Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

recon edit error
by Nicole Orme 04 Dec '17

04 Dec '17

Hello FreeSurfer Developers, I have been editing my MRI images using the recon edit tool. I have been editing the white matter so it does not include grey matter. When I click shift to remove the extra voxels included in white matter they are removed, which is what supposed to happen. Where I’m encountering a problem is sometimes I’ll have clicked the shift but are not holding the mouse down so it seems as if the entire image gets selected. I’ve attached a screenshot. I don’t know how to reverse this. It then will have all the images selected. If you could help me that would be great! Nicole

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Make binary ROIs appear 3d in Freeview
by Anna Mynick 04 Dec '17

04 Dec '17

Hi all, I’m using Tracula and would like to display some regions of interest (ROIs) along with the tracts produced by Tracula. I’m wondering whether there’s a way to visualize these ROIs with 3d texture in the same way that Tracula applies this 3d effect to its tracts. At present, my region of interest (see lower lefthand corner of image below, in yellow) can be viewed in concert with Tracula but doesn’t assume the same 3d texture. Is there a way to make it appear 3d like the tracts? For reference, the ROI is an .nii.gz file containing only 0s and 1s. Thanks for any help! Best, Anna

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Overlaying multiple results onto one surface
by Nguyen, Tin 04 Dec '17

04 Dec '17

Hello, I have been running different analyses through QDEC GUI for different covariates that describe a similar construct, for instance: * Model A: (cortical thickness) ~ (covariate 1) + (nuisance factors) * Model B: (cortical thickness) ~ (covariate 2) + (nuisance factors) * Model C: (cortical thickness) ~ (covariate 3) + (nuisance factors) * Model D: (cortical thickness) ~ (covariate 4) + (nuisance factors) * Model E: (cortical thickness) ~ (covariate 5) + (nuisance factors) As a result, I have 5 different brain images to illustrate each of the 5 models for their corresponding covariates. Is there way to overlay all 5 of the images onto a common space to have 1 representative brain image? This is to show overlapping effects, or the lack thereof, of the covariates. Thank you. -Tin

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Combining parcellated regions within an atlas?
by Michiko H. 04 Dec '17

04 Dec '17

Hi Freesurfer Experts, I was wondering what the best way of combining regions within a parcellation? For example, in the Schaefer 2017 functional atlas, there are regions such as: 7Networks_LH_DorsAttn_FEF_1 0 118 22 0 7Networks_LH_DorsAttn_FEF_2 0 119 17 0 7Networks_LH_DorsAttn_FEF_3 0 119 18 0 7Networks_LH_DorsAttn_FEF_4 0 119 19 0 7Networks_LH_DorsAttn_PrCv_1 0 119 20 0 7Networks_LH_DorsAttn_PrCv_2 0 119 21 0 If I would like to combine all the DorsAttn_FEF areas into 1 node and DorsAttn_PRCv areas into another, what is the best way to do this? I currently have an image that has been parcellated using this atlas that was brought into volumetric space. I would need to have a transformed re-parcellated file and a corresponding color LUT file. Would appreciate any help, thank you! Best, Michiko

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QDEC and comparing two conditions
by Rizvi, Batool 04 Dec '17

04 Dec '17

Hi FreeSurfer experts, We calculated the correlation between thickness two different behavioral conditions using QDEC. We now want to compare the spatial overlap and difference in thickness-correlation between the two behavioral conditions. We would like to do this both visually as well as statistically. Is there an option to do this either in QDEC or in the command line? Thanks for your time! Batool

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Concatenating .mgh surface space functional MRI runs
by Abisan - 04 Dec '17

04 Dec '17

Hi Freesurfer experts, I want to concatenate multiple preprocessed fMRI runs in the form of .mgh freesurfer surface space files (2-D matrices vertexes * time_frames). Is there a tool that can do this easily, or do you have other recommendations how to do this? Thank you!

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freesurfer design
by Dijkshoorn, A.B.C. (Aicha) 04 Dec '17

04 Dec '17

Dear freesurfer group, I have two questions: Can I compare one patient with a created control group in Freesurfer on the following outcome measures: cortical thickness, brain volume and gyrification? If so, how can you visualise that? When you do the cortical analysis with freesurfer can you account for covariates in the statistical model (before visualisation)? Kind regards, Aicha Dijkshoorn

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Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
by Taylor, Johnmark 04 Dec '17

04 Dec '17

Hello, A few quick questions about the "Per-Run" option in preproc-sess. I understand that in this option, each run's images are registered to the middle timepoint of that run, rather than the first timepoint of the first run. I was wondering, though: 1) Why is this the preferred option instead of per-session? 2) If motion-correction is only done internally to each run, then wouldn't between-run motion throw things off if you wanted to do a GLM spanning the whole scanning session (although I assume it'd be fine for single-run GLMs)? What ensures that the images line up properly between runs? Thank you very much, JohnMark

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mri_binarize
by John Anderson 04 Dec '17

04 Dec '17

Dear FS experts, I want to use mri_binarize to create (binarized and free of CSF and ventricles) mask from "aparc.DKTatlas+aseg". How can I substract CSF and ventricles from teh atlas using mri_binarize? Thanks John

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MRI protocol for hippocampal subfield segmentation
by Gabor Perlaki 04 Dec '17

04 Dec '17

I've two questions regarding hippocampal subfield segmentation: 1, Is there any article or other document which containes an optimal T2 protocol with detailed sequence parameters for hippocampal subfield segmentation? (eg. BW, echo time, repetition time, FOV, echo train, paralell imaging on/off, ...) We have a Siemens Prisma 3T scanner. 2, For T1, we use the suggested MPRAGE protocol by Andre (1mm*1mm*1mm). Is it OK or do we need a special protocol? Thank you, Gabor

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