Freesurfer

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19 participants
30088 discussions

Patch for -autorecon2
by Isabelle Deschamps, Miss 05 Dec '13

05 Dec '13

Dear FreeSurfer experts, Would it be possible to have the patch for this problem "Creation of the aseg.stats table fails when only running -autorecon1 or -autorecon2 because ribbon.mgz is not present"? Thank you very much in advance, Isabelle

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nuisance variable in qdec
by Cat Chong 05 Dec '13

05 Dec '13

Dear FreeSurfer Experts, We are trying to run a between group analysis (1 patient group 1 control group) within qdec. We are interested in investigating age-related thickness differences between groups. Our fixed factors are ‘group’ and our continuous covariate is ‘age’. We would like to control for other possibly confounding variables which should be declared as “nuisance factors, is that correct? Here is our problem. We like to put down “disease burden” (years subject has had the disease) as our nuisance factor, since it is likely possible that this has an effect on cortical thinning in our disease group. Yet, when we run the model, qdec crashes. Is this because the subjects in the control group have a “0” as disease burden? Could you advise us on another way of controlling for disease burden? Cheers, Catherine

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Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
by Skyler Gabriel Shollenbarger 05 Dec '13

05 Dec '13

Hi Anastasia, Thanks for your help. We updated to version 5.3 and received this error: INFO: Distances between consecutive points in test subject's space are 5 5 6 5 Writing output files to /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* dmri_train(44276) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice Cannot allocate memory We use Mac OS X 10.6.8 Snowleopard. Best, Skyler ----- Original Message ----- From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> To: "Skyler Gabriel Shollenbarger" <shollen2(a)uwm.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2013 1:19:55 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts Hi Skyler - I would *highly* recommend using the version of tracula in 5.3, as there have been improvements in both performance and speed. You can check the DWI to anatomical registration by overlaying the aparc+aseg from the dlabel/diff directory (which is in diffusion space) on the FA map. Does that look ok? a.y On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote: > Hi Anastasia, > > We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. Is there anything to do about poor registration? > > Thank you for the fast reply. Truly appreciated. > Skyler > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Skyler Gabriel Shollenbarger" <shollen2(a)uwm.edu> > Cc: Freesurfer(a)nmr.mgh.harvard.edu > Sent: Monday, December 2, 2013 4:27:37 PM > Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts > > > Hi Skyler - Are you using freesurfer 5.1 or 5.3? > > Most likely this issue is due to poor registration, either from the > individual DWI to the individual T1, or from the individual T1 to the > template space. Or it could be that there is a problem with the > aparc+aseg. > > a.y > > On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote: > >> Hi all, >> >> I've been running DTI using tracula (fs version 5) for over 1 week on 2 subjects. It appears that it is having difficulty finding satisfactory control point fit and has attempted over 1600 tries. Any help is greatly appreciated. >> See error below: >> >> INFO: Distances between consecutive points are 25 24 25 26 >> WARN: Could not find satisfactory control point fit - try 1665 >> Finding center streamline >> INFO: Step is 4 voxels >> WARN: Turning off FA check for center streamline >> INFO: Step is 4 voxels >> WARN: Turning off deviation check for center streamline >> INFO: Step is 4 voxels >> INFO: Length of center streamline is 96 voxels >> Selecting 5 points on center streamline >> INFO: Step is 4 voxels >> WARN: Defaulting to equidistant control points >> INFO: Selected control points are >> 108 193 84 >> 112 173 72 >> 98 153 75 >> 74 157 75 >> 74 184 86 >> INFO: Distances between consecutive points are 24 25 24 29 >> WARN: Could not find satisfactory control point fit - try 1666 >> Finding center streamline >> INFO: Step is 4 voxels >> WARN: Turning off FA check for center streamline >> INFO: Step is 4 voxels >> WARN: Turning off deviation check for center streamline >> INFO: Step is 4 voxels >> >> >> Best, >> Skyler >> >> > > > 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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FW: how do display a particular region for visucalization
by tulu 05 Dec '13

05 Dec '13

From: tulu [mailto:tulu@ms36.hinet.net] Sent: Wednesday, December 04, 2013 8:49 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: how do display a particular region for visucalization Dear freesurfer experts I try to display some of particular regions in freeview. The below figure is an example. Is there any script or step to do that ? Sincerely yours JLH CombinedNeuroimagingforAD2013.jpg

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Fwd: Re: Fwd: Some problems of the brain image after recon-all
by Xiaojun.Huang 05 Dec '13

05 Dec '13

-------- 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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R: Re: R: Re: Linear regression
by stdp82＠virgilio.it 04 Dec '13

04 Dec '13

Dear Douglas, thank you very much for you kind reply.In the paper I have 3 groups (2 diseases and 1 controls).I have performed cortical thickness analysis among groups, individuating relevant difference in the posterior regions. Next, for one group, I have used qdec to individuate statistically significant regions where NPS test scores and thickness were correlated. 3 nuisance factors was also added to regressor. All results were corrected for multiple comparisons by using a pre-cached cluster-wise Monte-Carlo Simulation.qdec analysis results have individuated a "composite region" (superior parietal cortex and precuneus) where NPS correlated with thinning. Now, if I understand, I should extract the mean thickness from superior parietal cortex and precuneus and I should perform a linear regression (and partial correlation) with an other statistical program (SPSS for example).Is there a better way to perform a regression the most possible similar to qdec computation? Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 4-dic-2013 17.35 A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] Linear regression On 12/02/2013 03:14 PM, stdp82(a)virgilio.it wrote: > Tank you very much. > > A-Do you mean the partial correlation coeff (PCC) at each voxel > averaged over region? > Finally a linear regression is done between cortical thickness of a > composite region and NPS. However the authors discuss every individual > region as related to disease. So a table with partials correlations of > individuals ROIs with NPS seems useful to support the discussion. What did you do in the paper? The reviewer mentions a "composite region". Did you average the thickness over that region and then do the regression with NPS? > > B- I'd like to obtain the covariance matrix of the regression made > between cortical thickness, group and covariates. How can I do it? > I'm not sure what you mean. Would this be a different matrix for each > vertex? > I cite the referee: "The authors must provide the covariance matrix of > the regression made between cortical thickness, group and covariates > as supplementary information in order to increase the value of the > results." Sorry, I don't understand what the reviewer is asking for. doug > > I don't have Matlab for mri_glmfit_pcc matlab. > > Stefano > > > > > ----Messaggio originale---- > Da: greve(a)nmr.mgh.harvard.edu > Data: 2-dic-2013 20.47 > A: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Linear regression > > > On 12/02/2013 02:22 PM, stdp82(a)virgilio.it wrote: > > Hi list, > > > > I have some questions, please. > > > > I performed linear regression by qdec to find the regions where the > > cortical thinning correlates with neuropsychological test (NPS), > > taking in account 3 nuisance factors. > > > > A- I individuated some posterior regions and now I'd like to build a > > table with partials correlations of individuals ROIs with NPS. How can > > I obtain the values for each region? > Do you mean the partial correlation coeff (PCC) at each voxel averaged > over region? You can get PCC maps using the mri_glmfit_pcc matlab > command. You can then do the averaging over region using mri_segstats. > > > > B- I'd like to obtain the covariance matrix of the regression made > > between cortical thickness,group and covariates. How can I do it? > I'm not sure what you mean. Would this be a different matrix for each > vertex? > > > > C- Is there a specific reference for qdec? > No, it is just a GLM so any GLM reference will do. > > > > Thank you very much, > > > > > > Stefano > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > 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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > > -- 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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how do display a particular region for visucalization
by tulu＠ms36.hinet.net 04 Dec '13

04 Dec '13

Dear freesurfer experts I try to display some of particular regions in freeview. The below figure is an example. Is there any script or manual descript how to do that ? Sincerely yours JLH <?xml:namespace prefix = v ns = "urn:schemas-microsoft-com:vml" /> <?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />

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mri_ca_normalize error
by Mark Plantz 04 Dec '13

04 Dec '13

Hello all, I am experiencing an error during the mri_ca_normalize step of auto-recon-1 using a non-default atlas (for infant brains). Essentially, "norm.mgz" and "ctrl_pts.mgz" are both outputting as blank files (completely black). However, brainmask.mgz looks completely fine, which leads me to believe that skull-stripping and alignment should be OK. Subsequently, zero control points were found during the "mri_ca_normalize" step. While mri_ca_normalize does not fail, I believe the lack of control points causes the following error in the "mri_ca_label" step: *searching scale 1 Z rot 2.3 * *searching scale 1 Z rot 2.5 * *searching scale 1 Z rot 2.8 * *searching scale 1 Z rot 3.0 * *searching scale 1 Z rot 3.3 * *searching scale 1 Z rot 3.5 * *searching scale 1 Z rot 3.8 * *searching scale 1 Z rot 4.0 * *searching scale 1 Z rot 4.3 * *searching scale 1 Z rot 4.5 * *searching scale 1 Z rot 4.8 * *searching scale 1 Z rot 5.0 * *searching scale 1 Z rot 5.3 * *searching scale 1 Z rot 5.5 * *searching scale 1 Z rot 5.8 * *searching scale 1 Z rot 6.0 * *searching scale 1 Z rot 6.3 * *searching scale 1 Z rot 6.5 * *searching scale 1 Z rot 6.8 global minimum found at slice 0.0, rotations (90.00, -0.00)* *final transformation (x=0.0, yr=90.000, zr=-0.000):* *-0.000 0.000 1.000 128.000;* *-0.000 1.000 -0.000 128.000;* *-1.000 0.000 0.000 128.000;* * 0.000 0.000 0.000 1.000;* *Segmentation fault* I am wondering if anyone knows why the control points would not be found and if there is anyway to solve the problem? I can also attach the .gca atlas that I am using if that would help. I also noticed that the "aseg.auto_noCCseg.mgz" file seems to have shifted significantly from the position of the GCA atlas. In fact, it shifted so far that some of the occipital lobe appears to have been cut out [I attached an image for details]. I am not sure if this is a related problem, but I figured I should mention it. I appreciate the help! Best, Mark

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how to extract DTI data with bvals/bvects
by ryu＠nmr.mgh.harvard.edu 04 Dec '13

04 Dec '13

Dear All, I used unpacksdcmdir to unpack DTI data from Bay 3. The log file shows "DTI is in non-moasic form, so cannot extract bvals/bvects" My question is how to get bvals/bvects files from unpack? The files look like: 42 DIFFUSION_HighRes ok 128 128 62 1 MR.1.3.12.2.1107.5.2.32.35162.2013031117224812856938134 43 DIFFUSION_HighRes ok 128 128 62 1 MR.1.3.12.2.1107.5.2.32.35162.2013031117224812950738135 44 DIFFUSION_HighRes ok 128 128 62 1 MR.1.3.12.2.1107.5.2.32.35162.2013031117224813055538136 45 DIFFUSION_HighRes ok 128 128 62 1 MR.1.3.12.2.1107.5.2.32.35162.2013031117224813122838137 46 DIFFUSION_HighRes ok 128 128 62 1 MR.1.3.12.2.1107.5.2.32.35162.2013031117224813209438138 47 DIFFUSION_HighRes ok 128 128 1 62 MR.1.3.12.2.1107.5.2.32.35162.2013031117224813279838139 Cheers, Jacky

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Problems with longitudinal analysis
by Knut J Bjuland 04 Dec '13

04 Dec '13

Hi, I have used a linear mixed model for longitudinal data analysis on a FreeSurfer 5.3, Matlab 2013b on a system with Ubuntu 12.04. I used mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh to concatenate thickness surf files, and smoothed with mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm30.mgh --fwhm-trg 30 --cortex –noreshape. I then used the same command and options in a Matlab script, as shown at http://freesurfer.net/fswiki/LinearMixedEffectsModel found in the example for mass-univariate data analyses. . I used this design matrix: interception, time, group, group*time, gender, gender*time, and I used two random effect on interception and time. I did not compare the two random effect models with one random effect model. I used this contrast vector C=[0 0 1 0 0] for these images which are included in the email. The script ran fine but when I looked at sig.mgh, it contained many visible quadrate shapes boxes even after FDR correction, and the image looks quite different than the image in the paper in Neuroimage (Spatiotemporal Linear Mixed Effects Modeling for the Mass-univariate Analysis of Longitudinal ). Any idea what went wrong here? Thank you! Best regards, Knut Jørgen

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