Freesurfer

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Re: [Freesurfer] Freesurfer Digest, Vol 150, Issue 14
by Caroline Beelen 12 Aug '16

12 Aug '16

The error is: "Mapping unhit to unknown. Found 137851 unhit vertices". The file is made, but when trying to select it from the annotation tab in Freeview, Freeview crashes too. Regards, Caroline -----Oorspronkelijk bericht----- Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens freesurfer-request(a)nmr.mgh.harvard.edu Verzonden: donderdag 11 augustus 2016 18:00 Aan: freesurfer(a)nmr.mgh.harvard.edu Onderwerp: Freesurfer Digest, Vol 150, Issue 14 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. aseg.stats data output (shi yao wang) 2. mri_glmfit-sim problem (miracle ozzoude) 3. Re: mri_glmfit-sim problem (miracle ozzoude) 4. Re: Registration of low-resolution EPI time series to CVS MNI (avoiding resampling) (Douglas N Greve) 5. Re: resample structural ROI in functional space? (Douglas N Greve) 6. Re: query about the "normal range" in aseg.stats (Douglas N Greve) 7. Re: aseg.stats data output (Douglas N Greve) 8. Re: Problems with QDEC (Douglas N Greve) 9. Re: group analysis/ region of interest (ROI) approach (Douglas N Greve) 10. Re: Inquiries about QDEC inflated surface (Douglas N Greve) 11. Re: FS V6.0 GTM PVC ROI definition (Douglas N Greve) 12. Re: Fw: Running recon-all with T1 and FLAIR (Douglas N Greve) 13. Re: myaparc (Douglas N Greve) 14. Re: Qdec Generate Stats Data Table Error (Douglas N Greve) 15. Re: bbregister problem in FS5.1 (Douglas N Greve) 16. Re: Error with qdec (Douglas N Greve) 17. Re: Assessing local correlations across 2 modalities (Douglas N Greve) 18. Re: FS V6.0 GTM PVC ROI definition (Pradeep) 19. Re: FS V6.0 GTM PVC ROI definition (Douglas N Greve) 20. Re: Retinotopy questions (Douglas N Greve) 21. how to run correlation analysis between cortical thickness and cognitive function (Liu Y) 22. Re: how to run correlation analysis between cortical thickness and cognitive function (Douglas N Greve) ---------------------------------------------------------------------- Message: 1 Date: Wed, 10 Aug 2016 12:38:45 -0400 From: shi yao wang <wangshiyao2009(a)gmail.com> Subject: [Freesurfer] aseg.stats data output To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CA+rJNW_0aSv=AtUCFtKM=BV_7iQZZL+AGFAC-wWct5VeAxr8AA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear FS experts: How can I only out put the volume value in the aseg.stats file? I applied following command: but it will produce a table with lots of values such as brainsegvol, brainsegvolnotvent, which I donot want to use. thanks asegstats2table --subjects 004 021 040 067 080 092 \ --segno 11 17 18 \ --tablefile aseg.vol.table

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Re: [Freesurfer] qdec error
by Jasinska, Kaja 12 Aug '16

12 Aug '16

Hello, When I'm loading qdec, I get the following error messages. Can you please help. Thanks. Kaja ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 405 vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 405 vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 405 vtkXOpenGLRenderWindow (0x7084e40): Could not find a decent visual ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 612 vtkXOpenGLRenderWindow (0x7084e40): GLX not found. Aborting. -- --- Kaja K. Jasinska, Ph.D. Post-Doctoral Research Associate Haskins Laboratories 300 George Street Suite 900 New Haven, CT 06511 USA: 203-865-6163 ext 315 Cote d’Ivoire: (+225) 77 62 42 28 Skype: kaja.jasinska kaja.jasinska(a)yale.edu<mailto:kaja.jasinska@yale.edu> www.haskins.yale.edu/staff/jasinska/<http://www.haskins.yale.edu/staff/jasinska/>

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Inter-rater and intra-rater reliability
by Annemarie Brandhofe 12 Aug '16

12 Aug '16

Dear FreeSurfer experts, I have a question regarding manual interventions during the recon-all script of FreeSurfer 5.3.0 (i.e. setting control points, performing white matter edits). How can we check for inter- and intra-rater reliability? In an earlier post you mentioned an intra- and inter-rater reliability study you did. Could you tell me the name of this publication? Thank you in advance for your help! Best regards, Anne

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Performing GLM within a Mask Specified by Another GLM
by Timothy Hendrickson 11 Aug '16

11 Aug '16

Freesurfer Support, Here is what I would like to do: I have run a GLM on the entire cortex to determine whether there are significant differences in LGI between patients and controls. I then would like run a different GLM just with the clusters outputted from the previous GLM. It would seem that the best thing to do is to set a mask representing the clusters from the first GLM and then run the second GLM on the mask. Is this a reasonable thing to do? What steps/commands would I perform in order to do something like this? Respectfully, -Tim Hendrickson Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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Using other brain template to calculate cortical thickness
by shi yao wang 11 Aug '16

11 Aug '16

Dear Douglas Thank you so much for your reply!! Another question: Can we use other brain template to calculate cortical thickness? If yes, How can I do it. thanks Lawrence

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how to run correlation analysis between cortical thickness and cognitive function
by Liu Y 11 Aug '16

11 Aug '16

Dear Expert, How to run the correlation analysis between cortical thickness and cognitive function with Qdec? Best regards, Yawu

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Re: [Freesurfer] FS V6.0 GTM PVC ROI definition
by Douglas N Greve 10 Aug '16

10 Aug '16

which "native" space? the pet native? the anatomical native? On 08/09/2016 05:46 PM, Pradeep wrote: > Hello Doug, > > The aux/seg.nii image which has all the ROI's defined does not seem to > be in the subject's native space or the CVS template space. > > How do I bring it to the subjects native space? > > Thanks, > Pradeep > > Screenshot from 2016-08-09 14:42:10.png > > On Tue, Jul 19, 2016 at 5:03 PM Pradeep <tpradeep(a)gmail.com > <mailto:tpradeep@gmail.com>> wrote: > > Thanks responding Doug! > > I am interested us using centrum semiovale as reference region. Is > there a way I can save the unsegmented white matter [5001& 5002] > during the gtmseg step or what would be its equivalent label in > the gtm_pvc results table? > > Thanks, > Pradeep > > On Thu, Jul 7, 2016 at 11:20 AM Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > > On 06/20/2016 08:25 PM, Pradeep wrote: > > Hello Freesrufer Team, > > > > I am trying to use the Partial volume correction procedure > implemented > > in the freesurfer 6 beta version and have a few questions. > > > > In your recent Neuroimaging paper, the left and right > hemispheres were > > combined by taking the average of the two as they did not > show any > > age-by-hemisphere interaction. > > > > I might have interpreted the Supplementary figure 1 > incorrectly, but > > the Geometric transfer matrix seem to show around 52 ROI's, > So were > > the L and R ROIs combined for the PVC results you reported > in that > > paper? Or were the same 52 used for the general PVC in the > FS pipeline? > They were combined only after the PVC calculation. For the > figure, I > changed the GTM to show the combined GTM. > > > > Do you have any concrete results to examine the effects of > the size > > variation over the ROIs used for PVC? > Not sure what you mean here. You can get the variance > reduction factor > for each ROI in the gtm.stats.dat file. This indicates how > much noise > reduction you can expect (assuming gaussian noise, etc) in > each ROI > given the size and anatomical distribution of the ROIs and PSF. > > Should a threshold be set for the sizes of these ROIs? > What do you mean? > > > > How were the white matter hypo-intensities dealt with while > generating > > the ROI masks? > I merged them with WM. I tried it with and without, and it did > not make > much of a difference. > doug > > > > > > Thanks, > > Pradeep > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 > <mailto:Freesurfer@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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Assessing local correlations across 2 modalities
by Elijah Mak 10 Aug '16

10 Aug '16

Dear Freesurfer Community, I am currently trying to investigate the local correlations across 2 modalities (i.e. Tau-PET and cortical thinning). I understand that this sort of questions has been conventionally addressed using the Biological Parametric Mapping (BPM) toolbox in MATLAB. Is there a way in Freesurfer to properly address this? My PET data have already been registered and projected to the surfaces for each individual. Thanks a lot. Best Wishes, Elijah -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Error with qdec
by Mahtab Farahbakhsh 10 Aug '16

10 Aug '16

Dear FreeSurfer, I am trying to compare my subjects to the healthy group, but when I put the matrix into qdec, I get the following error: Normalized matrix condition is 1e+08 Design matrix ------------------ 1.000 0.000 0.000 0.000 68.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 66.000 0.000; 1.000 0.000 0.000 0.000 40.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 35.000 0.000; 1.000 0.000 0.000 0.000 72.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 71.000 0.000; 1.000 0.000 0.000 0.000 22.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 22.000 0.000; 0.000 1.000 0.000 0.000 0.000 20.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 20.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 1. Your command line: mri_glmfit --y /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled --surf fsaverage lh --label /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/fsaverage/label/lh.aparc.label --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor-thickness-age.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-spelling-healthy-Intercept-thickness.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-spelling-healthy-Cor-thickness-age.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-X-gender2-diagnosis_spelling-Intercept-thickness.mat --C /Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-X-gender2-diagnosis_spelling-Cor-thickness-age.mat the table file is also attached to the mail. Would you please kindly guide me with this? Best Regards, Mahtab.

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bbregister problem in FS5.1
by Fred Sampedro 10 Aug '16

10 Aug '16

Dear FS experts, I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm trying to run bbregister to register a AV45-PET image to its corresponding FS processed T1 image. For that, I'm trying to run: bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1 And I keep getting segfaults: Log file is register.dat.log dom jul 24 16:44:19 CEST 2016 $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii Segmentation fault (core dumped) I have tried the same installation and command in two different computers and obtained the same segfault. I have also tried the same pipeline using instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same result. I didn't have this issue using freesurfer 5.3, but I need to use 5.1 for an ongoing project. I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits. Any help would be much appreciated, Thanks a lot in advance, Fred Sampedro

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