Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Problems dipslaying annotations in freeview
by Laura Taylor 18 Dec '13

18 Dec '13

Hi, I'm trying to load lh.aparc.a2009s.annot onto the lh pial surface of a subject. When I use the freeview gui and select lh.aparc.a2009s.annot under the annotations menu a strange multicolored surface is loaded. It looks like something that has been tie-dyed and not like the examples of parcellation that are shown on some of the freesurfer pages. I have attached a screenshot of the output that I get. Any help would be appreciated. Thank you, Laura

3 9

calculating ROI mean diffusivity
by Hamza Alshuft 18 Dec '13

18 Dec '13

Dear Freesurfer experts When I ran: mris_anatomical_stats -i 0 0.002 -l label/lh.roi.label -t / surf/lh.MD.mgh -b -f stats/lh.roi.stats subid lh to get the DTI value for a particular label, the function does not really take the thresholds I set into account as it displayed: only considering thicknesses in the range [0.0,0.0]. Is it because the range I want to detect is too small? Also, the result is always 0.001(mean DTI) +/-0.000 (std) for all the subjects and all the different labels. Thank you very much! Lily This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

2 1

extracting exact p values from QDEC
by Hubbard, Catherine S. 18 Dec '13

18 Dec '13

Hi, I've been using QDEC to run my GLM analyses. I want to obtain the exact p values and can't seem to locate them. I'm wondering if you can help me find a solution to this issue. Thanks so much. Kind regards, Catherine

2 1

Update aseg stats file
by Gomar, Jesus 18 Dec '13

18 Dec '13

Good morning, I have a group of subjects reconed with v5.1 and a group reconed with v5.3. In order to get the same aseg structures for all subjects in the stats file: Is there an option to update the aseg file only (like flags -cortparc & -parcstats for cortical measures)? Best, Jesus The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

1 0

Re: [Freesurfer] New features in TRACULA
by Anastasia Yendiki 18 Dec '13

18 Dec '13

Hi Ruth - If you apply the same mask to all the volumes in the DWI series, it's not a problem. The important thing is not to have applied any operation that would change the intensities of the images inside the brain. So these should NOT be the DWIs after the eddy_correct step, they should be before it. a.y On Tue, 17 Dec 2013, Ruth Carper wrote: > Thanks! I was able to run that with no problem. But as I read the wiki > closely I notice that with your TRACULA pipeline dmri_motion is processing > images that are still skull-on. Any thoughts on whether your algorithms > would work properly if the skull was removed prior to eddy correction? I > would think the rotation and translation measures would still be fine, but I > don't know how you've automated the 2 measures of signal dropout. My dwi > file is also skull removed. > > --Ruth > > ____________________________________________________________________________ > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > To: Ruth Carper <rcarper_99(a)yahoo.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Tuesday, December 17, 2013 1:28 PM > Subject: Re: [Freesurfer] New features in TRACULA > > > Hi Ruth - If you download the update and unzip it, you'll see an > executable called dmri_motion. You can run it without any arguments to see > the help text. > > Try something like this: > dmri_motion --dwi yourDWIs.nii.gz --mat your.ecclog --bval your.bvals --out > output.txt > > a.y > > On Fri, 13 > Dec 2013, Ruth Carper wrote: > > > > > Thanks. We haven't yet implemented TRACULA but have run eddy_correct on > all > > the brains in our existing pipeline and still have the ecc.log files. Is > > there a command line that would let us generate your motion measures > without > > running TRACULA? > > > > --Ruth > > > > > > > >___________________________________________________________________________ > _ > > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > To: Ruth Carper <rcarper_99(a)yahoo.com> > > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > Sent: Tuesday, December 10, 2013 8:28 PM > > Subject: Re: [Freesurfer] New features in TRACULA > > > > > > Hi Ruth - Glad to hear this is useful to you. The rotation and translation > > parameters are extracted from the affine registration of each DWI volume > > to the first volume, which in trac-all is performed by eddy_correct. > > > > a.y > > > > On Tue, 10 Dec 2013, Ruth Carper wrote: > > > > > Hi Anastasia, > > > We discussed your paper at our lab meeting yesterday so this was perfect > > > timing on the release of motion measures in your updated TRACULA. But > I > > > wasn't clear where the numbers are coming from in your new update. Is > > this > > > from EDDY? eddy_correct? Some other registration step? > > > > > > Thanks, > > > Ruth > > > > > > > > > > > > > > > > > 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 17 Dec '13

17 Dec '13

I would have thought that it would have gotten all of them. You can try something like --cwp .999999999 On 12/13/2013 01:03 PM, Jon Wieser wrote: > HI doug > thanks, that worked. it captured from 3-13 clusters for each contrast, not quite the 30-45 that I was seeing in the GUI. > perhaps theses are the most significant 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: Friday, December 13, 2013 11:43:29 AM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > use the command I gave you before just add --cwp .99 to it > doug > > > On 12/13/2013 12:25 PM, Jon Wieser wrote: >> Hi doug >> it's requesting the --sim option >> >> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 >> ERROR: must spec --sim >> >> >> >> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --sim >> ERROR: flag --sim requires four arguments >> >> >> what args do I give the --sim! >> >> 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: Friday, December 13, 2013 11:18:49 AM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> sorry, it is --cwp >> >> On 12/13/2013 12:12 PM, Jon Wieser wrote: >>> HI Doug >>> MRI_glmfit-sim didn't recognize the --cwd option >>> >>> >>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99 >>> ERROR: Flag --cwd unrecognized. >>> --glmdir MTA_ADHD_MJ --cwd .99 >>> >>> >>> >>> >>> >>> >>> ----- 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: Friday, December 13, 2013 10:54:19 AM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> >>> 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 6

Tracula error: libnetcdf.so.6
by Garikoitz Lerma-Usabiaga 17 Dec '13

17 Dec '13

Hi Anastasia, I've got this error when running -prep Tracula step. /usr/local/freesurfer/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory We have RedHat 6 (I tried in 2 different machines). Do you think it is some missconfiguration on our side? Can you think in anything we could try? thanks! Gari

2 2

Longitudinal Freesurfer & TRACULA quality control
by vbrunsch＠nmr.mgh.harvard.edu 17 Dec '13

17 Dec '13

Dear Freesurfer experts, I want to do a quality check on our imaging data. I used the longitudinal stream for SBA and as the first step for the longitudinal white matter analysis with TRACULA. We had two time points in our study and thus, in the freesurfer output directory there are 5 folders per subject (2 cross-sectional runs, 2 long runs and the base). 1. Would you recommend to use (all of) the QA_TOOLS on all of these 5 folders per subject for the SBA? 2. Independent of the previous question, for the longitudinal version of TRACULA would you recommend to use (all of) the QA_TOOLS on the freesurfer base folder only / additional folders? 3. In addition to the late visual check for well reconstructed pathways with freeview, is there another automated possibility to check the quality of the diffusion weighted images beforehand/do you think this is necessary? 4. On another note: If I understand correctly, in TRACULA bedpostX is used to reconstruct the pathways but then the mean over the voxels that were hit (by the MCMC sampling of the paths) of measures from the tensor model are taken as outputs. I wonder, is there also the possibility of using the partial volumes f1, f2,.. as output measures? Best, Vincent

4 5

Re: [Freesurfer] New features in TRACULA
by Anastasia Yendiki 17 Dec '13

17 Dec '13

Hi Ruth - If you download the update and unzip it, you'll see an executable called dmri_motion. You can run it without any arguments to see the help text. Try something like this: dmri_motion --dwi yourDWIs.nii.gz --mat your.ecclog --bval your.bvals --out output.txt a.y On Fri, 13 Dec 2013, Ruth Carper wrote: > > Thanks. We haven't yet implemented TRACULA but have run eddy_correct on all > the brains in our existing pipeline and still have the ecc.log files. Is > there a command line that would let us generate your motion measures without > running TRACULA? > > --Ruth > > > > ____________________________________________________________________________ > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > To: Ruth Carper <rcarper_99(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Tuesday, December 10, 2013 8:28 PM > Subject: Re: [Freesurfer] New features in TRACULA > > > Hi Ruth - Glad to hear this is useful to you. The rotation and translation > parameters are extracted from the affine registration of each DWI volume > to the first volume, which in trac-all is performed by eddy_correct. > > a.y > > On Tue, 10 Dec 2013, Ruth Carper wrote: > > > Hi Anastasia, > > We discussed your paper at our lab meeting yesterday so this was perfect > > timing on the release of motion measures in your updated TRACULA. But I > > wasn't clear where the numbers are coming from in your new update. Is > this > > from EDDY? eddy_correct? Some other registration step? > > > > Thanks, > > Ruth > > > > > > > > > > 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

Tracula error when running bedpostX (2nd step af trac-all)
by Matthieu Vanhoutte 17 Dec '13

17 Dec '13

Hello experts, I am running the ball-and-stick model fit in Tracula on FS 5.1 and come across the error: *WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri subjectdir is /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri Making bedpostx directory structure Queuing preprocessing stages /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 216: [: SGE: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 263: [: SGE: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 321: [: xbedpostx_pre: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 351: [: x: unexpected operator Queuing parallel processing stage /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 216: [: SGE: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 321: [: xbedpostx: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 351: [: x66: unexpected operator Queuing post processing stage /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 216: [: SGE: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 263: [: SGE: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 321: [: xbedpostx_post: unexpected operator /home/global//freesurfer5.1//bin/fsl_sub_seychelles: 351: [: x: unexpected operator Type /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri.bedpostX/monitor to show progress. Type /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. * I have attached my dmrirc file and trac-all.log. Best regards, Matthieu

2 3

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