whatever are all relevant/involved tools hope can help Colin Reveley

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error loading surface on one machine, but not another
by Ryan Mruczek 13 Dec '13

13 Dec '13

Hi All I created surfaces for a particular subject on one machine, and subsequently copied the entire subjects surface directory to another machine (both running OSX, although different versions). On the second machine, I cannot load the lh surfaces files. For example % tksurfer LS lh white produces the following output and error (last line): tksurfer LS lh white subject is LS hemi is lh surface is white surfer: current subjects dir: /Users/rmruczek/MR_DATA/surfaces surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/rmruczek/MR_DATA/surfaces/LS/surf checking for nofix files in 'white' Reading image info (/Users/rmruczek/MR_DATA/surfaces/LS) Reading /Users/rmruczek/MR_DATA/surfaces/LS/mri/orig.mgz surfer: Reading header info from /Users/rmruczek/MR_DATA/surfaces/LS/mri/orig.mgz mrisFindNeighbors: /Users/rmruczek/MR_DATA/surfaces/LS/surf/lh.white: face[0].v[0] = 0, but face 0 not in vertex 0 face list This is a problem for all of the left hemisphere surfaces on the new machine. The same command executes fine on the original machine. Also, the right hemisphere surfaces load fine on the second machine. I've double checked that the files were copied completely and were not truncated. Has anyone experienced something similar or have an idea of what is going on? Thanks! Cheers, Ryan

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segmentation incorrectly after recon-all
by Rujing Zha 13 Dec '13

13 Dec '13

Dear all, How can I fix the false segmentation in the attachment. Thanks. All the best. 2013-12-13 Rujing Zha

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problem creating annotation using mri_sample_parc?
by Markus Gschwind 13 Dec '13

13 Dec '13

Dear all, I am trying to create a annotation file from a ROI_file with multiple ROIs with values form 1:10 using mris_sample_parc I had verified that myROIfile and subject001/surf/rh.white and also mri/T1.mgz loadable together in freeview (=same space). when running the command mris_sample_parc -v -sdir subject001 rh ~/Documents/myROIfile.mgz rh.myROIfile.annot it first starts well, but then complains about could not open translation file /Applications/freesurfer/cma_parcellation_colors.txt However when trying to load the created annotation file it gives me the same never endign error: CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory ... etc. I guess that the annotation is not on the surface, but what am I doing wrong? Thank you in advance, Markus

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funcroi commands
by Emily Boeke 13 Dec '13

13 Dec '13

Hi Freesurfers, I would like to make sure I am using the funcroi commands correctly for anatomical and functional ROI analyses (using the aseg to anatomically constrain), and I have some questions about the commands. If I want to extract the average percent signal change in the whole left amygdala for a particular contrast, is this the correct version of the commands to run? 1. funcroi-config -seg aseg.mgz 18 -roi <name>.cfg -analysis <analysisname> 2. funcroi-sess -roi <name>.cfg -sf sf.txt -df sesspar 3. funcroi-table-sess -roi <name>.cfg -sf sf.txt -df sesspar -o <name>.txt -c <contrast> -m cespct If I want to extract the average percent signal change from an anatomically constrained functional ROI (e.g. an ROI representing activation in a certain contrast within the lh amygdala), is this the correct version of the commands to run: 4. funcroi-config -seg aseg.mgz 18 -roi <name>.cfg -analysis <analysisname> -contrast <contrast> -sign pos -thresh 1.3 5. funcroi-sess -roi <name>.cfg -sf sf.txt -df sesspar 6. funcroi-table-sess -roi <name>.cfg -sf sf.txt -df sesspar -o <name>.txt -a <analysisname> -c <contrast> -m cespct My questions are (regarding the second set of commands): -in the right hippocampus example under funcroi-config --help, the anatomical constraint is specified with --annot aseg.mgz 53, but it should be --seg aseg.mgz 53 like in my examples, correct? Otherwise you get an error. -Is it ok to use one analysis name in the funcroi-config file and another in funcroi-table-sess? Would that allow me to make an ROI from one analysis and use it to extract signal from another analysis? -If I get a message saying some subjects had "empty ROIs" and the value in the table for them is 0, does this mean that subjects had no activation (meeting the threshold specified) in the first contrast I specified (in funcroi-config) so no ROI could be created from their activation? -If I want to look at activation in more than one anatomical region (for example, bilateral amygdala), is there any way to do that with the -seg option? Pardon the long message. Thanks for the help! Emily

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Re: [Freesurfer] qdec analysis with 2 covariates
by Douglas N Greve 13 Dec '13

13 Dec '13

I'm sure that those clusters are not very significant. Try running mri_glmfit-sim with --cwd .99 to capture all clusters doug On 12/12/2013 03:27 PM, Jon Wieser wrote: > HI Doug, > here's a screen shot, showing the clusters and a scatter plot for one of the 45 clusters. > for this dataset, ussualy there is 0 or 1 clusters after monte carlo simulation. i'm not sure if they match one of the 45 clusters in qdec. i'l have to look into that. > > I would like to have a file which contains the data represented in the scatter plot, for all of the 45 clusters, vlaues of thickness for each subject. is that possible? > I tried runnin mri_surfcluster, but it only gave me the average data for that clusters, not the individual data. > > thanks! > > Jon > > ----- Original Message ----- > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Thursday, December 12, 2013 1:15:58 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > I'm not sure what is going on. Can you send a screen shot of the qdec > window when you see 40 clusters? It might be that it is showing clusters > regardless of the cluster significance. Do the 3 or 4 clusters created > when you run mri_glmfit-sim match clusters in qdec? > > On 12/10/2013 05:32 PM, Jon Wieser wrote: >> Hi Doug >> I'm looking at the effect of MJ usage, the effect of whetherthe subject has AHDH, and the interaction between MJ usage and ADHD >> our threshold is 1.3 >> >> i have attahced our qdec.table.dat file >> we are also looking at age and gender as covariates >> Jon >> >> Jon >> ----- Original Message ----- >> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)nmr.mgh.harvard.edu >> Sent: Tuesday, December 10, 2013 4:20:30 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> which contrast are you looking at in QDEC? Also, what is the voxel-wise >> threshold in QDEC? The value I gave in the command below is 1.3 but I >> got that from one of your CSD files. >> >> >> On 12/10/2013 05:10 PM, Jon Wieser wrote: >>> HI doug, >>> no, the summary files in the contrasts have the same # of cluster as the columns in their OCN.dat \ >>> the 40 cluster are seen in qdec when I run the "find cluster" and Goto max" button. most of these clusters go away in qdec when I run the montecarlo simulation >>> >>> Jon >>> ----- Original Message ----- >>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>> Sent: Tuesday, December 10, 2013 4:03:06 PM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> >>> So one of the contrasts has 40 clusters in the summary file but the >>> y.ocn.dat file only has a few columns? >>> >>> >>> On 12/10/2013 04:54 PM, Jon Wieser wrote: >>>> yes, that is what we want, but the files contain only 1-3 columns >>>> >>>> Jon >>>> >>>> ----- Original Message ----- >>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>>> Sent: Tuesday, December 10, 2013 3:44:50 PM >>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>> >>>> >>>> There should be a column for each cluster in contrast. Is that what you >>>> want? >>>> >>>> >>>> On 12/10/2013 04:37 PM, Jon Wieser wrote: >>>>> thanks, >>>>> I ran >>>>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs >>>>> >>>>> MTA_ADHD_MJ is my project file and has the results from qdec in it >>>>> >>>>> >>>>> it has produced: >>>>> >>>>> lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>> lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>>>> lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>>>> lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>>> lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>> lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>> lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>> lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>> lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>> lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>>> lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>> lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>> rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>> rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>>>> rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>>>> rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>>> rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>> rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>> rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>>> rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>> rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>> rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>>> rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>>> rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>> >>>>> >>>>> >>>>> these files have 120 rows. each row has a thickness value s >>>>> example >>>>> 2.71869 >>>>> 2.52448 >>>>> 2.50450 >>>>> 2.53677 >>>>> 2.58363 >>>>> 2.50404 >>>>> 2.42116 >>>>> 2.61757 >>>>> 2.51820 >>>>> 2.59009 >>>>> 2.42524 >>>>> 2.72043 >>>>> 2.59479 >>>>> 2.38014 >>>>> 2.41052 >>>>> 2.58483 >>>>> 2.49214 >>>>> 2.45870 >>>>> 2.51685 >>>>> 2.62981 >>>>> 2.59232 >>>>> >>>>> it appears that there is the thickness for each subject in the files >>>>> >>>>> I would like to have the thickness value, for each cluster, for every subject >>>>> >>>>> we have 120 subjects, with about 40 clusters >>>>> Jon >>>>> >>>>> ----- Original Message ----- >>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Sent: Tuesday, December 10, 2013 2:30:31 PM >>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>> >>>>> >>>>> OK, sorry, I thought qdec was running a script called mri_glmfit-sim but >>>>> it appears to be running the correction internally. That means that you >>>>> will have to run mri_glmfit-sim yourself, something like >>>>> >>>>> mri_glmfit-sim --glmdir glmdir --cache 1.3 abs >>>>> >>>>> doug >>>>> >>>>> >>>>> On 12/10/2013 02:53 PM, Jon Wieser wrote: >>>>>> i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the qdec output directory >>>>>> Jon >>>>>> >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)nmr.mgh.harvard.edu >>>>>> Sent: Tuesday, December 10, 2013 1:42:37 PM >>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>> >>>>>> >>>>>> Is there a cache.mri_glmfit-sim.log in the output folder? Can you send >>>>>> it to me? Also, please remember to post to the list. thanks! >>>>>> doug >>>>>> >>>>>> >>>>>> On 12/10/2013 02:30 PM, Jon Wieser wrote: >>>>>>> FS version 5.3 >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> Sent: Tuesday, December 10, 2013 1:05:26 PM >>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>> >>>>>>> >>>>>>> hmmm, it should be there. What version of FS are you using? >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 12/10/2013 12:57 PM, Jon Wieser wrote: >>>>>>>> i was getting the values for the command terminal, when I press the "find clusters and GOTo Max" button on the qdec GUI. >>>>>>>> there is no file named cache.th20.abs.y.dat or something similar. i did a "find" command to list all the *abs*.dat files in the directory >>>>>>>> >>>>>>>> qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>>>> qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat >>>>>>>> qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat >>>>>>>> qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat >>>>>>>> qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>>>> qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>>>> qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> these files contain: >>>>>>>> >>>>>>>> # CSD PDF/CDF >>>>>>>> # simtype null-z >>>>>>>> # anattype surface fsaverage lh >>>>>>>> # FixGroupSubjectArea 1 >>>>>>>> # merged 0 >>>>>>>> # contrast NA >>>>>>>> # seed 1271277527 >>>>>>>> # thresh 1.300000 >>>>>>>> # threshsign 0.000000 >>>>>>>> # searchspace 74612.965197 >>>>>>>> # nullfwhm 15.000000 >>>>>>>> # varfwhm -1.000000 >>>>>>>> # nrepetitions 10000 >>>>>>>> # NOTE: nreps and nrepetitions are both valid for volume data. >>>>>>>> # NOTE: nreps is invalid (-1) for surface data to assure. >>>>>>>> # NOTE: backwards INcompatibility. >>>>>>>> # $Id: volcluster.c,v 1.50.2.1 2011/03/28 15:32:36 greve Exp $ >>>>>>>> # nreps -1 >>>>>>>> # FixSurfClusterArea 1 >>>>>>>> # $Id: surfcluster.c,v 1.26.2.2 2011/11/10 16:01:11 greve Exp $ >>>>>>>> # nbins 100 >>>>>>>> # BinNo MaxClustBin MaxClustPDF MaxClustCDF GRFCDF MaxSigBin MaxSigPDF MaxSigCDF >>>>>>>> 0 204.826004 0.000500 0.999500 0.998289 2.456050 0.000500 0.999500 >>>>>>>> 1 220.348267 0.001800 0.997700 0.996805 2.811329 0.008100 0.991400 >>>>>>>> 2 235.870529 0.004300 0.993400 0.994388 3.166609 0.022200 0.969200 >>>>>>>> 3 251.392792 0.007100 0.986300 0.990673 3.521888 0.030300 0.938900 >>>>>>>> 4 266.915039 0.015600 0.970700 0.985251 3.877167 0.028900 0.910000 >>>>>>>> 5 282.437317 0.017500 0.953200 0.977702 4.232447 0.022600 0.887400 >>>>>>>> 6 297.959595 0.021400 0.931800 0.967628 4.587726 0.015200 0.872200 >>>>>>>> 7 313.481842 0.033600 0.898200 0.954689 4.943005 0.012300 0.859900 >>>>>>>> 8 329.004089 0.036100 0.862100 0.938634 5.298285 0.009800 0.850100 >>>>>>>> 9 344.526367 0.038000 0.824100 0.919325 5.653563 0.007300 0.842800 >>>>>>>> 10 360.048645 0.042500 0.781600 0.896747 6.008843 0.009200 0.833600 >>>>>>>> 11 375.570892 0.050000 0.731600 0.871009 6.364122 0.006900 0.826700 >>>>>>>> 12 391.093140 0.043400 0.688200 0.842332 6.719401 0.007100 0.819600 >>>>>>>> 13 406.615417 0.047300 0.640900 0.811034 7.074681 0.005500 0.814100 >>>>>>>> 14 422.137695 0.050700 0.590200 0.777508 7.429960 0.005500 0.808600 >>>>>>>> 15 437.659943 0.047400 0.542800 0.742195 7.785239 0.005200 0.803400 >>>>>>>> 16 453.182190 0.044100 0.498700 0.705560 8.140518 0.004900 0.798500 >>>>>>>> 17 468.704468 0.042700 0.456000 0.668070 8.495798 0.005100 0.793400 >>>>>>>> 18 484.226746 0.040600 0.415400 0.630176 8.851077 0.006100 0.787300 >>>>>>>> 19 499.748962 0.034900 0.380500 0.592300 9.206356 0.004800 0.782500 >>>>>>>> 20 515.271240 0.032200 0.348300 0.554820 9.561636 0.003600 0.778900 >>>>>>>> 21 530.793518 0.031400 0.316900 0.518067 9.916915 0.003400 0.775500 >>>>>>>> 22 546.315796 0.032400 0.284500 0.482320 10.272194 0.004000 0.771500 >>>>>>>> 23 561.838013 0.023800 0.260700 0.447809 10.627474 0.004800 0.766700 >>>>>>>> 24 577.360291 0.026100 0.234600 0.414711 10.982753 0.004500 0.762200 >>>>>>>> 25 592.882568 0.022700 0.211900 0.383160 11.338033 0.003300 0.758900 >>>>>>>> 26 608.404846 0.017500 0.194400 0.353244 11.693312 0.003100 0.755800 >>>>>>>> 27 623.927063 0.018200 0.176200 0.325018 12.048591 0.003700 0.752100 >>>>>>>> 28 639.449341 0.017400 0.158800 0.298504 12.403871 0.003800 0.748300 >>>>>>>> 29 654.971619 0.014900 0.143900 0.273697 12.759150 0.004400 0.743900 >>>>>>>> 30 670.493896 0.014200 0.129700 0.250569 13.114429 0.003700 0.740200 >>>>>>>> 31 686.016113 0.014300 0.115400 0.229078 13.469708 0.002800 0.737400 >>>>>>>> 32 701.538391 0.013100 0.102300 0.209165 13.824987 0.003800 0.733600 >>>>>>>> 33 717.060669 0.011700 0.090600 0.190763 14.180266 0.003700 0.729900 >>>>>>>> 34 732.582947 0.008500 0.082100 0.173798 14.535546 0.002900 0.727000 >>>>>>>> 35 748.105164 0.008400 0.073700 0.158191 14.890825 0.003200 0.723800 >>>>>>>> 36 763.627441 0.006800 0.066900 0.143861 15.246104 0.003300 0.720500 >>>>>>>> 37 779.149719 0.007100 0.059800 0.130727 15.601384 0.004600 0.715900 >>>>>>>> 38 794.671936 0.007200 0.052600 0.118707 15.956663 0.000000 0.715900 >>>>>>>> 39 810.194214 0.005400 0.047200 0.107723 16.311943 0.000000 0.715900 >>>>>>>> 40 825.716492 0.005400 0.041800 0.097698 16.667221 0.000000 0.715900 >>>>>>>> 41 841.238770 0.004800 0.037000 0.088559 17.022501 0.000000 0.715900 >>>>>>>> 42 856.761047 0.004600 0.032400 0.080237 17.377781 0.000000 0.715900 >>>>>>>> 43 872.283264 0.003200 0.029200 0.072665 17.733059 0.000000 0.715900 >>>>>>>> 44 887.805542 0.003400 0.025800 0.065783 18.088339 0.000000 0.715900 >>>>>>>> 45 903.327820 0.002200 0.023600 0.059531 18.443619 0.000000 0.715900 >>>>>>>> 46 918.850037 0.002600 0.021000 0.053855 18.798897 0.000000 0.715900 >>>>>>>> 47 934.372314 0.002200 0.018800 0.048707 19.154179 0.000000 0.715900 >>>>>>>> 48 949.894592 0.001900 0.016900 0.044040 19.509457 0.000000 0.715900 >>>>>>>> 49 965.416870 0.002200 0.014700 0.039810 19.864735 0.000000 0.715900 >>>>>>>> 50 980.939148 0.000700 0.014000 0.035979 20.220016 0.000000 0.715900 >>>>>>>> 51 996.461365 0.002100 0.011900 0.032510 20.575294 0.000000 0.715900 >>>>>>>> 52 1011.983643 0.000800 0.011100 0.029371 20.930573 0.000000 0.715900 >>>>>>>> 53 1027.505981 0.000800 0.010300 0.026530 21.285854 0.000000 0.715900 >>>>>>>> 54 1043.028198 0.001000 0.009300 0.023961 21.641132 0.000000 0.715900 >>>>>>>> 55 1058.550415 0.001000 0.008300 0.021638 21.996410 0.000000 0.715900 >>>>>>>> 56 1074.072754 0.000900 0.007400 0.019538 22.351692 0.000000 0.715900 >>>>>>>> 57 1089.594971 0.000900 0.006500 0.017640 22.706970 0.000000 0.715900 >>>>>>>> 58 1105.117310 0.000800 0.005700 0.015925 23.062248 0.000000 0.715900 >>>>>>>> 59 1120.639526 0.000100 0.005600 0.014375 23.417530 0.000000 0.715900 >>>>>>>> 60 1136.161743 0.000300 0.005300 0.012975 23.772808 0.000000 0.715900 >>>>>>>> 61 1151.684082 0.000800 0.004500 0.011711 24.128086 0.000000 0.715900 >>>>>>>> 62 1167.206299 0.000400 0.004100 0.010569 24.483368 0.000000 0.715900 >>>>>>>> 63 1182.728516 0.000200 0.003900 0.009538 24.838646 0.000000 0.715900 >>>>>>>> 64 1198.250854 0.000200 0.003700 0.008607 25.193924 0.000000 0.715900 >>>>>>>> 65 1213.773071 0.000300 0.003400 0.007767 25.549206 0.000000 0.715900 >>>>>>>> 66 1229.295410 0.000400 0.003000 0.007008 25.904484 0.000000 0.715900 >>>>>>>> 67 1244.817627 0.000400 0.002600 0.006323 26.259762 0.000000 0.715900 >>>>>>>> 68 1260.339966 0.000300 0.002300 0.005705 26.615044 0.000000 0.715900 >>>>>>>> 69 1275.862183 0.000400 0.001900 0.005147 26.970322 0.000000 0.715900 >>>>>>>> 70 1291.384399 0.000100 0.001800 0.004644 27.325600 0.000000 0.715900 >>>>>>>> 71 1306.906738 0.000000 0.001800 0.004190 27.680882 0.000000 0.715900 >>>>>>>> 72 1322.428955 0.000400 0.001400 0.003780 28.036160 0.000000 0.715900 >>>>>>>> 73 1337.951172 0.000100 0.001300 0.003410 28.391438 0.000000 0.715900 >>>>>>>> 74 1353.473511 0.000100 0.001200 0.003076 28.746719 0.000000 0.715900 >>>>>>>> 75 1368.995728 0.000100 0.001100 0.002775 29.101997 0.000000 0.715900 >>>>>>>> 76 1384.517944 0.000100 0.001000 0.002503 29.457275 0.000000 0.715900 >>>>>>>> 77 1400.040283 0.000300 0.000700 0.002258 29.812557 0.000000 0.715900 >>>>>>>> 78 1415.562500 0.000100 0.000600 0.002037 30.167835 0.000000 0.715900 >>>>>>>> 79 1431.084839 0.000000 0.000600 0.001838 30.523113 0.000000 0.715900 >>>>>>>> 80 1446.607056 0.000100 0.000500 0.001658 30.878395 0.000000 0.715900 >>>>>>>> 81 1462.129272 0.000200 0.000300 0.001495 31.233673 0.000000 0.715900 >>>>>>>> 82 1477.651611 0.000000 0.000300 0.001349 31.588951 0.000000 0.715900 >>>>>>>> 83 1493.173828 0.000200 0.000100 0.001217 31.944233 0.000000 0.715900 >>>>>>>> 84 1508.696167 0.000000 0.000100 0.001098 32.299511 0.000000 0.715900 >>>>>>>> 85 1524.218384 0.000000 0.000100 0.000990 32.654789 0.000000 0.715900 >>>>>>>> 86 1539.740601 0.000000 0.000100 0.000893 33.010071 0.000000 0.715900 >>>>>>>> 87 1555.262939 0.000000 0.000100 0.000805 33.365349 0.000000 0.715900 >>>>>>>> 88 1570.785156 0.000000 0.000100 0.000727 33.720627 0.000000 0.715900 >>>>>>>> 89 1586.307373 0.000000 0.000100 0.000655 34.075909 0.000000 0.715900 >>>>>>>> 90 1601.829712 0.000000 0.000100 0.000591 34.431187 0.000000 0.715900 >>>>>>>> 91 1617.351929 0.000000 0.000100 0.000533 34.786469 0.000000 0.715900 >>>>>>>> 92 1632.874146 0.000000 0.000100 0.000481 35.141747 0.000000 0.715900 >>>>>>>> 93 1648.396484 0.000000 0.000100 0.000434 35.497025 0.000000 0.715900 >>>>>>>> 94 1663.918701 0.000000 0.000100 0.000391 35.852306 0.000000 0.715900 >>>>>>>> 95 1679.441040 0.000000 0.000100 0.000353 36.207584 0.000000 0.715900 >>>>>>>> 96 1694.963257 0.000000 0.000100 0.000318 36.562862 0.000000 0.715900 >>>>>>>> 97 1710.485474 0.000000 0.000100 0.000287 36.918144 0.000000 0.715900 >>>>>>>> 98 1726.007812 0.000000 0.000100 0.000259 37.273422 0.000000 0.715900 >>>>>>>> 99 1741.530029 0.000100 -0.000000 0.000234 37.628700 0.715900 0.000000 >>>>>>>> >>>>>>>> ----- Original Message ----- >>>>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> Sent: Monday, December 9, 2013 5:02:41 PM >>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>> >>>>>>>> which file did you look in? It should have a name like >>>>>>>> cache.th20.abs.y.ocn.dat >>>>>>>> >>>>>>>> On 12/09/2013 05:09 PM, Jon Wieser wrote: >>>>>>>>> I found data for the average thickness all subjects for each cluster, but I haven't found the individual subject's thickness for each cluster. can you direct me to that data? >>>>>>>>> Jon >>>>>>>>> ----- Original Message ----- >>>>>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>> Sent: Monday, December 9, 2013 2:15:39 PM >>>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>>> >>>>>>>>> It is in one of the output files. Look for the .dat file in >>>>>>>>> mri_glmfit-sim --help >>>>>>>>> >>>>>>>>> On 12/09/2013 03:01 PM, Jon Wieser wrote: >>>>>>>>>> thanks doug, >>>>>>>>>> >>>>>>>>>> We've run a 2x2 analysis for thickness in Qdec and want the get the average thickness value for each cluster, for each subject. >>>>>>>>>> How can i get a table of thickness data , for feach subject in the analysis >>>>>>>>>> Jon >>>>>>>>>> >>>>>>>>>> ----- Original Message ----- >>>>>>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>> Sent: Monday, December 9, 2013 1:48:15 PM >>>>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Hi Jon, QDEC does not currently allow more than one covariates of >>>>>>>>>> interest. You will have to use the command-line stream (ie, >>>>>>>>>> mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) >>>>>>>>>> >>>>>>>>>> doug >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 12/05/2013 02:57 PM, Jon Wieser wrote: >>>>>>>>>>> HI freesurfer experts >>>>>>>>>>> >>>>>>>>>>> I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? >>>>>>>>>>> Thanks >>>>>>>>>>> Jon >>>>>>>>>>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 4

.nii file visualization in tkmedit
by Garikoitz Lerma-Usabiaga 13 Dec '13

13 Dec '13

Hi list, I am trying to visualize a .nii ROI coming from MEG, which is in Colin27 space. I can visualize it perfectly in mricron and tkmedit with the following command: tkmedit -f path/to/spm8/canonical/single_subj_T1.nii -overlay MEG_ROI.nii -fthresh 0.5 (single_subj_T1.nii is Colin27) but when I visualize it with: tkmedit Colin T1.mgz -overlay ./rC_vs_D_band1_0.01_left.nii -overlay-reg /home/glerma/glerma/GIT/bcblscripts/FREESURFER/ROI/Mikel_SingleSubject_to_Colin.dat -fthresh 0.5 -surface lh.white -aux-surface rh.white The result is wrong, and different from the first tkmedit. Should I convert the MEG_ROI.nii ni some specific way to make it work? Any suggestions? Thanks, Gari The registration matrix between single_subj_T1.nii and Colin27 is the following one: Colin 2.000000 2.000000 0.150000 9.999982714653015e-01 -1.096551306545734e-03 -1.517703873105347e-03 5.575752854347229e-01 1.516161020845175e-03 -1.406581024639308e-03 9.999977946281433e-01 -1.579373359680176e+00 -1.098683569580317e-03 -9.999984502792358e-01 -1.404915703460574e-03 6.750410795211792e-01 0 0 0 1 round (obtained with: bbregister --s Colin --mov path/to/spm8/canonical/single_subj_T1.nii --init-spm --reg from_SingleSubject_to_Colin.dat --t1 )

2 5

Fwd: qdec analysis with 2 covariates
by Jon Wieser 12 Dec '13

12 Dec '13

Hi Doug, Here's a screen shot, showing the clusters and a scatter plot for one of the 45 clusters. for this dataset, ussualy there is 0 or 1 clusters after monte carlo simulation. i'm not sure if they match one of the 45 clusters in qdec. i'l have to look into that. I would like to have a file which contains data similar to that represented in the scatter plot but for the average of the cluster, not just one vertex, for all of the 45 clusters, values of thickness for each subject. is that possible? I tried running mri_surfcluster, but it only gave me the average data for that clusters, not the individual data. thanks! Jon ----- Original Message ----- From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> To: "Jon Wieser" <wieser(a)uwm.edu> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Thursday, December 12, 2013 1:15:58 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates I'm not sure what is going on. Can you send a screen shot of the qdec window when you see 40 clusters? It might be that it is showing clusters regardless of the cluster significance. Do the 3 or 4 clusters created when you run mri_glmfit-sim match clusters in qdec? On 12/10/2013 05:32 PM, Jon Wieser wrote: > Hi Doug > I'm looking at the effect of MJ usage, the effect of whetherthe subject has AHDH, and the interaction between MJ usage and ADHD > our threshold is 1.3 > > i have attahced our qdec.table.dat file > we are also looking at age and gender as covariates > Jon > > Jon > ----- Original Message ----- > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)nmr.mgh.harvard.edu > Sent: Tuesday, December 10, 2013 4:20:30 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > which contrast are you looking at in QDEC? Also, what is the voxel-wise > threshold in QDEC? The value I gave in the command below is 1.3 but I > got that from one of your CSD files. > > > On 12/10/2013 05:10 PM, Jon Wieser wrote: >> HI doug, >> no, the summary files in the contrasts have the same # of cluster as the columns in their OCN.dat \ >> the 40 cluster are seen in qdec when I run the "find cluster" and Goto max" button. most of these clusters go away in qdec when I run the montecarlo simulation >> >> Jon >> ----- Original Message ----- >> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >> Sent: Tuesday, December 10, 2013 4:03:06 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> So one of the contrasts has 40 clusters in the summary file but the >> y.ocn.dat file only has a few columns? >> >> >> On 12/10/2013 04:54 PM, Jon Wieser wrote: >>> yes, that is what we want, but the files contain only 1-3 columns >>> >>> Jon >>> >>> ----- Original Message ----- >>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>> Sent: Tuesday, December 10, 2013 3:44:50 PM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> >>> There should be a column for each cluster in contrast. Is that what you >>> want? >>> >>> >>> On 12/10/2013 04:37 PM, Jon Wieser wrote: >>>> thanks, >>>> I ran >>>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs >>>> >>>> MTA_ADHD_MJ is my project file and has the results from qdec in it >>>> >>>> >>>> it has produced: >>>> >>>> lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>>> lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>>> lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>> lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>> lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>> lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>> lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>> lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>> lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>>> rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>>> rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>> rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>> rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>> rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>> rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>> rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>> rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> >>>> >>>> >>>> these files have 120 rows. each row has a thickness value s >>>> example >>>> 2.71869 >>>> 2.52448 >>>> 2.50450 >>>> 2.53677 >>>> 2.58363 >>>> 2.50404 >>>> 2.42116 >>>> 2.61757 >>>> 2.51820 >>>> 2.59009 >>>> 2.42524 >>>> 2.72043 >>>> 2.59479 >>>> 2.38014 >>>> 2.41052 >>>> 2.58483 >>>> 2.49214 >>>> 2.45870 >>>> 2.51685 >>>> 2.62981 >>>> 2.59232 >>>> >>>> it appears that there is the thickness for each subject in the files >>>> >>>> I would like to have the thickness value, for each cluster, for every subject >>>> >>>> we have 120 subjects, with about 40 clusters >>>> Jon >>>> >>>> ----- Original Message ----- >>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>>> Sent: Tuesday, December 10, 2013 2:30:31 PM >>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>> >>>> >>>> OK, sorry, I thought qdec was running a script called mri_glmfit-sim but >>>> it appears to be running the correction internally. That means that you >>>> will have to run mri_glmfit-sim yourself, something like >>>> >>>> mri_glmfit-sim --glmdir glmdir --cache 1.3 abs >>>> >>>> doug >>>> >>>> >>>> On 12/10/2013 02:53 PM, Jon Wieser wrote: >>>>> i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the qdec output directory >>>>> Jon >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)nmr.mgh.harvard.edu >>>>> Sent: Tuesday, December 10, 2013 1:42:37 PM >>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>> >>>>> >>>>> Is there a cache.mri_glmfit-sim.log in the output folder? Can you send >>>>> it to me? Also, please remember to post to the list. thanks! >>>>> doug >>>>> >>>>> >>>>> On 12/10/2013 02:30 PM, Jon Wieser wrote: >>>>>> FS version 5.3 >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)nmr.mgh.harvard.edu >>>>>> Sent: Tuesday, December 10, 2013 1:05:26 PM >>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>> >>>>>> >>>>>> hmmm, it should be there. What version of FS are you using? >>>>>> >>>>>> >>>>>> >>>>>> On 12/10/2013 12:57 PM, Jon Wieser wrote: >>>>>>> i was getting the values for the command terminal, when I press the "find clusters and GOTo Max" button on the qdec GUI. >>>>>>> there is no file named cache.th20.abs.y.dat or something similar. i did a "find" command to list all the *abs*.dat files in the directory >>>>>>> >>>>>>> qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>>> qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat >>>>>>> qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat >>>>>>> qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat >>>>>>> qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>>> qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>>> qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> these files contain: >>>>>>> >>>>>>> # CSD PDF/CDF >>>>>>> # simtype null-z >>>>>>> # anattype surface fsaverage lh >>>>>>> # FixGroupSubjectArea 1 >>>>>>> # merged 0 >>>>>>> # contrast NA >>>>>>> # seed 1271277527 >>>>>>> # thresh 1.300000 >>>>>>> # threshsign 0.000000 >>>>>>> # searchspace 74612.965197 >>>>>>> # nullfwhm 15.000000 >>>>>>> # varfwhm -1.000000 >>>>>>> # nrepetitions 10000 >>>>>>> # NOTE: nreps and nrepetitions are both valid for volume data. >>>>>>> # NOTE: nreps is invalid (-1) for surface data to assure. >>>>>>> # NOTE: backwards INcompatibility. >>>>>>> # $Id: volcluster.c,v 1.50.2.1 2011/03/28 15:32:36 greve Exp $ >>>>>>> # nreps -1 >>>>>>> # FixSurfClusterArea 1 >>>>>>> # $Id: surfcluster.c,v 1.26.2.2 2011/11/10 16:01:11 greve Exp $ >>>>>>> # nbins 100 >>>>>>> # BinNo MaxClustBin MaxClustPDF MaxClustCDF GRFCDF MaxSigBin MaxSigPDF MaxSigCDF >>>>>>> 0 204.826004 0.000500 0.999500 0.998289 2.456050 0.000500 0.999500 >>>>>>> 1 220.348267 0.001800 0.997700 0.996805 2.811329 0.008100 0.991400 >>>>>>> 2 235.870529 0.004300 0.993400 0.994388 3.166609 0.022200 0.969200 >>>>>>> 3 251.392792 0.007100 0.986300 0.990673 3.521888 0.030300 0.938900 >>>>>>> 4 266.915039 0.015600 0.970700 0.985251 3.877167 0.028900 0.910000 >>>>>>> 5 282.437317 0.017500 0.953200 0.977702 4.232447 0.022600 0.887400 >>>>>>> 6 297.959595 0.021400 0.931800 0.967628 4.587726 0.015200 0.872200 >>>>>>> 7 313.481842 0.033600 0.898200 0.954689 4.943005 0.012300 0.859900 >>>>>>> 8 329.004089 0.036100 0.862100 0.938634 5.298285 0.009800 0.850100 >>>>>>> 9 344.526367 0.038000 0.824100 0.919325 5.653563 0.007300 0.842800 >>>>>>> 10 360.048645 0.042500 0.781600 0.896747 6.008843 0.009200 0.833600 >>>>>>> 11 375.570892 0.050000 0.731600 0.871009 6.364122 0.006900 0.826700 >>>>>>> 12 391.093140 0.043400 0.688200 0.842332 6.719401 0.007100 0.819600 >>>>>>> 13 406.615417 0.047300 0.640900 0.811034 7.074681 0.005500 0.814100 >>>>>>> 14 422.137695 0.050700 0.590200 0.777508 7.429960 0.005500 0.808600 >>>>>>> 15 437.659943 0.047400 0.542800 0.742195 7.785239 0.005200 0.803400 >>>>>>> 16 453.182190 0.044100 0.498700 0.705560 8.140518 0.004900 0.798500 >>>>>>> 17 468.704468 0.042700 0.456000 0.668070 8.495798 0.005100 0.793400 >>>>>>> 18 484.226746 0.040600 0.415400 0.630176 8.851077 0.006100 0.787300 >>>>>>> 19 499.748962 0.034900 0.380500 0.592300 9.206356 0.004800 0.782500 >>>>>>> 20 515.271240 0.032200 0.348300 0.554820 9.561636 0.003600 0.778900 >>>>>>> 21 530.793518 0.031400 0.316900 0.518067 9.916915 0.003400 0.775500 >>>>>>> 22 546.315796 0.032400 0.284500 0.482320 10.272194 0.004000 0.771500 >>>>>>> 23 561.838013 0.023800 0.260700 0.447809 10.627474 0.004800 0.766700 >>>>>>> 24 577.360291 0.026100 0.234600 0.414711 10.982753 0.004500 0.762200 >>>>>>> 25 592.882568 0.022700 0.211900 0.383160 11.338033 0.003300 0.758900 >>>>>>> 26 608.404846 0.017500 0.194400 0.353244 11.693312 0.003100 0.755800 >>>>>>> 27 623.927063 0.018200 0.176200 0.325018 12.048591 0.003700 0.752100 >>>>>>> 28 639.449341 0.017400 0.158800 0.298504 12.403871 0.003800 0.748300 >>>>>>> 29 654.971619 0.014900 0.143900 0.273697 12.759150 0.004400 0.743900 >>>>>>> 30 670.493896 0.014200 0.129700 0.250569 13.114429 0.003700 0.740200 >>>>>>> 31 686.016113 0.014300 0.115400 0.229078 13.469708 0.002800 0.737400 >>>>>>> 32 701.538391 0.013100 0.102300 0.209165 13.824987 0.003800 0.733600 >>>>>>> 33 717.060669 0.011700 0.090600 0.190763 14.180266 0.003700 0.729900 >>>>>>> 34 732.582947 0.008500 0.082100 0.173798 14.535546 0.002900 0.727000 >>>>>>> 35 748.105164 0.008400 0.073700 0.158191 14.890825 0.003200 0.723800 >>>>>>> 36 763.627441 0.006800 0.066900 0.143861 15.246104 0.003300 0.720500 >>>>>>> 37 779.149719 0.007100 0.059800 0.130727 15.601384 0.004600 0.715900 >>>>>>> 38 794.671936 0.007200 0.052600 0.118707 15.956663 0.000000 0.715900 >>>>>>> 39 810.194214 0.005400 0.047200 0.107723 16.311943 0.000000 0.715900 >>>>>>> 40 825.716492 0.005400 0.041800 0.097698 16.667221 0.000000 0.715900 >>>>>>> 41 841.238770 0.004800 0.037000 0.088559 17.022501 0.000000 0.715900 >>>>>>> 42 856.761047 0.004600 0.032400 0.080237 17.377781 0.000000 0.715900 >>>>>>> 43 872.283264 0.003200 0.029200 0.072665 17.733059 0.000000 0.715900 >>>>>>> 44 887.805542 0.003400 0.025800 0.065783 18.088339 0.000000 0.715900 >>>>>>> 45 903.327820 0.002200 0.023600 0.059531 18.443619 0.000000 0.715900 >>>>>>> 46 918.850037 0.002600 0.021000 0.053855 18.798897 0.000000 0.715900 >>>>>>> 47 934.372314 0.002200 0.018800 0.048707 19.154179 0.000000 0.715900 >>>>>>> 48 949.894592 0.001900 0.016900 0.044040 19.509457 0.000000 0.715900 >>>>>>> 49 965.416870 0.002200 0.014700 0.039810 19.864735 0.000000 0.715900 >>>>>>> 50 980.939148 0.000700 0.014000 0.035979 20.220016 0.000000 0.715900 >>>>>>> 51 996.461365 0.002100 0.011900 0.032510 20.575294 0.000000 0.715900 >>>>>>> 52 1011.983643 0.000800 0.011100 0.029371 20.930573 0.000000 0.715900 >>>>>>> 53 1027.505981 0.000800 0.010300 0.026530 21.285854 0.000000 0.715900 >>>>>>> 54 1043.028198 0.001000 0.009300 0.023961 21.641132 0.000000 0.715900 >>>>>>> 55 1058.550415 0.001000 0.008300 0.021638 21.996410 0.000000 0.715900 >>>>>>> 56 1074.072754 0.000900 0.007400 0.019538 22.351692 0.000000 0.715900 >>>>>>> 57 1089.594971 0.000900 0.006500 0.017640 22.706970 0.000000 0.715900 >>>>>>> 58 1105.117310 0.000800 0.005700 0.015925 23.062248 0.000000 0.715900 >>>>>>> 59 1120.639526 0.000100 0.005600 0.014375 23.417530 0.000000 0.715900 >>>>>>> 60 1136.161743 0.000300 0.005300 0.012975 23.772808 0.000000 0.715900 >>>>>>> 61 1151.684082 0.000800 0.004500 0.011711 24.128086 0.000000 0.715900 >>>>>>> 62 1167.206299 0.000400 0.004100 0.010569 24.483368 0.000000 0.715900 >>>>>>> 63 1182.728516 0.000200 0.003900 0.009538 24.838646 0.000000 0.715900 >>>>>>> 64 1198.250854 0.000200 0.003700 0.008607 25.193924 0.000000 0.715900 >>>>>>> 65 1213.773071 0.000300 0.003400 0.007767 25.549206 0.000000 0.715900 >>>>>>> 66 1229.295410 0.000400 0.003000 0.007008 25.904484 0.000000 0.715900 >>>>>>> 67 1244.817627 0.000400 0.002600 0.006323 26.259762 0.000000 0.715900 >>>>>>> 68 1260.339966 0.000300 0.002300 0.005705 26.615044 0.000000 0.715900 >>>>>>> 69 1275.862183 0.000400 0.001900 0.005147 26.970322 0.000000 0.715900 >>>>>>> 70 1291.384399 0.000100 0.001800 0.004644 27.325600 0.000000 0.715900 >>>>>>> 71 1306.906738 0.000000 0.001800 0.004190 27.680882 0.000000 0.715900 >>>>>>> 72 1322.428955 0.000400 0.001400 0.003780 28.036160 0.000000 0.715900 >>>>>>> 73 1337.951172 0.000100 0.001300 0.003410 28.391438 0.000000 0.715900 >>>>>>> 74 1353.473511 0.000100 0.001200 0.003076 28.746719 0.000000 0.715900 >>>>>>> 75 1368.995728 0.000100 0.001100 0.002775 29.101997 0.000000 0.715900 >>>>>>> 76 1384.517944 0.000100 0.001000 0.002503 29.457275 0.000000 0.715900 >>>>>>> 77 1400.040283 0.000300 0.000700 0.002258 29.812557 0.000000 0.715900 >>>>>>> 78 1415.562500 0.000100 0.000600 0.002037 30.167835 0.000000 0.715900 >>>>>>> 79 1431.084839 0.000000 0.000600 0.001838 30.523113 0.000000 0.715900 >>>>>>> 80 1446.607056 0.000100 0.000500 0.001658 30.878395 0.000000 0.715900 >>>>>>> 81 1462.129272 0.000200 0.000300 0.001495 31.233673 0.000000 0.715900 >>>>>>> 82 1477.651611 0.000000 0.000300 0.001349 31.588951 0.000000 0.715900 >>>>>>> 83 1493.173828 0.000200 0.000100 0.001217 31.944233 0.000000 0.715900 >>>>>>> 84 1508.696167 0.000000 0.000100 0.001098 32.299511 0.000000 0.715900 >>>>>>> 85 1524.218384 0.000000 0.000100 0.000990 32.654789 0.000000 0.715900 >>>>>>> 86 1539.740601 0.000000 0.000100 0.000893 33.010071 0.000000 0.715900 >>>>>>> 87 1555.262939 0.000000 0.000100 0.000805 33.365349 0.000000 0.715900 >>>>>>> 88 1570.785156 0.000000 0.000100 0.000727 33.720627 0.000000 0.715900 >>>>>>> 89 1586.307373 0.000000 0.000100 0.000655 34.075909 0.000000 0.715900 >>>>>>> 90 1601.829712 0.000000 0.000100 0.000591 34.431187 0.000000 0.715900 >>>>>>> 91 1617.351929 0.000000 0.000100 0.000533 34.786469 0.000000 0.715900 >>>>>>> 92 1632.874146 0.000000 0.000100 0.000481 35.141747 0.000000 0.715900 >>>>>>> 93 1648.396484 0.000000 0.000100 0.000434 35.497025 0.000000 0.715900 >>>>>>> 94 1663.918701 0.000000 0.000100 0.000391 35.852306 0.000000 0.715900 >>>>>>> 95 1679.441040 0.000000 0.000100 0.000353 36.207584 0.000000 0.715900 >>>>>>> 96 1694.963257 0.000000 0.000100 0.000318 36.562862 0.000000 0.715900 >>>>>>> 97 1710.485474 0.000000 0.000100 0.000287 36.918144 0.000000 0.715900 >>>>>>> 98 1726.007812 0.000000 0.000100 0.000259 37.273422 0.000000 0.715900 >>>>>>> 99 1741.530029 0.000100 -0.000000 0.000234 37.628700 0.715900 0.000000 >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>> Sent: Monday, December 9, 2013 5:02:41 PM >>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>> >>>>>>> which file did you look in? It should have a name like >>>>>>> cache.th20.abs.y.ocn.dat >>>>>>> >>>>>>> On 12/09/2013 05:09 PM, Jon Wieser wrote: >>>>>>>> I found data for the average thickness all subjects for each cluster, but I haven't found the individual subject's thickness for each cluster. can you direct me to that data? >>>>>>>> Jon >>>>>>>> ----- Original Message ----- >>>>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> Sent: Monday, December 9, 2013 2:15:39 PM >>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>> >>>>>>>> It is in one of the output files. Look for the .dat file in >>>>>>>> mri_glmfit-sim --help >>>>>>>> >>>>>>>> On 12/09/2013 03:01 PM, Jon Wieser wrote: >>>>>>>>> thanks doug, >>>>>>>>> >>>>>>>>> We've run a 2x2 analysis for thickness in Qdec and want the get the average thickness value for each cluster, for each subject. >>>>>>>>> How can i get a table of thickness data , for feach subject in the analysis >>>>>>>>> Jon >>>>>>>>> >>>>>>>>> ----- Original Message ----- >>>>>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> Sent: Monday, December 9, 2013 1:48:15 PM >>>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>>> >>>>>>>>> >>>>>>>>> Hi Jon, QDEC does not currently allow more than one covariates of >>>>>>>>> interest. You will have to use the command-line stream (ie, >>>>>>>>> mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) >>>>>>>>> >>>>>>>>> doug >>>>>>>>> >>>>>>>>> >>>>>>>>> On 12/05/2013 02:57 PM, Jon Wieser wrote: >>>>>>>>>> HI freesurfer experts >>>>>>>>>> >>>>>>>>>> I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? >>>>>>>>>> Thanks >>>>>>>>>> Jon >>>>>>>>>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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.

1 0

Re: [Freesurfer] qdec analysis with 2 covariates
by Douglas N Greve 12 Dec '13

12 Dec '13

which contrast are you looking at in QDEC? Also, what is the voxel-wise threshold in QDEC? The value I gave in the command below is 1.3 but I got that from one of your CSD files. On 12/10/2013 05:10 PM, Jon Wieser wrote: > HI doug, > no, the summary files in the contrasts have the same # of cluster as the columns in their OCN.dat \ > the 40 cluster are seen in qdec when I run the "find cluster" and Goto max" button. most of these clusters go away in qdec when I run the montecarlo simulation > > Jon > ----- Original Message ----- > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Tuesday, December 10, 2013 4:03:06 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > So one of the contrasts has 40 clusters in the summary file but the > y.ocn.dat file only has a few columns? > > > On 12/10/2013 04:54 PM, Jon Wieser wrote: >> yes, that is what we want, but the files contain only 1-3 columns >> >> Jon >> >> ----- Original Message ----- >> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >> Sent: Tuesday, December 10, 2013 3:44:50 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> There should be a column for each cluster in contrast. Is that what you >> want? >> >> >> On 12/10/2013 04:37 PM, Jon Wieser wrote: >>> thanks, >>> I ran >>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs >>> >>> MTA_ADHD_MJ is my project file and has the results from qdec in it >>> >>> >>> it has produced: >>> >>> lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>> lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>> lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>> rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>> rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> >>> >>> >>> these files have 120 rows. each row has a thickness value s >>> example >>> 2.71869 >>> 2.52448 >>> 2.50450 >>> 2.53677 >>> 2.58363 >>> 2.50404 >>> 2.42116 >>> 2.61757 >>> 2.51820 >>> 2.59009 >>> 2.42524 >>> 2.72043 >>> 2.59479 >>> 2.38014 >>> 2.41052 >>> 2.58483 >>> 2.49214 >>> 2.45870 >>> 2.51685 >>> 2.62981 >>> 2.59232 >>> >>> it appears that there is the thickness for each subject in the files >>> >>> I would like to have the thickness value, for each cluster, for every subject >>> >>> we have 120 subjects, with about 40 clusters >>> Jon >>> >>> ----- Original Message ----- >>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>> Sent: Tuesday, December 10, 2013 2:30:31 PM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> >>> OK, sorry, I thought qdec was running a script called mri_glmfit-sim but >>> it appears to be running the correction internally. That means that you >>> will have to run mri_glmfit-sim yourself, something like >>> >>> mri_glmfit-sim --glmdir glmdir --cache 1.3 abs >>> >>> doug >>> >>> >>> On 12/10/2013 02:53 PM, Jon Wieser wrote: >>>> i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the qdec output directory >>>> Jon >>>> >>>> >>>> ----- Original Message ----- >>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)nmr.mgh.harvard.edu >>>> Sent: Tuesday, December 10, 2013 1:42:37 PM >>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>> >>>> >>>> Is there a cache.mri_glmfit-sim.log in the output folder? Can you send >>>> it to me? Also, please remember to post to the list. thanks! >>>> doug >>>> >>>> >>>> On 12/10/2013 02:30 PM, Jon Wieser wrote: >>>>> FS version 5.3 >>>>> >>>>> ----- Original Message ----- >>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>> To: "Jon Wieser" <wieser(a)uwm.edu>, Freesurfer(a)nmr.mgh.harvard.edu >>>>> Sent: Tuesday, December 10, 2013 1:05:26 PM >>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>> >>>>> >>>>> hmmm, it should be there. What version of FS are you using? >>>>> >>>>> >>>>> >>>>> On 12/10/2013 12:57 PM, Jon Wieser wrote: >>>>>> i was getting the values for the command terminal, when I press the "find clusters and GOTo Max" button on the qdec GUI. >>>>>> there is no file named cache.th20.abs.y.dat or something similar. i did a "find" command to list all the *abs*.dat files in the directory >>>>>> >>>>>> qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>> qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat >>>>>> qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat >>>>>> qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat >>>>>> qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>> qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>> qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> these files contain: >>>>>> >>>>>> # CSD PDF/CDF >>>>>> # simtype null-z >>>>>> # anattype surface fsaverage lh >>>>>> # FixGroupSubjectArea 1 >>>>>> # merged 0 >>>>>> # contrast NA >>>>>> # seed 1271277527 >>>>>> # thresh 1.300000 >>>>>> # threshsign 0.000000 >>>>>> # searchspace 74612.965197 >>>>>> # nullfwhm 15.000000 >>>>>> # varfwhm -1.000000 >>>>>> # nrepetitions 10000 >>>>>> # NOTE: nreps and nrepetitions are both valid for volume data. >>>>>> # NOTE: nreps is invalid (-1) for surface data to assure. >>>>>> # NOTE: backwards INcompatibility. >>>>>> # $Id: volcluster.c,v 1.50.2.1 2011/03/28 15:32:36 greve Exp $ >>>>>> # nreps -1 >>>>>> # FixSurfClusterArea 1 >>>>>> # $Id: surfcluster.c,v 1.26.2.2 2011/11/10 16:01:11 greve Exp $ >>>>>> # nbins 100 >>>>>> # BinNo MaxClustBin MaxClustPDF MaxClustCDF GRFCDF MaxSigBin MaxSigPDF MaxSigCDF >>>>>> 0 204.826004 0.000500 0.999500 0.998289 2.456050 0.000500 0.999500 >>>>>> 1 220.348267 0.001800 0.997700 0.996805 2.811329 0.008100 0.991400 >>>>>> 2 235.870529 0.004300 0.993400 0.994388 3.166609 0.022200 0.969200 >>>>>> 3 251.392792 0.007100 0.986300 0.990673 3.521888 0.030300 0.938900 >>>>>> 4 266.915039 0.015600 0.970700 0.985251 3.877167 0.028900 0.910000 >>>>>> 5 282.437317 0.017500 0.953200 0.977702 4.232447 0.022600 0.887400 >>>>>> 6 297.959595 0.021400 0.931800 0.967628 4.587726 0.015200 0.872200 >>>>>> 7 313.481842 0.033600 0.898200 0.954689 4.943005 0.012300 0.859900 >>>>>> 8 329.004089 0.036100 0.862100 0.938634 5.298285 0.009800 0.850100 >>>>>> 9 344.526367 0.038000 0.824100 0.919325 5.653563 0.007300 0.842800 >>>>>> 10 360.048645 0.042500 0.781600 0.896747 6.008843 0.009200 0.833600 >>>>>> 11 375.570892 0.050000 0.731600 0.871009 6.364122 0.006900 0.826700 >>>>>> 12 391.093140 0.043400 0.688200 0.842332 6.719401 0.007100 0.819600 >>>>>> 13 406.615417 0.047300 0.640900 0.811034 7.074681 0.005500 0.814100 >>>>>> 14 422.137695 0.050700 0.590200 0.777508 7.429960 0.005500 0.808600 >>>>>> 15 437.659943 0.047400 0.542800 0.742195 7.785239 0.005200 0.803400 >>>>>> 16 453.182190 0.044100 0.498700 0.705560 8.140518 0.004900 0.798500 >>>>>> 17 468.704468 0.042700 0.456000 0.668070 8.495798 0.005100 0.793400 >>>>>> 18 484.226746 0.040600 0.415400 0.630176 8.851077 0.006100 0.787300 >>>>>> 19 499.748962 0.034900 0.380500 0.592300 9.206356 0.004800 0.782500 >>>>>> 20 515.271240 0.032200 0.348300 0.554820 9.561636 0.003600 0.778900 >>>>>> 21 530.793518 0.031400 0.316900 0.518067 9.916915 0.003400 0.775500 >>>>>> 22 546.315796 0.032400 0.284500 0.482320 10.272194 0.004000 0.771500 >>>>>> 23 561.838013 0.023800 0.260700 0.447809 10.627474 0.004800 0.766700 >>>>>> 24 577.360291 0.026100 0.234600 0.414711 10.982753 0.004500 0.762200 >>>>>> 25 592.882568 0.022700 0.211900 0.383160 11.338033 0.003300 0.758900 >>>>>> 26 608.404846 0.017500 0.194400 0.353244 11.693312 0.003100 0.755800 >>>>>> 27 623.927063 0.018200 0.176200 0.325018 12.048591 0.003700 0.752100 >>>>>> 28 639.449341 0.017400 0.158800 0.298504 12.403871 0.003800 0.748300 >>>>>> 29 654.971619 0.014900 0.143900 0.273697 12.759150 0.004400 0.743900 >>>>>> 30 670.493896 0.014200 0.129700 0.250569 13.114429 0.003700 0.740200 >>>>>> 31 686.016113 0.014300 0.115400 0.229078 13.469708 0.002800 0.737400 >>>>>> 32 701.538391 0.013100 0.102300 0.209165 13.824987 0.003800 0.733600 >>>>>> 33 717.060669 0.011700 0.090600 0.190763 14.180266 0.003700 0.729900 >>>>>> 34 732.582947 0.008500 0.082100 0.173798 14.535546 0.002900 0.727000 >>>>>> 35 748.105164 0.008400 0.073700 0.158191 14.890825 0.003200 0.723800 >>>>>> 36 763.627441 0.006800 0.066900 0.143861 15.246104 0.003300 0.720500 >>>>>> 37 779.149719 0.007100 0.059800 0.130727 15.601384 0.004600 0.715900 >>>>>> 38 794.671936 0.007200 0.052600 0.118707 15.956663 0.000000 0.715900 >>>>>> 39 810.194214 0.005400 0.047200 0.107723 16.311943 0.000000 0.715900 >>>>>> 40 825.716492 0.005400 0.041800 0.097698 16.667221 0.000000 0.715900 >>>>>> 41 841.238770 0.004800 0.037000 0.088559 17.022501 0.000000 0.715900 >>>>>> 42 856.761047 0.004600 0.032400 0.080237 17.377781 0.000000 0.715900 >>>>>> 43 872.283264 0.003200 0.029200 0.072665 17.733059 0.000000 0.715900 >>>>>> 44 887.805542 0.003400 0.025800 0.065783 18.088339 0.000000 0.715900 >>>>>> 45 903.327820 0.002200 0.023600 0.059531 18.443619 0.000000 0.715900 >>>>>> 46 918.850037 0.002600 0.021000 0.053855 18.798897 0.000000 0.715900 >>>>>> 47 934.372314 0.002200 0.018800 0.048707 19.154179 0.000000 0.715900 >>>>>> 48 949.894592 0.001900 0.016900 0.044040 19.509457 0.000000 0.715900 >>>>>> 49 965.416870 0.002200 0.014700 0.039810 19.864735 0.000000 0.715900 >>>>>> 50 980.939148 0.000700 0.014000 0.035979 20.220016 0.000000 0.715900 >>>>>> 51 996.461365 0.002100 0.011900 0.032510 20.575294 0.000000 0.715900 >>>>>> 52 1011.983643 0.000800 0.011100 0.029371 20.930573 0.000000 0.715900 >>>>>> 53 1027.505981 0.000800 0.010300 0.026530 21.285854 0.000000 0.715900 >>>>>> 54 1043.028198 0.001000 0.009300 0.023961 21.641132 0.000000 0.715900 >>>>>> 55 1058.550415 0.001000 0.008300 0.021638 21.996410 0.000000 0.715900 >>>>>> 56 1074.072754 0.000900 0.007400 0.019538 22.351692 0.000000 0.715900 >>>>>> 57 1089.594971 0.000900 0.006500 0.017640 22.706970 0.000000 0.715900 >>>>>> 58 1105.117310 0.000800 0.005700 0.015925 23.062248 0.000000 0.715900 >>>>>> 59 1120.639526 0.000100 0.005600 0.014375 23.417530 0.000000 0.715900 >>>>>> 60 1136.161743 0.000300 0.005300 0.012975 23.772808 0.000000 0.715900 >>>>>> 61 1151.684082 0.000800 0.004500 0.011711 24.128086 0.000000 0.715900 >>>>>> 62 1167.206299 0.000400 0.004100 0.010569 24.483368 0.000000 0.715900 >>>>>> 63 1182.728516 0.000200 0.003900 0.009538 24.838646 0.000000 0.715900 >>>>>> 64 1198.250854 0.000200 0.003700 0.008607 25.193924 0.000000 0.715900 >>>>>> 65 1213.773071 0.000300 0.003400 0.007767 25.549206 0.000000 0.715900 >>>>>> 66 1229.295410 0.000400 0.003000 0.007008 25.904484 0.000000 0.715900 >>>>>> 67 1244.817627 0.000400 0.002600 0.006323 26.259762 0.000000 0.715900 >>>>>> 68 1260.339966 0.000300 0.002300 0.005705 26.615044 0.000000 0.715900 >>>>>> 69 1275.862183 0.000400 0.001900 0.005147 26.970322 0.000000 0.715900 >>>>>> 70 1291.384399 0.000100 0.001800 0.004644 27.325600 0.000000 0.715900 >>>>>> 71 1306.906738 0.000000 0.001800 0.004190 27.680882 0.000000 0.715900 >>>>>> 72 1322.428955 0.000400 0.001400 0.003780 28.036160 0.000000 0.715900 >>>>>> 73 1337.951172 0.000100 0.001300 0.003410 28.391438 0.000000 0.715900 >>>>>> 74 1353.473511 0.000100 0.001200 0.003076 28.746719 0.000000 0.715900 >>>>>> 75 1368.995728 0.000100 0.001100 0.002775 29.101997 0.000000 0.715900 >>>>>> 76 1384.517944 0.000100 0.001000 0.002503 29.457275 0.000000 0.715900 >>>>>> 77 1400.040283 0.000300 0.000700 0.002258 29.812557 0.000000 0.715900 >>>>>> 78 1415.562500 0.000100 0.000600 0.002037 30.167835 0.000000 0.715900 >>>>>> 79 1431.084839 0.000000 0.000600 0.001838 30.523113 0.000000 0.715900 >>>>>> 80 1446.607056 0.000100 0.000500 0.001658 30.878395 0.000000 0.715900 >>>>>> 81 1462.129272 0.000200 0.000300 0.001495 31.233673 0.000000 0.715900 >>>>>> 82 1477.651611 0.000000 0.000300 0.001349 31.588951 0.000000 0.715900 >>>>>> 83 1493.173828 0.000200 0.000100 0.001217 31.944233 0.000000 0.715900 >>>>>> 84 1508.696167 0.000000 0.000100 0.001098 32.299511 0.000000 0.715900 >>>>>> 85 1524.218384 0.000000 0.000100 0.000990 32.654789 0.000000 0.715900 >>>>>> 86 1539.740601 0.000000 0.000100 0.000893 33.010071 0.000000 0.715900 >>>>>> 87 1555.262939 0.000000 0.000100 0.000805 33.365349 0.000000 0.715900 >>>>>> 88 1570.785156 0.000000 0.000100 0.000727 33.720627 0.000000 0.715900 >>>>>> 89 1586.307373 0.000000 0.000100 0.000655 34.075909 0.000000 0.715900 >>>>>> 90 1601.829712 0.000000 0.000100 0.000591 34.431187 0.000000 0.715900 >>>>>> 91 1617.351929 0.000000 0.000100 0.000533 34.786469 0.000000 0.715900 >>>>>> 92 1632.874146 0.000000 0.000100 0.000481 35.141747 0.000000 0.715900 >>>>>> 93 1648.396484 0.000000 0.000100 0.000434 35.497025 0.000000 0.715900 >>>>>> 94 1663.918701 0.000000 0.000100 0.000391 35.852306 0.000000 0.715900 >>>>>> 95 1679.441040 0.000000 0.000100 0.000353 36.207584 0.000000 0.715900 >>>>>> 96 1694.963257 0.000000 0.000100 0.000318 36.562862 0.000000 0.715900 >>>>>> 97 1710.485474 0.000000 0.000100 0.000287 36.918144 0.000000 0.715900 >>>>>> 98 1726.007812 0.000000 0.000100 0.000259 37.273422 0.000000 0.715900 >>>>>> 99 1741.530029 0.000100 -0.000000 0.000234 37.628700 0.715900 0.000000 >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Sent: Monday, December 9, 2013 5:02:41 PM >>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>> >>>>>> which file did you look in? It should have a name like >>>>>> cache.th20.abs.y.ocn.dat >>>>>> >>>>>> On 12/09/2013 05:09 PM, Jon Wieser wrote: >>>>>>> I found data for the average thickness all subjects for each cluster, but I haven't found the individual subject's thickness for each cluster. can you direct me to that data? >>>>>>> Jon >>>>>>> ----- Original Message ----- >>>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>> Sent: Monday, December 9, 2013 2:15:39 PM >>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>> >>>>>>> It is in one of the output files. Look for the .dat file in >>>>>>> mri_glmfit-sim --help >>>>>>> >>>>>>> On 12/09/2013 03:01 PM, Jon Wieser wrote: >>>>>>>> thanks doug, >>>>>>>> >>>>>>>> We've run a 2x2 analysis for thickness in Qdec and want the get the average thickness value for each cluster, for each subject. >>>>>>>> How can i get a table of thickness data , for feach subject in the analysis >>>>>>>> Jon >>>>>>>> >>>>>>>> ----- Original Message ----- >>>>>>>> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> Sent: Monday, December 9, 2013 1:48:15 PM >>>>>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>>>>> >>>>>>>> >>>>>>>> Hi Jon, QDEC does not currently allow more than one covariates of >>>>>>>> interest. You will have to use the command-line stream (ie, >>>>>>>> mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) >>>>>>>> >>>>>>>> doug >>>>>>>> >>>>>>>> >>>>>>>> On 12/05/2013 02:57 PM, Jon Wieser wrote: >>>>>>>>> HI freesurfer experts >>>>>>>>> >>>>>>>>> I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? >>>>>>>>> Thanks >>>>>>>>> Jon >>>>>>>>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Freesurfer December 2013