Freesurfer November 2021

freesurfer@nmr.mgh.harvard.edu

77 participants
118 discussions

Re: [Freesurfer] Matlab Runtime download error (on MacOS)
by fsbuild 08 Nov '21

08 Nov '21

External Email - Use Caution Hello Stephanie, If you installed 7.2.0 using the Mac pkg installer, then FREESURFER_HOME is /Applications/freesurfer/7.2.0.  If you installed elsewhere however, then change FREESURFER_HOME in the command below to the appropriate path for your setup AND likewise change the path to the fs_install_mcr script You can try running the fs_Install_mcr script as follows, telling it do download and install the Matlab runtime environment for release 2014b, e.g., $ sudo FREESURFER_HOME=/Applications/freesurfer/7.2.0   /Applications/freesurfer/7.2.0/bin/fs_install_mcr  R2014b<much output deleted> … then if the install worked you should see … $ ls /Applications/freesurfer/7.2.0/MCRv84Contents/        bin/             help/            mcr/             remote/          runtime/         toolbox/MCR_license.txt  etc/             java/            patents.txt      resources/       simulink/        trademarks.txtappdata/         extern/          license.txt      polyspace/       rtw/             sys/ While the 7.2.0 release was built and tested with R2014b, this release is too old to be supported on M1 Macs by The Mathworks and so you may get run time errors.  This should be updated in a future point release of freesurfer though. - R. On Nov 8, 2021, at 16:26, Stephanie Otto <sotto(a)nevada.unr.edu> wrote:        External Email - Use Caution        Greetings Freesurfer Team,I am working on a new Macbook with the M1 chip. So far, I've had little issue with installation (7.2..0) and running recon-all. I am trying to run the thalmic nuclei and brainstem segmentations in preparation for running TRACULA, which required me to install the MCR package. I can't seem to make this work no matter what I try and I keep getting the following installation error:"./install: line 334: /var/folders/6m/d_9165656qdc255vpbs0byr40000gn/T/tmp.0tmo1FBB/bin/unknown/install_unix: No such file or directoryls: /var/folders/6m/d_9165656qdc255vpbs0byr40000gn/T/tmp.0tmo1FBB/install-target/v*: No such file or directory" I'm at my wits end here and would really appreciate any insight you may have on how to troubleshoot this. While I have you here, are there any known issues with running TRACULA on these new M1 machines? Thanks in advance for your help and time!Kind regards,Stephanie OttoDoctoral Candidate, Cognitive and Brain Sciences ProgramDepartment of Psychology, MSS 424/MS0296University of Nevada, Renosotto@nevada.unr.edu _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh..harvard.edu/mailman/listinfo/freesurfer

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Matlab Runtime download error
by Stephanie Otto 08 Nov '21

08 Nov '21

External Email - Use Caution Greetings Freesurfer Team, I am working on a new Macbook with the M1 chip. So far, I've had little issue with installation (7.2.0) and running recon-all. I am trying to run the thalmic nuclei and brainstem segmentations in preparation for running TRACULA, which required me to install the MCR package. I can't seem to make this work no matter what I try and I keep getting the following installation error: "./install: line 334: /var/folders/6m/d_9165656qdc255vpbs0byr40000gn/T/tmp.0tmo1FBB/bin/unknown/install_unix: No such file or directory ls: /var/folders/6m/d_9165656qdc255vpbs0byr40000gn/T/tmp.0tmo1FBB/install-target/v*: No such file or directory" I'm at my wits end here and would really appreciate any insight you may have on how to troubleshoot this. While I have you here, are there any known issues with running TRACULA on these new M1 machines? Thanks in advance for your help and time! Kind regards, Stephanie Otto Doctoral Candidate, Cognitive and Brain Sciences Program Department of Psychology, MSS 424/MS0296 University of Nevada, Reno sotto(a)nevada.unr.edu

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mri_label2label issues
by Trisanna Sprung-Much 08 Nov '21

08 Nov '21

External Email - Use Caution Hi there I created labels on surfaces of subjects (chimp) registered to a particular volumetric template. The labels were created on the surfaces in Freeview using Freesurfer 7.1. Since creating these labels, I improved the intensity inhomogeneity in the scans and re-ran the surfaces. When I try to use mri_label2label to transpose the labels to the new surfaces of each subject, the labels do not fall exactly where they should. In fact, the surfaces themselves have a slight translation in them (see snapshot). I assume this is because my registration to the template that I did prior to running recon-all is differing somehow between the 2 groups. However, I thought that this should not matter since mri_label2label --regmethod surface is using the sphere.reg to fsaverage. I am wondering if there is anything I can do to improve mri_label2label to avoid editing the labels manually? Thank you for your time, Trisanna -- Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute

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recon-all stuck at -fill on AWS batch processing
by Xin Qi 08 Nov '21

08 Nov '21

External Email - Use Caution Hello FreeSurfer Developers, We are attempting to use recon-all -all on T1w MRI image analysis. We tested it on AWS EC2 in a docker container successfully. The uname -a output the EC2 is Linux ip-10-193-42-20 5.11.0-1019-aws #20~20.04.1-Ubuntu SMP Tue Sep 21 10:40:39 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux. The docker file entrypoint is a job_script.py python code to call a subprocess of bash script, like recon-all using a python library called subprocess. When we used the same docker image with AWS ECS or batch processing, from the files created inside the processed subject's mri folder,* the recon-all stuck at "-fill" step because the input files (wm.mgz, aseg.auto_noCCseg.mgz, and transforms/talairach.lta) are created, but NO filled.mgz was created as the output file of "-fill " step in recon-all -autorecon2. * I have searched the list and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this? Also I have attached the reon-all.log in cas it is of any use. 1). FreeSurfer version: 7.2.0 2). Platform: AWS EC2 batch or ECS Fargate Looking forward to your feedback. Best Regards Xin

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Re: [Freesurfer] crash
by fsbuild 08 Nov '21

08 Nov '21

External Email - Use Caution Hello Nikolai, A posting from September lists some things you can try, https://secure-web.cisco.com/1PKZyepuYOeN_yDWbDmVHAh4TMYVweK8V3VAatHz0Mcg8M… I would try getting a new license file first.  I will send the text to your email as well. - R. On Nov 6, 2021, at 16:30, Nikolai Chapochnikov <nchapochnikov(a)gmail.com> wrote:        External Email - Use Caution        Hello,I just installed freesurfer 7.2.0 on mac os 11.6 using the pkg. Freeview opens, but as soon as I select a nii file to load, it crashes.Here is the report I get:MailScanner has detected a possible fraud attempt from "secure-web..cisco.com" claiming to be https://secure-web.cisco.com/16Gxapjkgf3ogWhosdJ4k4oFRwyTpquPg8gS5b… someone please help with this?Thank you very much!Nikolai_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer

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Brain Volume Extraction
by Mohanad Arafe 08 Nov '21

08 Nov '21

External Email - Use Caution Hello, I am new to FreeSurfer and I have a question regarding brain volume extraction. When I run recon-all on a patient, once the entire process is done, I get the brain volume levels from aseg.stats. I would like to know if there are any ways to do so without going through the entire process of 30+ steps. I need to extract brain volumes from ROIs of 100+ patients. Thank you

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Aseg and wm edits? + white/pial overlap near subcortical structures
by Kang, Jee Won 08 Nov '21

08 Nov '21

External Email - Use Caution Hello all, ? There are two topics I would appreciate your expert advice on: Topic 1: Aseg and wm edits I was going through the wiki and the archive of past inquiries and was unable to find a clear answer to whether you can make aseg edits and wm edits, and then re-run in Freesurfer at the same time. Furthermore, I was just a little unclear as to how exactly to perform aseg edits. According to this post: https://secure-web.cisco.com/1RxWuWDKVwztKCLSwXj6z1drGBPyh2kvn_19UWiYuyqKvR…,<https://secure-web.cisco.com/1RxWuWDKVwztKCLSwXj6z1drGBPyh2kvn_19UWiYuyqKvR…> you are supposed to edit aseg.manedit.mgz, and only make edits to wm.mgz if segmentation is still incorrect after re-running. The command suggested to be used is recon-all -s subject -autorecon2 -nogcareg -nocanorm -nocareg -autorecon3. However, according to this post: https://secure-web.cisco.com/12Lq8z3kDRX5hmVV3-U_tQM9lMGELV_rZuE0w7MEaZ6-3f… and the wiki page it references here: https://secure-web.cisco.com/1Ktb4SEXIjUqckJnfQRhLq0dVZmG77-DlcegK4GTCJhXvP…,<https://secure-web.cisco.com/1Ktb4SEXIjUqckJnfQRhLq0dVZmG77-DlcegK4GTCJhXvP…> you are supposed to edit aseg.presurf.mgz, and doesn't mention whether aseg edits are compatible with wm.mgz edits. The command these posts say you should run is recon-all -autorecon2-noaseg -autorecon3 -s subject, and this is also listed in the "OtherUsefulFlags" table. My questions are: 1) Does it matter which volume, aseg.presurf.mgz or aseg.manedit.mgz that you edit? 2) What is the proper command to use for re-running with aseg edits? 3) Can you make edits to wm.mgz and aseg edits and re-run with both edits being taken into account? For some background into why I've been looking into editing aseg segmentations, we have a sizeable portion of our data for whom the lateral ventricles are being mislabeled as wm (for some this is quite mild, for others it is pretty extensive). I know the -big-ventricles flag is an option, but we are not looking to re-run all of our subject with it at this time, as we have 100+ subjects. Topic 2: White/pial overlap near subcortical structures Sometimes, the pial surface near the subcortical structures will "pull back" too much, I've attached an example image. This "pull back" sometimes appears after I've re-run the subject after making wm edits, when it was not present in before re-running. In the attached example image, the original pial surface before re-running is in blue, the new pial surface is in red. The original white surface is in green, the new white surface is in yellow. I have the aparc+aseg.mgz and wm.mgz visible. As shown in the image, this "pull back" will often end up exclude a chunk of voxels from the aseg and aparc+aseg, even if there are wm.mgz voxels filled in that area. How important is it to fix errors in this area in general, and would aseg edits be appropriate since wm edits don't seem to address the problem? Thank you for your insight into these topics! Sincerely, Jee Won

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Confusion about discrete variable in the FSGD file
by Thalhammer, Melissa 08 Nov '21

08 Nov '21

External Email - Use Caution Dear FreeSurfer users, I am interested in cortical thickness differences between preterm (PT) and fullterm (FT) individuals. I have used DODS with mri_glmfit and wanted to regress out scanner (4 sites) and sex in the analysis, using the attached FSGD file. Both of the variables are discrete and I have found different information on how to include discrete variables into the model. I have followed Andrew Jahn's blog at first who includes discrete variables in the variable list just as continuous ones and specifies them with values of 0 or 1 (https://secure-web.cisco.com/1mCX947TtGflWAdnM3CtHlWXx5Aa4vkeu9B25dEdIVjquj…) I have adapted this procedure and have specified my gender values as 1 and 2 (simply because it was stated like this in the participants information sheet I have received). Recently, I have read a post on the mail archive, where Doug states: "you should not code gender and handedness as a continuous variables. In doing this, you are saying that you expect right handers to have 2x the thickness as left handers (or females to have 2x the thickness as males)" (https://secure-web.cisco.com/1A4RpPVoEFVSno401uhBm0BawiKw27S9-5VpEg7YyqN3rI…) When following this argument, this would also hold for continuous variables, i.e., a patient aged 50 would have 2x the thickness of a patient aged 25. So my question is how to correctly deal with discrete variables and why you have suggested to code gender as classes instead of variables. What is the actual difference? How does the model treat classes and variables? Cheers and many thanks in advance, Melissa Thalhammer

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adding covariates to a longitudinal glmfit model
by Zeng, Qi 08 Nov '21

08 Nov '21

External Email - Use Caution Hi Experts, After completing long_mris_slopes to get the rate of change and then concatenating them into one.mgh file for group analysis (mris_preproc). I am finally getting to mris_glmfit. Got a couple of questions along the way. 1). if I conducted long_mris_slopes, and got for example, lh.long.thickness-rate.fwhm10.fsaverage.mgh. Do I need to do a surface smoothing again (mri_surf2surf) before mris_glmfit? 2). I construct covariates in FSGD besides the group contrast that I am interested in. How do I add covariates into the glmfit model to control for the covariates as I contrast groups in terms of the rate of changing (CV vs. NCV groups) . Do I add them into --C as (1, -1, 0(age), 0(gender), 0(race)). mri_glmfit --y {$hemi}.{$meas}-rate.{$smoothness}.mgh --fsgd FSGD/{$study}.fsgd doss --C Contrasts/CV-NCV.mtx (1, -1) --C Contrasts/NCV-CV.mtx (-1, 1) --surf fsaverage {$hemi} --cortex --glmdir {$hemi}.{$meas}-rate.{$study}.{$smoothness}.glmdir Best, Zeno --

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tksurfer
by Arian Klows 08 Nov '21

08 Nov '21

External Email - Use Caution Hi experts, I recently downloaded the freesurfer and am testing it. I tried tksurfer, but the editor window is blank. Please see below. Can anyone please help me in resolving this issue!? [image: image.png] Is this an internal problem with my computer? If anyone knows an alternative way to visualize the window, please let me know. Thanks, A

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Freesurfer November 2021