Freesurfer January 2023

freesurfer@nmr.mgh.harvard.edu

87 participants
111 discussions

Image filter
by Ruifeng Dong 12 Jan '23

12 Jan '23

External Email - Use Caution Dear Freesurfer community, I wonder if Freesurfer uses any filter to deal with the noise in the image, before segmentation. If so, is the filter spatially local or nonlocal? Thanks. Best, Ruifeng

2 1

freeview: set file as read only
by Aaron Tanenbaum 12 Jan '23

12 Jan '23

External Email - Use Caution Hello, Is there a way to set a loaded volume as read only in freeview on the command line?

2 1

How to convert surface-based atlas to annotation?
by Andy Kim 11 Jan '23

11 Jan '23

External Email - Use Caution Dear FreeSurfer Developers, To analyze functional connectivity, I first got Shen 268 surface-based atlas from Neurovault. Now I want to extract average time series data from my subjects based on the atlas but I have no idea how to make annotation. All I have is .gii left and right hemispheres atlas files. When I tried mris_convert, it says: DA[0] has coordsys with intent NIFTI_INTENT_NONE (should be NIFTI_INTENT_POINTSET). Could you please give me any tips for making an annot file from surface-based atlas? Thank you in advance. Kind Regards, Andy (Junghyun) Kim

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Fw: error: Numerical argument out of domain; error: MRIhistogramLabelRegion: constant image\00
by adriana.jorge＠unibe.ch 11 Jan '23

11 Jan '23

External Email - Use Caution Hi FreeSurfer Developers, I'm trying to obtain brain parcellations/segmentations of a subject's brain, using T1 and T2 images, but when I execute the recon-all command, I get the following error message: error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image Segmentation fault Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux recon-all -s Test_withT2 exited with ERRORS at Tue Jan 10 13:17:00 CET 2023 The FreeSurfer version I'm currently using is the freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275, but I have also tried the exact same process (same command and same data) in the freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 version and got the exact same error message. When I tried running the recon-all again with the freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b version, no error was reported and the recon-all outputs were correct. Recon-all works for versions reesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 and freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 if I use only the T1 image. The recon-all logs for the 2 failed and the 1 successful attempts are attached here. Can you help me figure out what the issue is? Why can't I run the recon-all using both T1 and T2 in the latest versions? Best, Adriana Jorge

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ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage
by Yu Junhong (Dr) 11 Jan '23

11 Jan '23

External Email - Use Caution Hi there, I’ve been trying run recon-all on this public dataset https://secure-web.cisco.com/13AIuH-XEB3a4SQgLqeatTFX2txFlVseSmTdhYjjSnmJ3K… and I cant seem to complete the autorecon3 stage for any of the subjects. I’ve attached the log file. I’m using freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b #-------------------------------------------- #@# BA_exvivo Labels lh Mon Jan 9 05:39:18 +08 2023 ------------------------------------------------------------------------- ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version ------------------------------------------------------------------------- Linux hpc-gekko1 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-A00000300 exited with ERRORS at Mon Jan 9 05:39:18 +08 2023 I’ve also tried to recon-all with freesurfer 7.3.2. however I got stuck at the autorecon2 stage instead ERROR: cannot find or read transforms/talairach.m3z error: No such file or directory error: transforms/talairach.m3z: could not open transform I’m wondering if there is anything wrong with the data? The input file can be downloaded here https://secure-web.cisco.com/1kuOf_Y-BPoVdkGgGQL_IV4l7nF5eQ5cy4kb3Lu9CxxDEa… Thanks Junhong ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

2 2

Elephant brain MRI segmentation
by Malav Shah 11 Jan '23

11 Jan '23

External Email - Use Caution Hi all, I am trying to extract cortical thickness of elephant brain neocortex with structural MRI data. I have figured out a pipeline I can use to generate WM-GM and GM-pial matter surfaces. However, I feel stuck at the segmentation level. As a lot of MRI segmentation tools are optimised for human MRI with probability maps, they are not much helpful with elephant brain segmentation. Can anyone help me with these brains segmentation using other image processing tools? Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391

1 0

Re: [Freesurfer] mri_mask error exits returns a zero exit status
by fsbuild 10 Jan '23

10 Jan '23

External Email - Use Caution Just curious what output (if any) is echoed to the terminal when the failure occurs. - R. On Jan 10, 2023, at 13:23, Aaron Tanenbaum <aaron.b.tanenbaum(a)gmail.com> wrote:        External Email - Use Caution        Hello,FYI, I recently noticed that mri_mask returns a zero exit status when it is unable to write the output._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

To post on list
by hcw11 09 Jan '23

09 Jan '23

External Email - Use Caution hcw11(a)sfu.ca

1 0

Re: [Freesurfer] Virtualbox ova unzip password
by hcw11 09 Jan '23

09 Jan '23

External Email - Use Caution Hi, I am writing to request the password to unzip the virtual box containing Freesurfer 7 image. Thank you. Best, Debbie

1 0

TRACULA cluster statistics visualization
by Makenna B McGill 09 Jan '23

09 Jan '23

External Email - Use Caution Hi Freesurfer Developers, I'm using FS v7.2 to conduct along-tract statistics using trac-all -stat, and I was wondering how to best visualize and interpret the results of the cluster-wise correction in freeview. I referenced this page ( https://secure-web.cisco.com/1Wn0Jo3ZhV2QIp8R6uvzRorN2zYdL69NgfN7PXt5cTq22h…) which describes how to do this for uncorrected statistics, and used dmri_trk2trk to embed the *perm.th13.abs.sig.cluster.mgh files produced by mri_glmfit-sim into the template .trk files (--in $FREESURFER_HOME/trctrain/hcp/syn/"$tract".display.trk). However, I'm noticing inconsistencies in the location along the tract of significant clusters between the projection of the uncorrected statistics in freeview, projection of the corrected statistics in freeview, and the cluster location as indicated by the cluster summary file (*perm.th13.abs.sig.cluster.summary.txt). I've attached the cluster summary file for FA in the rh.cst tract as an example. My understanding is that for pathways with superior-inferior orientation, points along the tract are ordered from superior to inferior. Given that this significant cluster is at a VoxX of 68 (of 80 total points along the tract), I would have thought that this cluster would be located at a more inferior position along the right cst -- instead, the cluster appears to be located superiorly. Similar to this FS user ( https://secure-web.cisco.com/1W2wWzty4LvZ-noLr4zvkjNMq5qwway38c9kYyxk8c8a4A…) I'm wondering: (1) Am I missing something regarding this embedding process? (2) Is it appropriate to embed the *perm.th13.abs.sig.cluster.mgh file to visualize the results of the cluster-wise correction? Please let me know if there is any other information you'd like me to provide. Any thoughts on where I might be going wrong would be greatly appreciated. Thank you! Best, Makenna *Makenna McGill *(she/her) Doctoral Student in Clinical Psychology The University of Texas at Austin

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Freesurfer January 2023