Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

WM lobes and Corpus Callosum
by Bharadwaj, Pradyumna - (prad) 19 Jan '17

19 Jan '17

Hi, I've been trying to create WM lobes using the following steps: 1) mri_annotation2label --lobesStrict 2) Outputting the labels from step 1, & creating a simpler annotation without limbic and insular lobes 3) Labeling the WM using mri_aparc2aseg (mri_aparc2aseg --s MySub --annot Step2AnnotationFile --labelwm --hypo-as-wm --wmpar-dmax 20 --rip-unknown However, as the corpus callosum is not labelled as wm, it is not included in any WM lobe. Is there any workaround to assigning the corpus callosum to the different WM lobes or do I have to manually edit aseg.mgz to change the corpus callosum's value to match that of WM ? Thanks, -Prad

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License error when open Tkmedit
by Hao wen 19 Jan '17

19 Jan '17

Hello, FS experts: I installed FS 5.3 and the tkmedit version is stable5, but when I open tkmedit, it always give me the error: ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. But FS 5.3 works fine with the license file license.txt, so I just copy the content of license.txt to .license in the dir of $FREESURFER_HOME, and it still gives me this error,, here is the command ls -la to display all the files:[cid:d53d9bb8-296c-465b-bd70-3712bc44e337] My freesurfer works fine with Freeview or tksurfer, just not work with tkmedit, I even change the .license's right with : chmod +x $FREESURFER_HOME/.license Still does not work, Any advice?? Thanks Hao

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Attrition in longitudinal analysis
by Greenberg, Jonathan 19 Jan '17

19 Jan '17

Dear FreeSurfer users I conducted a longitudinal study with 3 timepoints: baseline, 8 weeks and 24 weeks. Between baseline and 8 weeks participants were randomized to one of 3 training programs. I want to assess changes in gray matter volume from baseline to 8 weeks, and baseline to 24 weeks, and also determine how these changes correlate with various behavioral outcome measures. The correlations will be conducted in SPSS, so I need to export values from each time point to enter into the regression matrix. The issue is that about 20 people dropped out after the 8 week assessment. So to just ask the question about changes in brain structure I created two different processing streams, one for all 75 subjects who have pre and 8 week data, and a second one for the 58 individuals who have pre and 24 week data. Therefore, participants who have data for all 3 time points had their pre and 8-week data analyzed in both processing streams. These separate processing streams yield different pre values for these individuals (e.g. the hippocampal volume of participant X at “pre” in the first processing stream is different than the pre hippocampal volume of the same participant in the second processing stream). My question is about the proper way to combine data from these two processing streams so that I have one Excel column for each of the 3 time points to be analyzed in SPSS with all participants included. One approach would be to use the values from the second processing stream (which includes the 24 week time point) for the participants who have all 3 time points, and use the data from the first processing stream only for those who are missing the 24 week time point. But I am not sure whether this is acceptable given the discrepancy in values between the two processing streams. So, is there better way to combine the data from both streams into these 3 time-point columns? Thank you Jonathan

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Re: [Freesurfer] V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream
by Antonin Skoch 19 Jan '17

19 Jan '17

Dear Martin, one more thing: When the error is large and present in both timepoints (as is my case), I think that necessity of editing the same error in both timepoints can easily lead to error (maybe even demonstrated as false positive effect) caused by non-systematic editing. When editing comprises many voxels one cannot realistically assure the perfect consistence in editing. Editing only once (in base) and initialize mri_ca_label in long from base can avoid this problem. So I think the initialization of mri_ca_label from base is not a bad option for such cases. What do you think? Antonin Hi Antonin, the -noasegfusion is not really supported and a left over from initial testing when we first developed the stream. I will take a look at it and probably remove the flag (or implement it in a way that it really initializes with the aseg from the base, although I think this is not desirable, unless one really assumes there is no/ or very little change between time points. About aseg edits in longitudinal processing, please look at our edit wiki page: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#aseg.mgz <https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#aseg.mgz> “ ASEG edits can be done in cross, base and long. Recommendation: Edit in long only if you want to correct the volume of important structures. Edit in base if surfaces need to be changed due to incorrect labeling of aseg. Not necessary to edit in cross. The segmentation in the long runs is initialized with a fused aseg (a weighted average of the cross sectional asegs). Thus any edits done to the cross sectionals are incorporated indirectly into the long stream. But since the fused aseg is used only for the initialization, it can happen that manual edits from the cross get removed again. Therefore, to correct the volume, just edit the long." So for your ventricle correction, you could either clean up the cross data and hope it caries over to the long (it should), or directly edit the long aseg. Best, Martin > On 16 Jan 2017, at 23:23, Antonin Skoch <a...(a)ikem.cz> wrote: > > Dear experts, > > I am testing the longitudinal stream with V6beta version. > > The recon-all -help says for -noasegfusion: > > Do not create 'fused' aseg from the longbase timepoints, which would normally > be used to initialize the ca_labeling. Instead, initialize using the longbase > aseg.mgz. > > As I looked to recon-all code it seems that in case of -noasegfusion there is > no use of -r and -ri parameters and therefore no "initialization". Could you > please comment on? > > My second query is regarding manual edits: > > In one subject the manual editing of aseg was necessary due to ventricle > mislabeling. I edited the aseg.presurf in base template and subsequently run > longitudinal stream via > > recon-all -long tpID templateID -noasegfusion -all > > From the last sentence of -noasegfusion help I (wrongly) expected that my > aseg.presurf edits in base template would be incorporated for -long recon. > However, this was not the case, the edits have not been incorporated at all. > Looking at the recon-all code the aseg.presurf from base is never used for > -long. > > I thought that I could incorporate manual edits from base by manual copying > of aseg.presurf from base to long directory. As I looked for the way how the > manual aseg edits are handled in recon-all, they are identified by using the > difference between the files aseg.auto and aseg.manedit which contains manual > edits. Therefore I think that the copying from base is not an option, I > expect that this would replace segmentations not only in manual edit regions, > but in all regions where the aseg.auto of base and aseg.auto of -long differs > (they do not have the same input) which is undesirable. So I think I do not > have any other option than to edit aseg.presurf in -long again. > > Could you please comment on how to optimally handle such situations? > > Regards, > > Antonin Skoch > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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(no subject)
by Hao wen 19 Jan '17

19 Jan '17

Hello: I am using QATool in Freesurfer, and the script requires FS 5.1 and also works for 5.3 which i am using, but when i run it, it always gives me error about license: ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. But FS 5.3 works fine with the license file license.txt, so I just copy the content of license.txt to .license in the dir of $FREESURFER_HOME, and it still gives me this error, here is the content of these two license files: Password: alexandre.routier(a)gmail.com 24787 *CZJRu8f2ozyc FShcQvYXXTGaI any idea? Thanks in advance

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Re: [Freesurfer] PETSURFER Tutorial Problems <Repost>
by Anderson Napolitano 18 Jan '17

18 Jan '17

Hi Zeke, That resolved the issue. Thank you very much. Warmest Regards, Anderson Napolitano ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Wednesday, January 18, 2017 10:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 155, Issue 27 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. installation fail :( (Shapiro, Allison L) 2. Re: TRACULA in FreeSurfer 6.0 trac-paths error (Derek A Pisner) 3. PETSURFER Tutorial Problems <Repost> (Anderson Napolitano) 4. question about cortical volume group analyses (Ritobrato Datta) 5. Re: V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream (Antonin Skoch) 6. FS Anatomic ROIs Atlas (Da, Xiao) 7. Anatomical ROI parcellation (Aya Kabbara) 8. Re: Anatomical ROI parcellation (Anthony Dick) 9. Re: FS Anatomic ROIs Atlas (Douglas N Greve) 10. Re: V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream (Antonin Skoch) 11. WM lobes and Corpus Callosum (Bharadwaj, Pradyumna - (prad)) 12. Re: WM lobes and Corpus Callosum (Yendiki, Anastasia) 13. Re: mri_vol2surf (Zhivago) 14. 'nuisance factors adjusted' values (hiroki.sato(a)med.tohoku.ac.jp) 15. recon-all error (Freesurfer) ( Gwang-Won Kim ) 16. Question (N Saf) 17. Re: mri_vol2surf (Bruce Fischl) 18. Neuroimaging postdoctoral position (Tiril Pedersen Gurholt) 19. Re: Question (Bruce Fischl) 20. mris_make_surfaces error with bbr-init-header (Sneha Pandya) 21. Re: mris_make_surfaces error with bbr-init-header (Bruce Fischl) 22. Re: Fwd: QDEC versus Terminal annotation (Douglas N Greve) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Jan 2017 16:50:29 +0000 From: "Shapiro, Allison L" <ALLISON.SHAPIRO(a)ucdenver.edu> Subject: [Freesurfer] installation fail :( To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CB7C3006-2F82-44E5-BE71-0A5354DF90B6(a)ucdenver.edu> Content-Type: text/plain; charset="utf-8" Dear FreeSurfer support, I am a new user of the Freesurfer program and attempted to install everything this morning on my Mac OSx 10.11.6 (El Capitan). To preface everything, I updated my XQuartz program before installing, and I do not have Matlab on this computer and understand that I can?t use the fMRI functionality without this, but this is not my goal. The installation appeared to go as planned, but when I went to test the installation with the commands: $> <source_freesurfer> $> freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red I received the following error: -bash: $: command not found I was not able to decipher this error with The Google, so I am hoping that you can help. Thank you so much for your time! Best Wishes, Allie Allison L B Shapiro, MPH, PhD Postdoctoral Research Fellow LEAD Center | Colorado School of Public Health Office 303.724.7708 ?Those who dare to fail miserably can achieve greatly? - JFK

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Roi parcellation
by Aya Kabbara 18 Jan '17

18 Jan '17

Thank you.. Actually, I realized that using tksurfer I can do a manual parcellation. However, I need an automatic parcellation. Is there a way? Get Outlook for Android<https://aka.ms/ghei36>

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Postdoc position and PhD studentships available at Cardiff, UK {Disarmed}
by Jiaxiang ZHANG 18 Jan '17

18 Jan '17

[Apologize for cross-posting] Dear all, We are seeking applicants for 1 postdoc position and 2 fully-funded PhD studentships at Cardiff University Brain Research Imaging Centre (CUBRIC). These posts link to a project funded by the European Research Council (ERC). The successful candidates will work with Dr Jiaxiang Zhang and other collaborators to understand the neural mechanisms of intentional decision, using multimodal brain imaging and brain stimulation. We encourage applicants from different disciplines, including cognitive neuroscience, imaging neuroscience, psychology, computer science, mathematics or physics. Job specs and application details are available online (see links below). For informal enquiries about the project, please contact Dr Jiaxiang Zhang ( zhangj73(a)cardiff.ac.uk) with your CV. A. 3-year postdoc position (Deadline: Feb 16, 2017) http://krb-sjobs.brassring.com/TGWEbHost/jobdetails.aspx?par tnerid=30011&siteid=5460&AReq=5577BR B. 3.5-year PhD studentship 1, focusing on MEG (Deadline: Feb 1, 2017) https://www.findaphd.com/search/ProjectDetails.aspx?PJID=80235&LID=281 <http://krb-sjobs.brassring.com/TGWEbHost/jobdetails.aspx?partnerid=30011&si…> C. 3-year PhD studentship 2 (Deadline: Feb 24, 2017) https://www.findaphd.com/search/ProjectDetails.aspx?PJID=82157&LID=281 The successful candidates will be based at CUBRIC. CUBRIC houses a unique combination of state-of-the-art facilities and world-leading expertise, with 4 human MRI systems (2 x Siemens Prisma, 1 x Siemens Connectom, 1 x Siemens 7T), MEG, EEG, TMS, tDCS, clinical research units and testing labs. Further details of CUBRIC can be found on our web-page ( http://sites.cardiff.ac.uk/cubric) Dr. Jiaxiang Zhang Cardiff University Brain Research Imaging Centre (CUBRIC) School of Psychology Cardiff University Maindy Road, Cardiff, CF24 4HQ Lab: http://ccbrain.org Faculty: http://psych.cf.ac.uk/zhang Email: zhangj73(a)cardiff.ac.uk Tel: +44 (0)29 2087 0471 <+44%2029%202087%200471>

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volume based GLM group analysis(whole brain and ROI).
by miracle ozzoude 18 Jan '17

18 Jan '17

Hello Freesurfer, I would like to do a GLM volume based analysis using the cortical volumes from desikan atlas (structural not functional). However, I can't find the steps/tutorials on how to do this on the freesurfer website. Does anyone know how to do this using freesurfer? Basically, I want to perform analysis similar to surface based cortical thickness ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) Thank you. Best, Paul

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installation fail :(
by Shapiro, Allison L 18 Jan '17

18 Jan '17

Dear FreeSurfer support, I am a new user of the Freesurfer program and attempted to install everything this morning on my Mac OSx 10.11.6 (El Capitan). To preface everything, I updated my XQuartz program before installing, and I do not have Matlab on this computer and understand that I can’t use the fMRI functionality without this, but this is not my goal. The installation appeared to go as planned, but when I went to test the installation with the commands: $> <source_freesurfer> $> freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red I received the following error: -bash: $: command not found I was not able to decipher this error with The Google, so I am hoping that you can help. Thank you so much for your time! Best Wishes, Allie Allison L B Shapiro, MPH, PhD Postdoctoral Research Fellow LEAD Center | Colorado School of Public Health Office 303.724.7708 “Those who dare to fail miserably can achieve greatly” - JFK

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Freesurfer January 2017