Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30064 discussions

Re: [Freesurfer] Samseg lesion mask holes
by Cerri, Stefano,PHD 31 Mar '23

31 Mar '23

Hi Evie, --save-probabilities and --save-posteriors will save two different things for lesions. The former is an initialization of lesions based on intensity and location constraints, and the latter is a probability map of seg.mgz after we also introduce lesion shape constraints (Cf Fig.4 of https://www.sciencedirect.com/science/article/pii/S1053811920309563) The output of --save-probabilities should give you a very noisy lesion probability map with lots of false positives (at least this is my experience). In your case, it seems that too many *true* lesions are removed when the shape model is introduced. Would you be able to provide the command you're using to segment your T2-FLAIR scans? Which --lesion-mask-pattern values are you using for this input combination? Stefano Evie Neylon Tue, 28 Mar 2023 07:15:17 -0700 External Email - Use Caution Dear experts, I am running SAMSEG to segment MS lesions from T2 FLAIR scans. I wanted to create a lesion mask in order to obtain lesion volumes and lesion counts, so I used mri_binarize on seg.mgz to obtain all voxels with the value 99. However, upon visualising this mask I see that there are holes in the mask in regions that are quite clearly lesions based on the FLAIR image. I see in seg.mgz that these voxels are instead assigned incorrectly to a different tissue, as the lateral ventricle, for example. I wondered if this misassignation of tissue was due to the chosen threshold (0.3) so I added the --save-probabilties flag to look at the probability maps too, and I see that actually the probability map thresholded at 0.3 does not contain holes. The probability map actually seems more accurate in general and picks up on more of the hyperintensities. This is important for my desired outputs (i.e. accurate lesion counts/volumes). So I wondered if it was possible to explain a little why these holes might be occurring in the final segmentation but not the probability map? Would it be incorrect to derive the lesion mask from the probability map instead? Apologies I cannot attach the images of the data. TIA, Evie _______________________________________________ Freesurfer mailing list Freesurfer(a)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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Regressing out unconditioned stimulus
by Gillian Grennan 30 Mar '23

30 Mar '23

External Email - Use Caution Hi Freesurfer Developers, I am analyzing a fear conditioning imaging study and am attempting to regress out the shock/unconditioned stimulus by adjusting the modulation weights in my par file. I set the stimuli presented with the shock (CS+) with a modulation weight of -1 and set all other unshocked/unpaired stimuli (CS- and fixation) with a weight of 1. Similarly, we have a few CS+ trials where the participants are expecting a shock but didn't receive one -- I have been setting these with a modulation weight of 1 similar to the CS- and fixation stimuli. I attached a copy of our .par file. Could you let me know if this makes sense for our analyses? Best, Gillian Grennan

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kvlThresholdImage: command not found
by Song, Xinrui 30 Mar '23

30 Mar '23

External Email - Use Caution Hello Dear Developers, I am trying to segment ex vivo hemisphere brains following instructions here "https://secure-web.cisco.com/1aMllqwj8kw45W6STdIjlcZduOuYMIQpzI8UIeO-4ITFYp…". I was just proceeding to the Segment White Matter section and found that none of the kvl commands can be found in my installation. They are also not found in the freesurfer/bin folder. I searched the archive and found that there was one case that's very similar to mine, but it occurred back in 2012 and on a Mac distribution. (https://secure-web.cisco.com/1l-Cmn5p7-rI6gQsdH_JGo18SYVHYKwuPuWwgNbpZRVRkl…) Freesurfer version: freesurfer_ubuntu20-7-dev_amd64.deb Platform: WSL-Ubuntu on Windows.

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error with synthsr in Mac M1
by hmarzban＠student.ubc.ca 30 Mar '23

30 Mar '23

External Email - Use Caution Hi developers, I'm Using freesurfer-darwin-macOS-dev.pkg (the ) which is developed in march 2023. Also my system is Apple M1 max (MacOS Ventura 13.2.1). When I run synthsr, I receive an error: mri_synthsr --i /Users/Hyperfine/028 --o /Users/Hyperfine/028/synthsr --threads 2 --lowfield Traceback (most recent call last): File "/Applications/freesurfer/dev/python/scripts/mri_synthsr", line 10, in <module> import surfa as sf File "/Applications/freesurfer/dev/python/lib/python3.8/site-packages/surfa/__init__.py", line 19, in <module> from .image import Volume File "/Applications/freesurfer/dev/python/lib/python3.8/site-packages/surfa/image/__init__.py", line 1, in <module> from .framed import FramedImage File "/Applications/freesurfer/dev/python/lib/python3.8/site-packages/surfa/image/framed.py", line 24, in <module> from surfa.image.interp import interpolate File "surfa/image/interp.pyx", line 1, in init surfa.image.interp ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 80 from PyObject Have you had a similar issue before? Any advice? Many thanks in advance. Regards Hengameh

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Re: [Freesurfer] HPC Usage - Moving On from CentOS7
by Horn, Mitchell Jacob 30 Mar '23

30 Mar '23

As an update I’ve tested another run (bert, 7.2.0, no flags, recon-all) on an OS-8 system but set LD_PRELOAD to the 7 system’s libm.so: export LD_PRELOAD=/alma/cos7lib/libm.so recon-all …. And that produced the equivalent results of all my CentOS7 runs: [Table Description automatically generated with low confidence] I believe this is very important information to the general community for stability with the imminent and inevitable switch to OS-8 HPC platforms. Best, Mitch

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Seed-based fcMRI: mean BOLD post nuisance regressor
by Vinke, Louis N.,PHD 30 Mar '23

30 Mar '23

Hello, After running a seed-based connectivity 1st level analysis on an individual subject, is it possible to pull out the mean BOLD activation (across all time-points; all runs) in a way that any “noise” in the time-series has already been regressed out (i.e., motion, ventricle, csf, wm, global mean, high/low pass filter)? I imagine it is one of the outputs in the analysis folder and not found within any particular FC seed sub-folder (containing pcc.nii.gz, etc.). In other words, one may run different seed-based connectivity analyses, but the mean activation estimate will not change so long as the nuisance parameters stay the same. The meanfunc overlay looks to be what I’m interested in, but unclear if this is created after regressing out nuisance parameters. Thanks. -Louis

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(no subject)
by Rachel Wagner 30 Mar '23

30 Mar '23

External Email - Use Caution Please unsubscribe me

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Pass code
by BREUILLY MARINE 30 Mar '23

30 Mar '23

External Email - Use Caution Hello, I have downloaded the FreeSurfer Vitrual VM images for my research project and a pass code is required to open the image. As mentioned in the guidelines https://secure-web.cisco.com/1oZit62PBJoLikTlTdvtgmPiBPc4ThiBZJNpYfu6IvCxQz…, we need to send an email to the help list. Could you please send me the pass code for FS_7_2_0_ubuntu_18_04_06.ova.7z ? Thank you in advance, Best regards, ---- Marine BREUILLY Chercheure postdoctorale Plateforme LyMIC CIQLE, Faculté de médecine Rockefeller, Université Claude Bernard Lyon 1 8 avenue Rockefeller, 69008 LYON tel: +33(0)660033005

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errors with running recon-all -autorecon1
by 张思敏 29 Mar '23

29 Mar '23

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to run the command: recon-all -subjid <subname> -autorecon1. I'm getting the an error message and the error log reads as follows: error: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Then I run the command: recon-all -subjid <subname> -autorecon1. I get the same error as before. Finally, I run the command: tkregister2 --s subjid --fstal. But I am new to Freesurfer so I can't get the meaning of the output after running that command. How do I know if this is true？I‘ve attached the tkregister2.png and the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0 2) Platform: MacOS release 10.15.7 (Catalina) 3) uname -a: Darwin zsilencedeMacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_644) recon-all.log: see attached 5) tkregister2.png: see attached Thanks!

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Tracula, trac-all, bug in interreg
by Tan Li Kuo 29 Mar '23

29 Mar '23

External Email - Use Caution Hi, I've been trying to configure Tracula to use different inter-subject registration methods. It fails for type #3 (robust cost) and #4 (nonlinear CVS). From the trac-all script (line #1634), it looks like Tracula points to different trctrain templates depending on the registration method used (mni, rob, cvs, syn, fnt). The problem is, the FreeSurfer distribution appears to only include template files for mni and syn. E.g., $FREESURFER_HOME/trctrain/hcp/mgh_1001 Basic info: 1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 2) Platform: Ubuntu 22.04.1 LTS 3) uname -a: Linux medphys-rtx 5.15.0-53-generic #59-Ubuntu SMP Mon Oct 17 18:53:30 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Thanks! -- Tan Li Kuo Medical Physics, Dept. Biomedical Imaging Faculty of Medicine Universiti Malaya -- " PENAFIAN: E-mel ini dan apa-apa fail yang dikepilkan bersamanya ("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat-pendapat, rumusan-rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Malaya adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut. DISCLAIMER: This e-mail and any files transmitted with it ("Message") is intended only for the use of the recipient(s) named above and may contain confidential information. You are hereby notified that the taking of any action in reliance upon, or any review, retransmission, dissemination, distribution, printing or copying of this Message or any part thereof by anyone other than the intended recipient(s) is strictly prohibited. If you have received this Message in error, you should delete this Message immediately and advise the sender by return e-mail. Opinions, conclusions and other information in this Message that do not relate to the official business of University of Malaya shall be understood as neither given nor endorsed by any of the forementioned. "

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