Freesurfer June 2024

freesurfer@nmr.mgh.harvard.edu

47 participants
51 discussions

Inquiry About Using Freeview's ROI/Voxel Edit Tool on Surface File
by Dai, Y. (Yuxuan) 27 Jun '24

27 Jun '24

External Email - Use Caution Dear Freesurfer support team, Hope this email finds you well. I am writing to ask about using Freeview's ROI/Voxel edit tool on the surface file. To be more specific, my situation is that I need to customize regions of interest by manually drawing areas on the surface file and then storing the selected voxels, and I'm wondering if it's possible to do so with Freeview. I have found some previous scripts suggesting that this can be done using tksurfer. However, I understand that tksurfer has been deprecated for quite some time, and we are also eager to transition to a more updated tool. Yet, compared to tksurfer, freeview seems to be less flexible in terms of surface editing. It appears that I cannot find a surface operation tool in freeview that is similar to tksurfer. Moreover, tksurfer accepts customized parameter recipes (such as revphaseflag, usefdr, fthresh, etc.), configured through a .tcl file, but this option is no longer functional in freeview. If I want to continue using my old tksurfer configuration for surface display, is there a way to translate all those options to freeview? Thanks for your assistance in advance. Best, Yuxuan

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MRI watershed error
by Gaurav Ambwani 27 Jun '24

27 Jun '24

External Email - Use Caution Dear Freesurfer developers, I took a 1mm T1 MRI of the MNI152 skull stripped it using HD brain extraction tool in 3D slicer, and then I registered it in fsl to a skull stripped version of a T1 weighted image of a Stroke patient (which I got from Openneuro). The purpose of doing this is to, get the aseg.mgz file and overlay that onto the MRI of the stroke patient. Previously I have taken the T1 1mm MNI image and received an aseg.mgz file which I have overlayed onto my MNI registered T1 weighted stroke MRI and that worked perfectly. However, This time I have taken the T1 1mm MNI image registered that to my stroke T1 MRI, and the registered image hasn't gone through freesurfer. I have attached the recon-all.log file in this email. Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Uname -a: Linux DESKTOP-HV9KQQ6 5.10.16.3-microsoft-standard-WSL2 #1 SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Distributor ID: Ubuntu Description: Ubuntu 22.04.4 LTS Release: 22.04 Codename: jammy I am using a WSL in windows 11 (64 bit) Thank you, Best Wishes, Gaurav Ambwani.

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Differences between lme_mass_fit_vw and lme_mass_fit_Rgw
by Dan Levitas 26 Jun '24

26 Jun '24

External Email - Use Caution Hello, I've been analyzing a dataset consisting of two groups (control, clinical), each with two timepoints (tp1, tp2), following FreeSurfer's LME longitudinal analysis pipeline, to assess cortical thickness differences. Given the relative simplicity of my data, I've only specified a single random effect (intercept). In the FreeSurfer section on spatiotemporal models, it begins with "*Spatiotemporal models are more powerful to detect effects in your data than traditional vertex-wise models when two or more random effects are included in the longitudinal statistical model.*" However, I've currently been using the spatiotemporal model approach (lme_mass_fit_EMinit, lme_mass_RgGrow, lme_mass_fit_Rgw) with the single random effect, but am curious if this is inappropriate and instead need to use the mass-univariate (lme_mass_fit_vw) workflow? Dan

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Recon-all manual edits - multiple re-runs
by Blujus, Jenna 25 Jun '24

25 Jun '24

External Email - Use Caution Hi all, I have processed a set of T1w data through recon-all (v7.3.2) and am now making manual edits, if necessary. I have had a few cases where control points, wm.mgz, and brainmask edits are needed and incorporated via 'recon-all -autorecon2-cp -autorecon3 -s ${id}'. However, upon inspection of the updated outputs following the initial manual edits, further edits are required only to the wm.mgz to fix new topological errors. To incorporate the second round of wm edits, would I need to rerun recon-all from the control point stage to incorporate *all* edits (i.e., first round [control points, wm, brainmask]) or just from the wm stage with recon-all -autorecon2-wm -autorecon3 -s ${sid}? Essentially, I am asking if each time recon-all is re-run does it progressively build off of previous edits? Let me know if you need any clarification. Thanks in advance, Jenna

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Registering Two Anatomical Images
by Andrew Jahn 25 Jun '24

25 Jun '24

External Email - Use Caution Hello, I have a raw anatomical image called raw.mgz, which I have manually annotated using Freeview; the resulting annotations are saved in a file called seg.mgz. I want to compare this to the annotations automatically generated by recon-all, so I ran the image through the recon-all processing stream. However, the original dimensions of the raw.mgz image are 256x209x256, and recon-all resamples the image to 256x256x256 resolution. If I want to compare the amount of overlap between my annotations and those generated by FreeSurfer - specifically, the aparc+aseg.mgz file created by recon-all - what is the best way to register the seg.mgz file to aparc+aseg.mgz? I looked through the documentation of mri_vol2vol, but I wasn't sure which registration file to use. Is it one of the transformation files contained in the "transforms" folder from the image that has been processed through recon-all? Thank you! -Andy

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Recon-all for a common template
by Chen Yang 24 Jun '24

24 Jun '24

External Email - Use Caution Dear Freesurfer Developers, my data is from 50 preschoolers and I created my own group template from these kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti file (see attached). Then we'd like to process this group template in Freesurfer to reconstruct the cortical surfaces as the individual brain images. My question is, how can i do the recon-all with the template? Because I only have this template file I feel I don't have enough input files(?). Thanks in advance! Best regards, Chen -- Chen Yang PhD Student Independent Research Group 'Milestones of Early Childhood Development' Max Planck Institute for Human Cognitive and Brain Sciences Email:yangc@cbs.mpg.de

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Become a member of the International Society for Tractography (IST)
by Maxime Descoteaux 21 Jun '24

21 Jun '24

External Email - Use Caution ** *We are thrilled to officially announce the launch of the International Society for Tractography (IST) <http://www.tractography.io>. Our goal is to facilitate fundamental advances in the field of tractography that are only possible via an interactive community dedicated to sharing a broad range of talent and knowledge. This includes planning engaging events such as webinars, educational workshops, and conferences, as well as promoting large-scale collaborations across institutions and international borders. * * It’s now time to sign up and become a member <http://www.tractography.io/become_a_member/>. The first year (July 1st 2024 - June 30th 2025), membership will be free! Exciting things to watch out for: * Our new website [www.tractography.io <http://www.tractography.io>] * IST is on X <https://x.com/tractography>[@tractography] and LinkedIn <https://www.linkedin.com/company/international-society-for-tractography/> * TheTract-Anat Club <http://www.tractography.io/tractanat_club/>with recordings posted on our YouTube channel <https://www.youtube.com/@SocietyTractography>. * A dedicated collection "Neuroanatomy and Tractography" in Brain and Structure Function <https://link.springer.com/collections/jfccijhacc> * And more to come (2025 conference in Bordeaux, France) Looking forward to interacting! On behalf of the board of directors and scientific committee Maxime Descoteaux, Flavio Dell’Acqua, Kathleen Rockland, Catherine Lebel, Derek Jones, Lauren O’Donnell, Ariel Rokem, Pratik Mukherjee, Shawna Farquharson, Alexander Leemans, Graham Little, and Laurent Petit *

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Renaming Freesurfer subject directories for data sharing
by Dan Fitch 20 Jun '24

20 Jun '24

External Email - Use Caution Hi folks, Our subject identifiers that we push through Freesurfer are internal-only. We have a public-facing set of IDs, and we'd like to include anonymized Freesurfer data in the BIDS that we share. So: we need to take the stuff we have in $SUBJECT_DIR and transform it. Unfortunately, this isn't as simple as just renaming the directories, as many of the outputs and logs include "# subjectname sub-XXXX" comments and cmdlines that include the subject name. 1. Is there an extant method to rename subject directories? I've searched around on Github and on this list's archives; came up blank. 2. Would it be enough to walk the directories and replace all instances of e.g. "sub-1234" with "sub-30000"? Or do subject numbers get embedded in binary headers/metadata, as well? The extra-fun touch is that we are not actually allowed to SEE the mapping from internal IDs to public-facing IDs, so any tool we provide for this translation needs to be useable by someone who is unfamiliar with Freesurfer. (Don't ask.) Then we will also need to de-face all the images, of course. Any tips or leads appreciated; otherwise, I'll build a thing and eventually post about it here. Dan Fitch Research Engineer University of Wisconsin-Madison Institute on Aging

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Re: [Freesurfer] Brain in a Box
by Huang, Yujing 20 Jun '24

20 Jun '24

Hi Hebah, You don’t need to install Surfa separately. It is part of your Freesurfer installation. Surfa Volume takes .mgz/.mgh, .nii/.nii.gz formats. Once you sourced your Freesurfer environment, use ‘fspython’ to access the Python distribution shipped with your Freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux What I showed in previous message was from an interactive fspython session. You can write your own python scripts to use Surfa. On Surfa github, there are some documentations on how to use the library. In your sourced Freesurfer environment, use ‘fspython’ to run your scripts. Best, Yujing From: Hebah Tanveer <hebah.tanveer(a)biotexmedical.com> Sent: Tuesday, June 18, 2024 10:32 AM To: Huang, Yujing <YHUANG43(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Brain in a Box External Email - Use Caution Hi, Yujing! I am new to the field of neuroimaging and want to better understand how to run Surfa. I'll need to install Python+IDE, C+IDE, and then run pip install surfa in my computer's command window? What is the file format of the slice images that Surfa will intake? Best, Hebah On Tue, Jun 18, 2024 at 7:26 AM Huang, Yujing <YHUANG43(a)mgh.harvard.edu<mailto:YHUANG43@mgh.harvard.edu>> wrote: I'm wondering if the bbox() implementation in Surfa (https://github.com/freesurfer/surfa/tree/master) will achieve the task? surfa.image.framed.bbox() (https://github.com/freesurfer/surfa/blob/master/surfa/image/framed.py#L203) computes the bounding box of the image data greater than zero. I tried it on bert orig.mgz, >>> import surfa as sf >>> bert='/usr/local/freesurfer/dev/subjects/bert/mri/orig.mgz' >>> vol=sf.load_volume(bert) >>> vol sf.Volume(shape=(256, 256, 256), dtype=uint8) >>> vol.shape (256, 256, 256) >>> bbox=vol.bbox() >>> bbox (slice(47, 207, None), slice(3, 255, None), slice(3, 252, None)) Yujing -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Wighton, Paul Sent: Monday, June 17, 2024 5:34 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Brain in a Box Hi Hebah, Interesting application. You could try running mri_synthstrip then analyse the resulting binary mask to determine the first and last slices in each direction. -Paul ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Hebah Tanveer <hebah.tanveer(a)biotexmedical.com<mailto:hebah.tanveer@biotexmedical.com>> Sent: Monday, June 17, 2024 5:18 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Brain in a Box External Email - Use Caution I'm trying to determine the smallest rectangular prism that a brain will fit in based on its MRI scan. My strategy is as follows: I am moving through the brain axially, sagittally, and coronally to see where the brain "starts" appearing and "stops" appearing. Then, I'm subtracting the amount of no-brain slices from the total number of slices and multiplying the result by the slice thickness. This should get me the length (sagittal plane), width (coronal plane), and height (axial plane) of a box that contains the brain. Is there a function within FreeSurfer that can automate this process of determining "first and last sight of brain" ? It is quite time consuming to manually check hundreds of patients! Best, Hebah _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Re: [Freesurfer] freesurfer launching error
by fsbuild 19 Jun '24

19 Jun '24

External Email - Use Caution  The info at the end of this posting about updating sshd_config in your Linux image might be helpful if you have not already tried it (enable X-forwarding, use local X11  host)https://stackoverflow.com/questions/62363023/x11-forwarding-from-wsl2-fails You could try updating WSL which I don’t think is updated along with the OS.  Looks like that command is,  wsl —update Some postings indicate that WSL2 now has its own X-server, WSLg,  but that it does not work as well as VcXsrv,https://www.reddit.com/r/wsl2/comments/172urvu/wsl2_no_longe… Another posting about using WSLg is,https://superuser.com/questions/1682522/gui-apps-not-working-in-wsl2-for… If the above does not work, maybe try uninstalling and re-installing VcXsrv. -R. On Jun 18, 2024, at 06:56, yunus soleymani <soleymani.yunus(a)yahoo.com> wrote:        External Email - Use Caution        hi everyone, recently after a major Windows 11 update, I can not launch Freeview in my WSL Ubuntu machine despite having VcXsrv working in the background,  and encountered the following error:  QXcbConnection: Could not connect to display 10.255.255.254:0Could not connect to any X display. do you have any idea to troubleshoot this error? I appreciate any help you can provideBest,Yunus _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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