Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

FreeSurfer container recipe?
by Bennet Fauber 06 Apr '23

06 Apr '23

External Email - Use Caution In reply to mail from Mitchell Horn, Douglas Greve replied > The math libraries changed between 7 and 8, nothing we can do about it. When I > have to run things on a centos8 machine, I generally run in a centos7 singularity > container (which we might be able to make available, without support:) Would it be possible to get just the Singularity definition file for the CentOS 7 Singularity image that you use posted to the FS wiki? We're happy to do the building, but having a file that lists the needed prerequisites that need to be installed via yum prior to installing FreeSurfer would be very helpful. It would also help to see how you handle the needed FSL components, and I think at least some portion of ANTs is needed for TRACULA, so even just which binaries are needed would be a help, too.. Thanks for considering this request, which I hope is not as burdensome as providing the fully built container.

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-gcareg dropped from -autorecon2-volonly
by Christopher Markiewicz 06 Apr '23

06 Apr '23

External Email - Use Caution Hi all, This is a duplicate of a bug report on GitHub (https://secure-web.cisco.com/1C5EnDIMtZh6wk0SJMqe8l166ycKmSdnL5atT3CIHDPAY1…) `DoGCAReg` was removed from `-autorecon2-volonly` in commit 4b9af5fc8c559e944400b885ef89f3682f94e0da, but this seems unrelated to the commit message. It's still in `-autorecon2`. Is there a reason it shouldn't be present, or was this a mistake? This issue affects versions 7.3.0+. Apologies for doubling up if you saw it; my impression is the mailing list is more actively monitored. Best, Chris

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Open research assistant position at Ohio State University
by Osher, David E. 06 Apr '23

06 Apr '23

External Email - Use Caution The Cognition and Brain Circuitry Laboratory at the Ohio State University is recruiting a research assistant. Primary duties include: conducting neuroscience research on the functional and structural architecture of the human brain, and its role in cognition; programming, running, and analyzing behavioral and brain-imaging experiments using functional magnetic resonance imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and behavioral assessments; scoring and coding data; performing statistical analyses using programs such as, MATLAB, Python, and shell scripting; recruiting research participants; maintaining participant databases; developing outreach letters. The position is available for one year with the possibility of extension based on satisfactory performance and availability of funds. Required qualifications include: Bachelor's degree in psychology, neuroscience, cognitive science, computer science, data science, engineering, physics, or math; conduct of social science research is required; experience in a social science research capacity. Highly desired: strong mathematical, statistical, and coding skills (e.g., MATLAB, Python, shell scripting); strong interpersonal skills for interacting with a diverse group of people; strong organizational skills. This position is an excellent opportunity for individuals considering future graduate studies in cognitive and computational neuroscience (every one of our research assistants has successfully been admitted into doctoral programs!). We are seeking an aspiring, self-motivated researcher with strong coding/programming skills who is excited about the brain, cognitive neuroscience, and/or clinical disorders and demonstrates evidence of a serious interest in a career in the field. If you are interested in being considered for these positions, please apply online at https://secure-web.cisco.com/1TciY0h9Hnogs0Vsz6IpkMg3S9JvHoraefFGDv9JWfB8mv… and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. David Osher at osher.6(a)osu.edu The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status. _____________________________________ David E. Osher, Ph.D. Assistant Professor of Psychology The Ohio State University davidosher.com<https://secure-web.cisco.com/1-CVKBQsgAyt6sw0qCo0o_YrQ6nEs-h_DI1v27Nd4YqU30…>

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some issues of -inflate operation
by 韦亚辉 06 Apr '23

06 Apr '23

External Email - Use Caution On Tues, 4 April 2023, YaHui Wei wrote:Hello freesurfers, I am getting some problems in pial reconstruction that the pial can not expand well to the real surface (result is below). Thus I’ve tried to check the ?h.inflated and ?h.inflated.nofix and found they had a large offset from the volume. The image below shows the volume, ?h.smoothwm and ?h.inflated. I wonder if the offset causing the pial reconstruction error, and if so how can I solve this problem. Can I get your suggestions? Thanks.

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mri_glmfit correction across lobes
by John Anderson 06 Apr '23

06 Apr '23

External Email - Use Caution Hello Freesurfer, Currently, I am using the Petsurfer manual, which is easily understandable and clear. Nonetheless, I have a question regarding the "mri_glmfit" step. As far as I know, this command is used to correct data for multiple comparisons among all the ROIs in the aparc+aseg.mgz file. Can you please confirm if my understanding is correct? mri_glmfit.bin --y lh.all.suvr.sm05.proj0.5.nii.gz --fsgd 2G0C.fsgd --C patients_vs_controls.mtx --surf fsaverage lh --cortex --glmdir lh.patinets_vs_controls In particular, I am interested in correcting data across lobes instead of across all ROIs. I followed the steps mentioned in the FS forum to create lobes, and I can observe lobe annotations in the wmparc.mgz file. I am curious to know whether using the "--annot" flag will adjust the p-values across different lobe ROIs instead of all ROIs in the aparc+aseg.mgz file. I have attempted this, but it appears to only change the name of the annotation in the final statistics file, and the p-value remains the same. Do I need to include any additional arguments in the command? Thanks for your help John

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lh.inflated and rh.inflated generated by mris_inflate is biased
by 韦亚辉 05 Apr '23

05 Apr '23

External Email - Use Caution On Tues, 6 April 2023, YaHui Wei wrote:Hello freesurfers, I found the ?h.inflated and ?h.inflated.nofix and found they had a large offset from the volume. The image below shows the volume, ?h.smoothwm and ?h.inflated. How can I solve this problem. Can I get your suggestions? Thanks.

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Updating to Current Version of Freesurfer
by Lauren Stephens 05 Apr '23

05 Apr '23

External Email - Use Caution Hello, We have been using Freesurfer v7.1.1 to process our data. We want to update to the v7.3.2. Can we continue to use the files from v7.1.1 which have our edits applied on the 7.3.2 version? Do we need to re-run recon-all on the files now using the 7.3.2 version? Thank you.

2 1

[FreeSurfer] error in talairach_afd
by Krystal Xiwing Yau 05 Apr '23

05 Apr '23

External Email - Use Caution Dear FreeSurfer experts, I am encountering the error below: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) As suggested, I have visited the website and followed these steps (https://secure-web.cisco.com/1sysqwtJ3yrcNBi951zfg6ki_eIkKSA8LC8npRZ7GbT_Bf…) However, I cannot move the bars as indicated; plus, there are no T1.mgz generated and the surf folder is empty. [cid:47451ebe-9ef9-4af4-8165-7a9c27bb0881] Much appreciated if anyone could advise. Thank you very much, Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

2 3

synthstrip error
by Salil Soman 05 Apr '23

05 Apr '23

External Email - Use Caution Hi, I am passing synthstrip an nii.gz file, and it keeps giving the error "ValueError: cannot determine file format from extension for test " (full error below). Any suggestions on how to fix this issue? The nifti files was made from dicom images using dcm2nnix. Thanks! Salil Configuring model on the CPU Running SynthStrip model version 1 Input image read from: test.nii.gz Traceback (most recent call last): File "/usr/local/freesurfer/7.3.2//python/scripts/mri_synthstrip", line 245, in <module> image.save(args.out) File "/usr/local/freesurfer/7.3.2/python/lib/python3.8/site-packages/surfa/core/framed.py", line 274, in save save_framed_array(self, filename, fmt=fmt) File "/usr/local/freesurfer/7.3.2/python/lib/python3.8/site-packages/surfa/io/framed.py", line 136, in save_framed_array raise ValueError(f'cannot determine file format from extension for {filename}') ValueError: cannot determine file format from extension for test

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How to use custom fill with up to other labels flag
by Dilara Erişen 05 Apr '23

05 Apr '23

External Email - Use Caution Hi, I want to create ROI labels by dividing the activation cluster from functional localizer scan into visual areas. I used to be able to do this by projecting the activation cluster together with visual area labels I have generated with retinotopy analysis onto the surface using tksurfer and using the flags: "up to functional values below threshold", "up to unlabeled" and "up to other labels". For example, if I want to fill the above threshold vertices in V2, it will fill it up to V1/V2 and V2/V3 boundaries. However, now that I moved my analysis pipeline to Freeview I'm having problems with "up to other labels" options. It prints "Did not fill/remove any vertices" on the terminal and nothing happens on the Freeview screen. Here are the steps I take: - I load the surface together with the overlay (functional localizer activation) and labels (from the retinotopy analysis: V1, V2 and V3) - I select the custom fill option and click on a vertex inside the visual area label. - I select "create new label" with "up to functional values below threshold", "up to unlabeled" and "up to other labels". - nothing happens (see attachment) Is this not the way the "up to other labels" option is intended to be used? If so, can you suggest another way to achieve my goal? Or is this a bug? Thank you, Dilara 1. FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76bhow 2. Platform: 22.04 LTS (Jammy Jellyfish) 3. uname -a: Linux ada 5.15.0-43-generic #46-Ubuntu SMP Tue Jul 12 10:30:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

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