Freesurfer February 2022

freesurfer@nmr.mgh.harvard.edu

83 participants
132 discussions

GLM analysis - volume and surface area
by Laura Willers de Souza 21 Feb '22

21 Feb '22

External Email - Use Caution Hello FreeSurfer Developers, I would like to know if it is correct to perform volume and surface area analysis using freesurfer's GLM!? In several mailing list questions I have already seen instructions for performing these types of analysis. But I understand that freesurfer does vertex-wise analysis in the 2D surface space. So, it is not clear to me how it is possible to evaluate a 3D measurement, as volume, with a 2D method!? I've also read that surface area analysis via vertex-wise analysis doesn't make much sense. The best would be to do ROI-based analysis. Can you explain that to me? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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vertex indices in EPI space - mri_surf2vol registration issues
by Gomez, Daniel 21 Feb '22

21 Feb '22

Dear FS users, I’m trying to get surface indices from surfaces generated with recon-all into a volume in native functional/EPI space. I’m using mri_surf2vol for that, though if there is a better alternative solution, I’m happy to take it. My issue is that the output index volume (vtxvol) I get from mri_surf2vol does not seem to ever be properly aligned/registered with the target space. Here's the command I run (I'm interesting in vtxvol.nii.gz) mri_surf2vol --reg anat2epi.dat --hemi lh --vtxvol vtxvol.nii.gz --fillribbon --outvol foo.nii.gz --template epi.nii.gz --mkmask Upon further investigation, I learn I can’t get the projection to work properly even if I try projecting the surface onto the native anatomical space. As in: mri_surf2vol --hemi lh --vtxvol vtxvol.nii.gz --fillribbon --outvol foo.nii.gz --template ../mri/orig.mgz --mkmask --identity sub-01 Given the output vtxvol doesn't even have the same dimensions as the template specified in the command line, it makes me think I’m doing something wrong: > nib-ls vtxvol.nii.gz ../mri/orig.mgz vtxvol.nii.gz float32 [320, 320, 320] 1.00x1.00x1.00 sform ../mri/orig.mgz uint8 [320, 320, 320] 0.75x0.75x0.75 What is the proper way to get vertex indices in EPI space? Thank you, Daniel -- Daniel Gomez, Ph.D. MR Physics and Instrumentation Group A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 USA dgomez1(a)mgh.harvard.edu

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Confusing Permissions Error
by Jacoby, John 21 Feb '22

21 Feb '22

Hi all, I have a recon that looks like it ran (almost) to completion, but then threw a permissions error in the stdout and directed me to the log. I can't determine what the issue might have been. I've attached the .log file as well as .error and .done files. I'll also paste the end of the stdout below because for some reason the permissions error was not captured by the log file. I appreciate any insight anyone can give. Best, John end of stdout: tee: /autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log: Permission denied setting seed for random number generator to 1234 total integrated curvature = 26.759*4pi (336.266) --> -26 handles ICI = 173.9, FI = 1548.0, variation=24893.111 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. @#@FSTIME 2022:02:17:09:34:06 mris_curvature N 4 e 1.41 S 0.03 U 1.30 P 94% M 157860 F 0 R 20801 W 0 c 20 w 53 I 0 O 2176 L 1.29 1.25 1.20 @#@FSLOADPOST 2022:02:17:09:34:07 mris_curvature N 4 1.29 1.25 1.20 Linux erso.nmr.mgh.harvard.edu 4.18.0-365.el8.x86_64 #1 SMP Thu Feb 10 16:11:23 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux tee: /autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log: Permission denied recon-all -s sub-LALM61_ses-LALM61 exited with ERRORS at Thu Feb 17 09:34:08 EST 2022 tee: /autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log: Permission denied tee: /autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log: Permission denied For more details, see the log file /autofs/vast/bandlab/studies/kyoto_preliminary/data/derivatives/freesurfer/sub-LALM61_ses-LALM61/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting BugReporting - Free Surfer Wiki<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> top. Bug Reporting. Submitting a request for help . When submitting a request for help with your problems please be aware that the developers will try and repeat your ... surfer.nmr.mgh.harvard.edu

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Subject ID error with bbregister
by Tisdall, Dylan 21 Feb '22

21 Feb '22

External Email - Use Caution Hi all, Quick question on a puzzling error with bbregister version 7.1.1. When I run: bbregister --s 126346 --mov mgz/7T_MEMPRAGE --init-reg 7Tto3Tinit.lta --reg 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 I get the error: ERROR: must spec a subject id which I thought I'd done with the --s flag. What am I missing? Even more odd, if I just move the to the end of the command, bbregister will run, but eventually fails with: error: mghRead(/hom/mtisdall/Research/7TAnalysis/subject//subject-unknown/mri/orig.mgz, -1): could not open file Is there something obvious I'm doing wrong with these two command lines that cause these behaviors? Thanks, Dylan

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Re: [Freesurfer] Subject ID error with bbregister
by Glasser, Matt 21 Feb '22

21 Feb '22

External Email - Use Caution Hi Dylan, I call bbregister with --s in the same place you have it. Is it possible there is something wrong with $SUBJECTS_DIR when you are calling bbregister? Matt. On 2/21/22, 2:43 PM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Tisdall, Dylan" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of mtisdall(a)pennmedicine.upenn.edu> wrote: Hi all, Quick question on a puzzling error with bbregister version 7.1.1. When I run: bbregister --s 126346 --mov mgz/7T_MEMPRAGE --init-reg 7Tto3Tinit.lta --reg 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 I get the error: ERROR: must spec a subject id which I thought I'd done with the --s flag. What am I missing? Even more odd, if I just move the to the end of the command, bbregister will run, but eventually fails with: error: mghRead(/hom/mtisdall/Research/7TAnalysis/subject//subject-unknown/mri/orig.mgz, -1): could not open file Is there something obvious I'm doing wrong with these two command lines that cause these behaviors? Thanks, Dylan _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1wND93MoprFSyHH-F94sUpXKmf26HHTyp_vwiNVZHarL9o… ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] Question glm analysis g4v0
by Laura Willers de Souza 21 Feb '22

21 Feb '22

External Email - Use Caution Got it! The 4 groups I'm testing are: CU cortisol low; CU cortisol high; CI cortisol low; CI cortisol high. So if I found a significant cluster for this contrast, can I interpret that the cortical thickness of this region of the cluster is affected by both the diagnosis and cortisol levels? In this case I made the correction of multiple comparisons with positive direction. That means that the worse the diagnosis and the cortisol levels (CI cortisol high) the more the cortical thickness of this region of the cluster will be affected, or to draw this conclusion would I need the results of the other contrasts as well? Thanks so much for all the help! Best, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil ________________________________ De: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Enviado: quinta-feira, 17 de fevereiro de 2022 20:25 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Assunto: Re: [Freesurfer] Question glm analysis g4v0 No, that was only for interactions between the covariates and the groups On 2/17/2022 10:05 AM, Laura Willers de Souza wrote: External Email - Use Caution Hello FreeSurfer Developers, I am performing a GLM analysis to assess cortical thickness between 4 groups, without any covariates. I followed exactly what is on the wiki MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1U3sqGZa-FRgmgKfJEevEk2EOd_uv7vQJWJjf_LYazWAn4…<https://secure-web.cisco.com/1VuhMA49mKmIDKH_rGPy4c67MdbjL6bNv2i_WwNDwvMA5-…> In a previous analysis (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1RhFqzblDwAITsckPrr706fDxu-1VP5A0p_2Z1L_dV6eBL…<https://secure-web.cisco.com/1qw-8Oc7vg0Tc3_ilXhnADw1_lWmUuUCQVr-MNNAiNRRR1…>), Dr Douglas had told me that before any analysis I should test whether the interaction is significant or not. I would like to know if this also applies to this case, the interaction being tested by contrast number 7 of the wiki. Thanks in advance! Best, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1opnu8lzUFtpkWbHA-714sXrzRJWxeI-j3CsFLaYe-LC2A…

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Postdoc opportunity at UCLA
by Arpana Annie Gupta 21 Feb '22

21 Feb '22

External Email - Use Caution POST-DOCTORAL RESEARCH FELLOW CENTER FOR NEUROBIOLOGY OF STRESS AND RESILIENCE UNIVERSITY OF CALIFORNIA LOS ANGELES Background: The Center for Neurobiology of Stress and Resilience in the Division of Digestive Diseases at the University of California Los Angeles is seeking a full time Post-Doctoral Research Fellow for an R01-funded project studying the brain-gut microbiome mechanisms of action underlying obesity. The Center is a multidisciplinary team conducting clinical, translational and basic research with human populations. The postdoctoral fellow will work directly with Dr. Arpana “Annie” Gupta, PhD and other faculty collaborators. This project uses multimodal MRI sequences combined with measures of the gut microbiome and dimensional neuropsychiatric behavioral measures (i.e. tasks, questionnaires, heart rate variability, digital phenotyping, cognitive and clinical measures) to study structural and functional circuit dynamics in obesity. There will be opportunities to develop translational and clinical research skills (e.g. target discovery, individualized treatment development and biomarker/predictor development), in addition to analysis methods and pipelines to address basic and pathophysiological systems biology questions. There will be many opportunities to lead high impact publications starting on day one. We will be working with existing unique datasets in addition to creating new ones. Extensive mentorship will be provided to facilitate the transition to an independent research career. Duties and Responsibilities: The Post-Doctoral Fellow’s responsibilities will include, but are not limited to: 1. Model complex datasets including imaging, gut microbiome, inflammation, behavioral and clinical data. 3. Coordinate the acquisition of data working with a team of research assistants. 4. Be able to contribute to manuscripts, grants and publish Qualifications: 1. Ph.D. in Engineering, Epidemiology, Mathematics, Statistics, Computer Science or a related field. 2. Strong proficiency and independence with large data analysis platforms (such as neuroimaging or microbiome platforms), multivariate modeling strategies and network connectivity analyses. 3. Established quantitative and statistical skills, including strong programming skills and comfort with diverse computing environments. Comfortable using R. 4. Background in bioinformatics systems/cognitive neuroscience, neuroanatomy or psychological/clinical constructs. 5. A demonstrated capacity to write first author publications. 6. Great writing skills, motivated and driven to publish. Additional Qualifications: 1. Connectomics network analysis and machine learning modeling confer a very significant advantage. Additional Information: This is a 2 to 5-year term position with great opportunities for training in human systems biology, translational/clinical applications and diverse integrated methodologies. Applications can be submitted via https://secure-web.cisco.com/1cL6LdftaUrm2V4leqOxIwAsivDpS5DwRpOwjDHVkMasSU… <https://secure-web.cisco.com/1cL6LdftaUrm2V4leqOxIwAsivDpS5DwRpOwjDHVkMasSU…> If you have any questions please email Dr. Arpana Gupta (AGupta(a)mednet.ucla.edu <mailto:AGupta@mednet.ucla.edu>) and include a CV, cover letter and names of three references. Arpana "Annie" Gupta, Ph.D. Associate Professor Director: Neuroimaging Core G. Oppenheimer Center for Neurobiology of Stress and Resilience Ingestive Behavior and Obesity Program UCLA Vatche and Tamar Manoukian Division of Digestive Diseases David Geffen School of Medicine UCLA CHS 42-210, 10833 Le Conte Avenue | Los Angeles, CA 90095-7378 Email: agupta(a)mednet.ucla.edu <mailto:agupta@mednet.ucla.edu> https://secure-web.cisco.com/178l8jWLTKq8hEg73cz2xNMQqXOZCFR7JJ5Cukg7_1LCNx… | Twitter: @AGuptaCNS This message (including any attachments) contains confidential information intended for a specific individual and purpose, and is protected by law. If you are not the intended recipient, you should delete this message and any disclosure, copying, or distribution of this message, or the taking of any action based on it, by you is strictly prohibited.

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Fw: Freeview problem - can't see surfaces, hidden behind volumes
by Harriet Dempsey-Jones 20 Feb '22

20 Feb '22

External Email - Use Caution Hi there, I am having a weird problem with freeview… When l load some volumes and some surfaces together, I can’t see the surfaces because they are hidden ‘behind’ the volumes. They normally sit on top, but now I can only see them if I toggle off the volumes – which is not useful as I need both at once. They are definitely in alignment as I can see them when I toggle, and when I look at old data that I know I could view properly (and surfaces-volumes are in alignment) I have the same issue. I can't move them up, as you can only move position within volumes and surfaces. I tried to attach a video but my email got bounced for being too large - happy to send directly if it is helpful I am using the below code to load things (though have also manually loaded stuff in freeview). The code has not changed since it worked in the past… I have tried searching the freesurfer help, but can’t find anything on my issue… Any help would be appreciated Thanks! Harriet p.s., I am using freesurfer/ freeview on a remote machine of my university. They inform me no updates have been performed CODE freeview -v mri/T1.mgz \ mri/brainmask.mgz \ mri/wm.mgz:visible=0 \ -f surf/lh.smoothwm:edgecolor=yellow \ surf/lh.pial:edgecolor=red \ -viewport cor -layout 1

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Re: [Freesurfer] Linux Novice (VM_67 root vs. developer permissions)
by fsbuild 20 Feb '22

20 Feb '22

External Email - Use Caution Hello Randy, You can set SUBJECTS_DIR (via export command) to point a directory, e.g., where you have write permission.  You always have permission to write to your home directory, which in the VM is the path /home/developer.  The home directory path is saved in the shell environment variable $HOME. So you could make a writeable directory for subjects under developer’s home directory.  (Below, pwd command = print working directory path). $ echo $SUBEJCTS_DIR/usr/local/freesurfer/7.2.0/subjects$ cd $HOME$ pwd/home/developer$ mkdir subjects_new$ cd subjects_new$ pwd/home/developer/subjects_new$ export SUBJECTS_DIR=$HOME/subjects_new$ echo $SUBJECTS_DIR/home/developer/subjects_new It should work to drag and drop a file *from* Windows Explorer *into* the VM using the Linux file browser GUI in developer’s home directory (or where you have write permission).  That is the example on page 19 of the VBox_load_image.pdf doc found under https://secure-web.cisco.com/12je3qk7PjFfZ8id7gOdQ3NmuWY5iAVuERB… The example is dragging in the single license file (assuming you downloaded it on the Windows side). You can also run a browser directly in the linux VM (uses the Windows host network connection) and download files directly into the VM from any web location, e.g., the license file.  There should be a Firefox browser icon to double click on in the upper left hand corner of the VM window under “Activities”.  Firefox downloads files into /home/developer/Downloads which you can navigate to via “cd” in the LInux terminal or you can go there via the Linux file browser GUI.   If you have some cloud storage, e.g., which comes with a free Google account, then another option besides dragging in files or creating a mount point in the VM from the Windows side - is to use the cloud storage to swap (upload/download) files between the VM and any other computer using the web browsers. - R. On Feb 20, 2022, at 11:21, daedalus39(a)aol.com wrote:        External Email - Use Caution        Dear Freesurfers,I am a Linux novice.  Syntax is my major weakness.  On the other hand, I have been working with Windows for over 30 years.I was able to get the VM_67 up and running.  I had some prior experience using VM for a brief time in 2014 (ver5.3) so I wasn't starting completely from scratch. I figured out how to share with my host (Win 10) and have one of my own test images in my sf-shared folder (I also copied it to the Desktop).I can navigate to /usr/local/... /subjects and I made a directory in "/subjects/" (realized I needed "sudo mkdir, but then I was successful).  However, after having done that, it occurred to me that that wasn't the right thing to do anyway.When I tried using the folder GUIs to drag/drop/copy the image into the test folder (old Windows habit), it simply rejected the action.  I'm assuming this is a permissions issue (everything in FS is "root" and everything in the VM is "developer'), but I am very spooked about using some type of chmod statement here.  If that's the only way to resolve this, would you be able to share some guidance and sample syntax to allow me to import the test image using the GUI?  Thanks in advance for any help you can provide.  This may also help others who need to do the same if I/we can resolve this (i.e., search archives). -Randy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Linux Novice (VM_67 root vs. developer permissions)
by daedalus39＠aol.com 20 Feb '22

20 Feb '22

External Email - Use Caution Dear Freesurfers, I am a Linux novice. Syntax is my major weakness. On the other hand, I have been working with Windows for over 30 years. I was able to get the VM_67 up and running. I had some prior experience using VM for a brief time in 2014 (ver5.3) so I wasn't starting completely from scratch. I figured out how to share with my host (Win 10) and have one of my own test images in my sf-shared folder (I also copied it to the Desktop). I can navigate to /usr/local/... /subjects and I made a directory in "/subjects/" (realized I needed "sudo mkdir, but then I was successful). However, after having done that, it occurred to me that that wasn't the right thing to do anyway. When I tried using the folder GUIs to drag/drop/copy the image into the test folder (old Windows habit), it simply rejected the action. I'm assuming this is a permissions issue (everything in FS is "root" and everything in the VM is "developer'), but I am very spooked about using some type of chmod statement here. If that's the only way to resolve this, would you be able to share some guidance and sample syntax to allow me to import the test image using the GUI? Thanks in advance for any help you can provide. This may also help others who need to do the same if I/we can resolve this (i.e., search archives). -Randy

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Freesurfer February 2022