Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

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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CORTICAL Thicknesses
by amirhossein manzouri 23 Sep '13

23 Sep '13

Hi, In the attached Slice image of a processed brain, there is a yellow line which defines the WM and red line for the cortex but in segmentation some WM have been segmented as cortex and some part of cortex have not been segmented ! Would you please let me know how to handle the situation while I am reporting cortical thicknesses of my data? -- Best regards, Amirhossein Manzouri

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Re: [Freesurfer] qdec analysis and covariates
by Anita van Loenhoud 23 Sep '13

23 Sep '13

Oh, I meant to reply to an older post, but that didn't work apparently. Below the original post. This person does a group analysis, with gender and age as covariates.You adviced to first do a DODS and look for a age-by-group interaction. If there's no interaction, he/she could continue with DOSS. My questions is (since I'm doing a similar analysis) whether it's also necesary to check for a age-by-gender interaction? Or is this not important since gender is a covariate instead of an independent variable? Thanks! Anita Douglas N Greve Mon, 29 Nov 2010 07:27:30 -0800 Yes, that looks fine. The only other thing to decide is whether to use DODS (different offset different slope) or DOSS (different offset same slope). The default is DODS, but if you don't think that there is an age-by-group interaction, then you can get more power using DOSS. If you use DODS, then you should probably de-mean the ages (ie, subtract the grand mean age over all subjects from the age of each individual). doug Roser Sala wrote: Hi, We are doing a group analysis using qdec with two groups, and we would like to include gender and age as covariates. Which is the best option in order to perform a simple t-test (group1>group2 and group2>group1) and including the two covariates? (we would like them to have 'zero' weighting in the contrast matrix) We realized that if we include 'age' as a continous factor in the dialog, qdec is performing rather an interaction analysis than a covariate. So, would it be ok to include group and gender as fixed factors and age as nuisance, and then select the output as 'Does the average thickness accounting for gender differ between group1 and group2' (age as nuisance variable)? By checking all the possibilities this seemed the best option for us, but we would like to get a confirmation that we are doing it right. Many thanks Roser

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Re: [Freesurfer] qdec analysis and covariates
by Anita van Loenhoud 23 Sep '13

23 Sep '13

Hi, I have a question related to this post. Besides an age-group interaction, wouldn't it also be neccesary to check for an age-gender interaction?

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dilate a label?
by Yang, Daniel 22 Sep '13

22 Sep '13

Hi FreeSurfer Experts, Is it possible to dilate a label using command line? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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break down a label?
by Yang, Daniel 22 Sep '13

22 Sep '13

Dear FreeSurfer Experts, If I have a label that spans across multiple anatomical regions, is it possible to automatically break it down according to aparc.annot? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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Sulcal depth variations
by Damien MARIE 21 Sep '13

21 Sep '13

Hello everyone, I'm working on a group analysis of cortical thickness, surface area, curvature and sulcal depth with FreeSurfer 5.3. However I'm in trouble concerning the interpretation or the meaning of my results, especially concerning curvature and sulcal depth. I understood that curvature can be positive when it concerns sulcus or positive in case of gyrus. According to my result it would be almost the same for sulcal depth. The value of sulcal depth is positive on a sulcus while it is negative on a gyrus. Am I correct? All the best, Damien Marie

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Freesurfer September 2013