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Loading control points into freeview from command line
by Jonathan Holt 24 Sep '13

24 Sep '13

Is there a way to do this? jon

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Re: [Freesurfer] Viewing auxiliary and main volumes simultaneously
by Jonathan Holt 24 Sep '13

24 Sep '13

Never mind, page up/page down are separate from arrow keys. thanks bruce On Sep 24, 2013, at 1:09 PM, Jonathan Holt <whatsdac(a)umich.edu> wrote: > forgot to cc list > >> You'd think that was it, but that simply moves the brain around in it's box, it doesn't change slices. The only way i can go through slices is by grabbing them with the cursor in the 3D view, but I can't navigate slice by slice that way >> >> >> On Sep 24, 2013, at 12:50 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >> >>> Hi Jon >>> >>> try page up/page down >>> >>> cheers >>> Bruce >>> >>> >>> On Tue, 24 Sep 2013, Jonathan Holt wrote: >>> >>>> Thanks bruce >>>> >>>> I'm realizing free view is a ton more powerful than tkmedit. I can't figure out how to navigate through the brain slice by slice like I could in tkmedit. >>>> >>>> jon >>>> On Sep 24, 2013, at 12:22 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>>> >>>>> there is an opacity slider in freeview you can use for this >>>>> >>>>> cheers >>>>> Bruce >>>>> On Tue, 24 Sep 2013, Jonathan Holt wrote: >>>>> >>>>>> Is there any way to accomplish this? >>>>>> >>>>>> Jon >>>>>> _______________________________________________ >>>>>> 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. >>>>> >>>> >>>> >>>> >>>> >> >

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Re: [Freesurfer] Viewing auxiliary and main volumes simultaneously
by Bruce Fischl 24 Sep '13

24 Sep '13

Hi Jon try page up/page down cheers Bruce On Tue, 24 Sep 2013, Jonathan Holt wrote: > Thanks bruce > > I'm realizing free view is a ton more powerful than tkmedit. I can't figure out how to navigate through the brain slice by slice like I could in tkmedit. > > jon > On Sep 24, 2013, at 12:22 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > >> there is an opacity slider in freeview you can use for this >> >> cheers >> Bruce >> On Tue, 24 Sep 2013, Jonathan Holt wrote: >> >>> Is there any way to accomplish this? >>> >>> Jon >>> _______________________________________________ >>> 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. >> > > > >

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complex repeated measure model
by Jacobs H (NP) 24 Sep '13

24 Sep '13

Dear FreeSurfers, I am struggling with how to set the fsgd-file and contrast file for a probably complex model. I have two groups: old and young participants. For each participant, I have one T1-weighted image, on which I would like to perform the cortical thickness analyses. This T1 image was collected at baseline. The variable of interest is cognitive performance defined on three different occasions (during which we applied an intervention). We want to investigate susceptibility for this intervention over time, as reflected in this cognitive outcome score. The idea is to investigate whether susceptibility for this intervention is associated with different cortical thickness patterns in old versus in young persons. Is there a way to capture this in one test and then do posthoc pariwise comparisons? Thanks! Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

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LME toolbox for VBM-style data?
by Seán Froudist Walsh 24 Sep '13

24 Sep '13

Dear FreeSurfers, I was wondering if anyone had tried to use the MATLAB LME toolbox that you kindly developed for volume based VBM-style data? Either way would you be able to impart some initial advice as to considerations that should be made etc? Best wishes and many thanks, Sean

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label stats?
by Yang, Daniel 23 Sep '13

23 Sep '13

Dear FreeSurfer Experts, Is there a way to use command line to obtain the stats (e.g., area) for a given label? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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Thalamic subdivisions
by O'Shea,Andrew 23 Sep '13

23 Sep '13

Hello FS-Experts, I was wondering if there has been any work done to subdivide the thalamus segmentation (aseg volume) into smaller sub-sections, similar to what has been done with the hippocampus (using -hippo-subfields)? I am measuring longitudinal changes in the volume of the thalamus from pre to post treatment comparing a treatment group and waitlist control group. I have found significant results over the whole left thalamus but I was wondering if maybe a smaller sub-field was driving the results or if the changes were evenly distributed amongst the whole region? Any input would be greatly appreciated. -Andrew

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Re: [Freesurfer] Watershed and Normalization Problem
by Erica Tatham 23 Sep '13

23 Sep '13

Hi Bruce and Team, I have uploaded the subject dir to the File Drop under "Watershed and Normalization Problem". Thank you very much for taking a look at these files. Cheers! Erica Hi Erica if you upload this subject dir we will take a look cheers Bruce On Thu, 12 Sep 2013, Erica Tatham wrote: Hello Freesurfer People, Below is the error that I have been receiving after running a recon-all. There seems to be a problem in the normalization stage. I checked the orig.mgz and the transform.xfm, and both seem to be reasonable. I was hoping for some guidance/expert advice for how to precede from here. I have not tried to add control points as I am fairly novice to freesurfer and not quite sure how to complete this task. Thank you for any advise you are able to give, Cheers, Erica Error: *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Erica Tatham, B.Sc M.Sc. Candidate McMaster Integrative Neuroscience Discovery & Study McMaster University 1280 Main St W., Hamilton On Email: tathamel(a)mcmaster.ca

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AD vs ctrl in 1.5T strange results
by zach.petr＠post.cz 23 Sep '13

23 Sep '13

Hi all, we ran FS with confirmed 30 AD/ctrls and got wierd results: hippocampi almost equal and many regions (accumbens, BG and others) greater volume greater in AD compared to controls. On the other hand cort surface area was smaller in AD as well as temporal gyri and many other gyri. What could be the case? Thanks Petr

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High intensity GM being omitted
by Jonathan Holt 23 Sep '13

23 Sep '13

Attached is an image that describes my issue. WM in the temporal region is being omitted after running recon-all. Most of the omitted voxels are in the 120-130 range. It's causing an issue with the underlying WM voxels as well, they've simply disappeared. I can see how this voxel intensity limit would help omit dura, vessels, and other high intensity objects but in this case it's a bit of an issue and I'm not sure how to A) rectify it (I could replace the WM voxels?) B) keep it from happening again. Is there a way to give freesurfer an intensity threshold to work with? Please advise! Jon

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