Freesurfer June 2022

freesurfer@nmr.mgh.harvard.edu

84 participants
123 discussions

Nii to Img file
by Rachel Wagner 15 Jun '22

15 Jun '22

External Email - Use Caution Hello, Thank you for your assistance! I am trying to convert an nii nifti file to an img file within free surfer. I’ve used the mri convert function and did create the img file, but I’m getting an error message in SPM when I try to co-register it to another img file. Is there a particular way I should be converting an nii file? My only other thought is that potentially I’m not exporting properly. I am using ubunu VM on a windows computer, and need to export the two img files from ubuntu to my windows files so I can upload them in matlab. Is there a preferred way to export files out of the ubuntu VM? Thanks very much again, Rachel

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Re: [Freesurfer] SPM to FreeSurfer
by fsbuild 15 Jun '22

15 Jun '22

External Email - Use Caution Hello Rachel, SUBJECTS_DIR is preset in the terminal window to point to the example subjects already provided with the freesurfer distribution under /usr/local/freesurfer/7.2.0/subjects.  You will see subject names under that directory like “bert”.  That SUBEJCTS_DIR setting is printed out when you start a new terminal window. But it is not intended you process your own subjects there.  You don’t have permission to copy data into that location unless you use the “sudo” command. It’s preferable to set SUBJECTS_DIR to point to a subdirectory where you have permission to read and write your own subject data files such as /home/developer   If you put your data under there, then you can set SUBEJCTS_DIR to instead be, $ export SUBJECTS_DIR=/home/developer/subjects… under which you would presumably have directories referenced by subject name. To see the value of SUBEJCTS_DIR in the terminal window,$ echo $SUBJECTS_DIR To see the value of all environment variables in the terminal window,$ env | sort You can change what SUBJECTS_DIR is set to in the terminal window by editing the file /home/developer/.bashrc  I would put any export command to change SUBJECTS_DIR from the subejcts provided with freesurfer at the end of that file. - R. On Jun 15, 2022, at 17:04, Rachel Wagner <rwagne2(a)uwo.ca> wrote:        External Email - Use Caution        Hello,  I am trying to take my SPM images and cortically project them with free surfer (SpmPainting - Free Surfer Wiki (harvard.edu) As it might be quite obvious, I have very little experience using these softwares. I am typing in the suggested code as follows: developer@developer-VirtualBox:~$ mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.imgmri_convert /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz brain.imgreading from /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz...error: mghRead(/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz, -1): could not open filedeveloper@developer-VirtualBox:~$ ^Cdeveloper@developer-VirtualBox:~$ Is there something I am doing incorrectly? Thank you!Rachel_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] FreeSurfer Passcode - Apologies!
by fsbuild 15 Jun '22

15 Jun '22

External Email - Use Caution Hello Rachel, You should have just received the info for the Freesurfer Ubuntu VM. Replies to these requests are now being sent directly to the email of the requestor and are no longer copied to the Freesurfer list so as not to generate extra  list. From: Rachel Wagner <rwagne2@uwo.ca>Date: Wednesday, June 15, 2022 at 1:33 PMTo: Sennott, Liam Ricker <LSENNOTT@mgh.harvard.edu>Subject: FreeSurfer Passcode - Apologies!        External Email - Use Caution        Hello,  I hope this finds you well. My apologies for emailing you personally, I am a bit desperate - I am attempting to subscribe to the mailing list offered by the developers of FreeSurfer, as I need to email for the passcode I require to access the software. I am having trouble subscribing (for some reason I’m not getting the subscription confirming email) and thus cannot contact the listed email. I am wondering if you might be able to offer an alternative way to get in touch for the passcode I need to expand the archive (I downloaded the ubuntu VM and WinRAR)? Thanks!Rachel Wagner 

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Re: [Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system with errors
by fsbuild 15 Jun '22

15 Jun '22

External Email - Use Caution If you boot into recovery mode, there is an fsck option available there you can try.   I will send some screenshots of booting into recovery mode to your email directly. - R. On Jun 14, 2022, at 21:06, Joanna L Eckhardt <jeckhardt(a)health.ucsd.edu> wrote:        External Email - Use Caution        Dear FS Help Team, I run FS on Ubuntu VM Virtualbox 6.1 on Windows. Out of nowhere, my Virtualbox is no longer opening and has errors. See screenshots below. First screen looks like this upon launching the Virtualbox and so I click Ubuntu and then it shows the error /dev/sda1 contains a file system with errors, check forced. I tried doing a website fix that I found online: fsck -f /dev/sda1 but it did not work. Do you have any insights on how to resolve this issue? Thank you very much for your time and assistance!All my best,Joanna <image.png><image.png>Joanna EckhardtNeurosciences Graduate ProgramUniversity of California, San Diego_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Ubuntu VM Error - /dev/sda1 contains a file system with errors
by Joanna L Eckhardt 14 Jun '22

14 Jun '22

External Email - Use Caution Dear FS Help Team, I run FS on Ubuntu VM Virtualbox 6.1 on Windows. Out of nowhere, my Virtualbox is no longer opening and has errors. See screenshots below. First screen looks like this upon launching the Virtualbox and so I click Ubuntu and then it shows the error /dev/sda1 contains a file system with errors, check forced. I tried doing a website fix that I found online: fsck -f /dev/sda1 but it did not work. Do you have any insights on how to resolve this issue? Thank you very much for your time and assistance! All my best, Joanna [cid:471109e4-6e90-411d-b653-14572ec8662b] [cid:06b19041-fce6-416f-97cc-faeb5576040e] Joanna Eckhardt Neurosciences Graduate Program University of California, San Diego

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recon-all -s exited with ERRORS
by Wang, Yu 14 Jun '22

14 Jun '22

External Email - Use Caution Hi, FreeSurfer Developers, I am attempting to use the recon-all to reconstruction, I successfully run this command in some subjects, but it also failed in around 1/3 of subjects. And after running the recon-all of this 1/3 subjects. It will show “mri_watershed error:GLOBAL region of the brain empty” and I already solve this with the command “recon-all -skullstrip -no-wsgcaatlas -s smwrc1NT816”. And after working with this, I tried to use the command “recon-all -autorecon2 -autorecon3 -s smwrc1NT816” and it shows the output as without given some detailed reasons: recon-all -s smwrc1NT816 exited with ERRORS at Mon Jun 13 13:54:10 CDT 2022 For more details, see the log file /Applications/freesurfer/7.2.0/subjects/smwrc1NT816/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/15s_oFH-kAftN57mqGI2bcqN1hKf4R5zXE_fPPasU_i9bJa… I’ve searched over the internet and did not find the reasons and solutions of my problems. And I will attached the recon-all.log in case it's of any use. I try to work out on two machine, and they show the same problems : 1. FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b and freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 2. Platform: MacOs 11.4 and ubantu 20.04.4 3. uname -a:Darwin WANGs-MBP.attlocal.net 20.5.0 Darwin Kernel Version 20.5.0: Sat May 8 05:10:31 PDT 2021; root:xnu-7195.121.3~9/RELEASE_ARM64_T8101 arm64 or: Linux sulu 5.4.0-113-lowlatency #127-Ubuntu SMP PREEMPT Wed May 18 15:12:18 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 1. recon-all.log: see attached (this one is run by macOS) I will be appreciated if you can give me a hand with these problems. And looking forward to your reply. Sincerely, Yu

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mris_preproc read error
by Joanna L Eckhardt 14 Jun '22

14 Jun '22

External Email - Use Caution Dear FreeSurfer Help Team, I am working through the FreeSurfer tutorial on cannabis using Ubuntu VM on windows (FS version 7.1.1). I am on the group analysis portion of the tutorial attempting to run mris_preproc. However, I am receiving the following error upon running the script: error: No such file or directory error: mghRead(/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/rh.thickness.fwhm10.fsaverage.mgh, -1): read error I wonder if something has been going wrong with recon-all as I believe it is saying that there is an error with one of the outputs in sub-101? Recon-all has been running in a suspiciously short time (~5 hours), but I do not know enough about the processing steps to know what might be occurring wrong in recon-all or in trying to run mris_preproc. Please let me know if I can send you anything else to provide more information on the issue. Thank you for your time and assistance. Best wishes, Joanna

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Incorporating samseg segmentation into the recon-all pipeline
by Cerri, Stefano 14 Jun '22

14 Jun '22

Hi Julian, You can use the command "samseg" with the --recon flag. See the helper function for more details (--help) Stefano External Email - Use Caution /Hello everyone,/ /We have been utilizing freesurfer for our brain morphometry and processing pipelines, and have recently tested the samseg segmentation algorithm on a clinical cohort./ /With respect to some regions, we currently prefer its results to the ones generated by the standard freesurfer segmentation algorithm. / /As SAMSEG only provides volume calculation (please correct me if I am wrong) and does not feature cortical thickness measurements,/ /I was wondering if the recon-all pipeline can be modified to utilize the samseg segmentation instead, and if so, which script(s) or chain of commands would be a good starting point to implement this./ /Looking forward to your feedback,/ /Julian / Julian McGinnis PhD Candidate TUM-Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany Department of Computer Science, Technical University of Munich, Munich, Germany Email:julian.mcgin...@tum.de _______________________________________________ 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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mri_label2vol with fill-ribbon option
by Wu, Junjie 14 Jun '22

14 Jun '22

External Email - Use Caution Dear Freesurfer experts,, I tried to use mri_label2vol with fill-ribbon option to covert the surface-based label of perirhinal cortex into the volume (an ROI in mgz file). However, when I typed "mri_label2vol --fill-ribbon --label lh.entorhinal_exvivo.thresh.label --o lh.entorhinal_exvivo.thresh.nii --identity" in the command line, an error popped up, saying "ERROR: Option --fill-ribbon unknown". Do you have any solution in order to make it work? Thanks, Junjie

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Exciting Postdoc Position at UCLA
by Arpana Annie Gupta 13 Jun '22

13 Jun '22

External Email - Use Caution Dear Freesurfer Community, We are looking for a postdoc fr this exciting position (2-3 years)- details below https://secure-web.cisco.com/1wp5qnfMl6kH8tGZQqKIFBkrm-7MMorOxY-JjeSnDeCwRf… <https://secure-web.cisco.com/1wp5qnfMl6kH8tGZQqKIFBkrm-7MMorOxY-JjeSnDeCwRf…> Thanks Annie 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 a U54-funded project studying sex-related differences in the brain-gut-microbiome interactions related to visceral pain. This project is focused on the sex-specific effect of gut microbial metabolites, and estrogen levels on ascending arousal pathways originating in distinct brainstem nuclei to change the activity and connectivity of brain networks involved in symptom generation in irritable bowel syndrome. As a part of an multidisciplinary research team the fellow will apply advanced computational, neuroimaging, biostatistical, and bioinformatics approaches to assess the interaction between various levels of biological data (e.g., microbiota, metabolites, sex hormones, multimodal brain and brainstem imaging data), clinical variables (symptom severity, widespread pain) and sex. There will be opportunities to develop translational and clinical neuroscience research skills (e.g., target discovery, individualized treatment development and biomarker/predictor development), in addition to state-of-the-art analytical skills to address basic and pathophysiological systems biology questions. The G Oppenheimer Center for Neurobiology of Stress and Resilience (CNSR) is an interdisciplinary, translational Center funded by the National Institutes of Health, and by philanthropic support. The overall research goals of the CNSR are to better understand the interactions between mind brain and body in health and disease, and to develop novel management strategies for optimal health and for complex chronic disorders. Center investigators are conducting clinical, translational and basic research with human populations, using interventions (e.g., diet, cognitive behavioral therapy) alongside deep phenotyping including neuroimaging, mutli-omics profiling (gut microbiome, metabolomics, inflammatory biomarkers, psychosocial and behavioral assessments. You will work directly with Arpana “Annie” Gupta, PhD and Jennifer Labus, PhD and an array of faculty collaborators across UCLA, and beyond. There will be many opportunities to lead high impact publications starting on day one, working with existing rich and 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: Develop longitudinal multimodal MRI data analysis streams (functional connectivity, task-based fMRI, diffusion tractography and volumetrics). Analyze complex multi-omics datasets including imaging, gut microbiome, metabolomics, behavioral and clinical data. Prepare and submit manuscripts Mentor graduate and undergraduate students Be inquisitive, curious and publish! Required Qualifications: Ph.D. in Neuroscience, Neuropsychology, Bioinformatics, Biostatistics, Engineering, Computer Science or a related field. Strong proficiency and independence with various neuroimaging analysis platforms, multivariate modeling strategies and network connectivity analyses. Established quantitative and statistical skills, including strong programming skills and comfort with diverse computing environments. Experience with R, Linux, Matlab or Python preferred. Background in systems/cognitive neuroscience, neuroanatomy and psychological/clinical constructs. A demonstrated capacity to drive first author publications. Excellent communication and writing skills, motivated and driven to publish. Preferred Qualifications: Connectomics network analysis and machine learning modeling confer a very significant advantage. Management/coding of neuroimaging databases (XNAT or others). 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 https://secure-web.cisco.com/1Td84IwBPHD8C0Xja4FKyZS6G3wT_dgKSL5Vqmzs05avLQ… | 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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Freesurfer June 2022