Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

Re: [Freesurfer] how to include Schaefer atlas into freesurfer and compute surface statistics
by Kate Marvel 14 Jan '20

14 Jan '20

External Email - Use Caution Thank you very much! Much appreciated Prof Leo. On Tue, Jan 14, 2020, 6:46 PM Thomas Yeo <yeoyeo02(a)gmail.com> wrote: > Hi Kate, > > You can see the instructions here: > https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc… > > The gcs files will be incorporated into freesurfer at some point. > Aihuiping (cc-ed) will attach the gcs files in the next email. > > Thanks, > Thomas > > On Wed, Jan 15, 2020 at 7:40 AM Kate Marvel <kmarvel54(a)gmail.com> wrote: > >> Dear Freesurfer team, >> >> I would like to include Schaefer atlas into freesurfer. The Schaefer >> atlas can be found in the link below: >> >> >> https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc… >> >> My question is how can I integrate the atlas in the freesurfer so that I >> can run recon-all and calculate the statistics using Schaefer >> parcellations, just like aparc_DK40 or aparc_a2009s atlases already >> pre-installed in freesurfer >> >> >> Thank you, >> >> -- >> kate >> >

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how to include Schaefer atlas into freesurfer and compute surface statistics
by Kate Marvel 14 Jan '20

14 Jan '20

External Email - Use Caution Dear Freesurfer team, I would like to include Schaefer atlas into freesurfer. The Schaefer atlas can be found in the link below: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc… My question is how can I integrate the atlas in the freesurfer so that I can run recon-all and calculate the statistics using Schaefer parcellations, just like aparc_DK40 or aparc_a2009s atlases already pre-installed in freesurfer Thank you, -- kate

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Re: [Freesurfer] Right Lateral Ventricle Omitted from white and pial surfaces
by Rachel Hoel 14 Jan '20

14 Jan '20

External Email - Use Caution Thank you, I am still checking in with my supervisors about sending the subject. For now, if we are only interested in looking at grey matter data, do we need to be concerned if the subcortical segmentation isn’t accurate? Best, Rachel

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Skipping bias field correction
by Patrick 13 Jan '20

13 Jan '20

External Email - Use Caution Dear Freesurfer experts, I am trying to run recon-all but I want to skip bias field estimation and correction step. I have tried the following: 1) Run recon-all by specifiying -nonuintensitycor2) Running recon-all by specifying "motioncor" followed by "talairach" (additionally copying "orig" file and renaming it as "nu" However, in both the cases, it looks like Freesurfer is still running bias correction. How can I go about skipping bias field correction? Thanks and RegardsPatrick

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Re: [Freesurfer] average subject with 5th order icosahedron tesselation
by Marina Fernández 13 Jan '20

13 Jan '20

External Email - Use Caution That's it! Thank you Doug! Best wishes, Marina.

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hippocampal subfield segmentation question
by Gabor Perlaki 12 Jan '20

12 Jan '20

External Email - Use Caution We have a sagittal 1 mm isotropic whole-brain 3D T1 mprage (morphometry protocol suggested on Freesurfer's page) and a coronal anisotropic (0.4mm inplane, 2mm thickness, similar to ADNI protocol) T2 measurement acquired perpendicular to the hippocampus. We'd like to use both measurements simultaneously in the segmentation. However, on the fswiki it is suggested that T2 should be coarsely aligned to the main T1 scan, but I'm not sure about how to understand it, especially since our 3D T1 is acquired in sagittal plane, while T2 is in coronal. (a) Should T1 and T2 acquired in the same (e.g. coronal plane) with the same or little angulation? or (b) Is it enough if they are just aligned based on the physical/anatomical coordinate system (which is automatically ensured if both images were acquired in the same session with no repositioning and little or no head movement of the subject between the two measurements)? Best, Gabor

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Noise reduction + Eddy current reduction
by Adam Rytina 11 Jan '20

11 Jan '20

External Email - Use Caution Hello all, I want to apply the denoising and eddy current reduction on input images 3DT1 and 3D Flair. Are there any algorithms in Freesurfer to perform the noise and eddy current reduction? Does recon-all involve denoising and eddy current reduction? If so, in which processing stage? Thanks a lot Regards Adam

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Extract specific LGI values
by Tien Pham 11 Jan '20

11 Jan '20

External Email - Use Caution Dear FreeSurfer Experts, I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI changes in my data set with two time points using longitudinal pipeline. Now I would like to extract the regional LGI and gray matter volume in my longitudinal results using QDEC to draw the ROIs which is showed significant differences, label it and map to all subjects. Then I get the LGI value of the ROI I saved before using the command below: cd $SUBJECTS_DIR mris_anatomical_stats -l lh.untitled.label \ -t lh.pial_lgi \ -b \ -f subject_id/stats/lh.untitled.stats subject_id lh And this is the result: [toyama-no-iMac:/applications/freesurfer/subjects] toyama% mris_anatomical_stats -l lh.frontoinsula.label \ ? -t lh.pial_lgi \ ? -b \ ? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh limiting computations to label lh.frontoinsula.label. using thickness file lh.pial_lgi. reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz... reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white... reading input pial surface /applications/freesurfer/subjects/VC019_1/surf/lh.pial... reading input white surface /applications/freesurfer/subjects/VC019_1/surf/lh.white... table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 6595 4368 15935 3.311 0.895 0.158 0.077 135 19.7 lh.frontoinsula.label As I saw there was no columns showing the LGI value, I did similar with gray matter volume, the result displayed the different in some values of the columns. Could you please help me to explain about this? Thank you very much. Best regards, Tien Pham

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Re: [Freesurfer] Amygdala Segmentation T1.v20 Command
by Deng, Yushan Wisteria 10 Jan '20

10 Jan '20

Hi Eugenio, Please see attached for the list of files. Thank you so much for your kind help! Best, Wisteria Date: Wed, 8 Jan 2020 08:12:04 +0000 From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Amygdala Segmentation T1.v20 Command To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <4B81084F-8361-40FA-851E-D30180DC8D23(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Thanks, Wisteria. Can you please send us the list of files under the mri directory of any subject? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

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mri_glmfit-sim for longitudinal pipelines
by Swati Rane 10 Jan '20

10 Jan '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare longitudinal cortical thinning rates (pc1) between 3 groups using mri_glmfit using FreeSurfer 6.0. The tutorial suggests that you could use the multiple comparisons corrections that come with it but does not comment on using the mri_glmfit-sim option. I just want to confirm whether there is anything prohibiting me from using mri_glmfit-sim. Are there any set of parameters that should be set differently when using pc-1 instead of thickness files? Also, would you do a stricter correction and stick to the longitudinal model or prefer the linear mixed effects model and do a FDR? How do you decide between the two? Thanks! Swati

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Freesurfer January 2020