Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

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

2 1

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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TRACULA multiple sessions output question
by Fotiadis, Panagiotis 18 Jun '24

18 Jun '24

External Email - Use Caution Hello, First of all, thank you for the fantastic software! I have a cohort of individuals with multiple DWI sessions each, and I have been using TRACULA with a configuration file similar to that of Example 3 (“Cross-sectional study, multiple diffusion scans per session”) shown in https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc to analyze them. I have ran all three steps of the analysis (preproc, bedp, and path) successfully for all subjects, but I was a little confused as to whether TRACULA can save the individual statistics for each DWI session of each subject. So far, when I’m looking under each subject’s …/dpath/$white_matter_tract/ directory I can see only one pathstats.byvoxel.txt (and one pathstats.overall.txt) file. 1. Does that correspond to only one (perhaps the least noisy) or the average stats file across all DWI sessions for that subject? 2. I can see that some files (such as the control point niftis) are saved for all DWI sessions, but is there a way to get the aforementioned stats files (and corresponding diffusion measure and white matter tract maps) for each DWI session per subject? Thank you in advance! Best, Panos ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

1 1

Brain in a Box
by Hebah Tanveer 18 Jun '24

18 Jun '24

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

3 2

freesurfer launching error
by yunus soleymani 18 Jun '24

18 Jun '24

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

1 0

Cannot find mri/transforms/talairach.m3z file
by Dan Levitas 17 Jun '24

17 Jun '24

External Email - Use Caution Hello, I am following the longitudinal freesurfer pipeline ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) and getting this error on the final (LONG) portion: *ERROR: cannot find or read transforms/talairach.m3z* I can confirm that recon-all ran successfully during the CROSS and BASE portions; it is only when I attempt to perform recon-all -long that things fail. My suspicion is that CA registration was not performed during CROSS, as I used -synthseg (and -synthstrip) in that recon-all command. I'm unsure if I need to go back and specify -careg in the CROSS recon-all command (e.g. *recon-all -autorecon2 -careg*), or if there is some way to bypass this error. I tried appending -nocareg to the end of my LONG recon-all command, but this errored out with the following output: *mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/transforms/cc_up.lta sub-1000_ses-2pre.long.sub-1000 will read input aseg from aseg.auto_noCCseg.mgzwriting aseg with cc labels to aseg.auto.mgzwill write lta as /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/transforms/cc_up.ltareading aseg from /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/aseg.auto_noCCseg.mgzerror: mghRead(/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/aseg.auto_noCCseg.mgz, -1): could not open file* Thanks for the assistance. Dan

2 4

How to get the parcellations to the initial space as before running recon all
by Reji, A. (Amal, Student M-EE) 17 Jun '24

17 Jun '24

External Email - Use Caution Hi, I was trying to get the mesh files for cortical parcellations after running recon all. I used the Ernie data set which is the example dataset given by SimNIBS.<https://simnibs.github.io/simnibs/build/html/dataset.html> I did recon all to the Ernie dataset and I got the parcellations. Now I want to get these parcellations to the same space as the space of Ernie. How can I convert the parcellations in the initial space? Looing forward to hearing from you Regards Amal Reji

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