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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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Error
by Kirill Elin 10 Jan '20

10 Jan '20

External Email - Use Caution Dear FreeSurfer Developers, I am trying to run the script and the recon-all command and getting Exited with errors output. 1. FreeSurfer Version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2. Platform, VM Ware Workstation 15, host OS: Windows 10, Guest: Ubuntu ubuntu-18.04.3-LTS, 64 Bit, 2 GB RAM 3. See the log file and the screenshot. In the script I have not found any other errors so I am not even sure, what I should be looking for. If it plays a role, my MRI folder, where original T1s are as well as the output folder are in the shared folder (shared between the host windows OS and the virtual machine). I would be grateful if you could help me out with this. Thank you in advance. Sincerely yours, Kirill

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Right Lateral Ventricle Omitted from white and pial surfaces
by Rachel Hoel 10 Jan '20

10 Jan '20

External Email - Use Caution Dear Freesurfer Developers, In one of our recons I'm seeing that the right lateral ventricle is partially excluded from the white matter and pial surfaces (screenshots attached). The aseg.mgz has no label for the omitted region. We are using v6.0. What is recommended for fixing this type of error? Filling in the wm.mgz where the omission is? Thanks in advance, Rachel

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single-trial analysis of BOLD data in FSFAST
by Katsumi, Yuta 10 Jan '20

10 Jan '20

Dear Doug, I would like to perform GLM on a trial-by-trial basis in FSFAST. That is, I'm interested in obtaining beta estimates per trial and using them as input for group-level analyses of activation patterns (e.g., MVPA) or functional connectivity (e.g., beta series correlations). I've done this in the past using SPM to analyze data in volume space, and now would like to take a similar approach using FSFAST to analyze data in surface space. Would you please advise how I might be able to implement this? Thanks in advance for your input. Best, Yuta

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funcroi-sess annotation issue
by Lewis, Lydia R. 10 Jan '20

10 Jan '20

Hello Freesurfer Team, I am running the fsfast analysis stream for resting state data and recently came across an issue with the funcroi-sess command. I originally used funcroi-config to configure the rois with the -annot aparc.a2009s $ROI flag to seed each of the regions from the 2009 annotation. But when I tried to do funcroi-sess I got the following error ERROR reading $projectdir/sess01/rest/lh_G_and_S_frontomargin.fc/tmp.funcroi-sess.lh.G_and_S_frontomargin/label/lh.lh_G_and_S_frontomargin.label It seems like this is because first command (mri_annotation2label) generates labels with slightly different names, such as $projectdir/sess01/rest/lh_G_and_S_frontomargin.fc/tmp.funcroi-sess.G&S_frontomargin.fc/label/lh.G&S_frontomargin.label. For instance, if I edit the config file to: roiname lh.G_and_S_frontomargin annot aparc.a2009s G&S_frontomargin fillthresh 0 analysis lh_G_and_S_frontomargin.fc the funcroi-sess command works fine. As a solution, I edited my script to change the annotations to 1) remove the hemisphere from the prefix, and 2) replace G_and_S with G&S. With these changes, the funcroi-sess command seems to be working correctly. I just wanted to get some feedback on whether this was a valid solution, or if this error is occurring because of some other larger issue that I will need to fix/be aware of. For reference I am using the stable6 version of freesurfer. Thanks for your time, Lydia Lewis

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