Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

MCR install for parcellation
by Antonio Di Renzo 09 May '24

09 May '24

External Email - Use Caution Messers FreeSurfer developers, I dowloaded MCR zip file for linux in /home/vboxuser/Downloads from MatLab website. I extracted files in new foldern named Matlab_Component_Runtime_R2014b in Downloads. I am trying to install Matlab Component Runtime, but the the following command: fs_install_mcr R2014b does not work. Where can I find the right step by step MCR installation guide? Thank you, Antonio

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Postdoc Positions in Cognitive Neuroscience/ Neuroimaging Genomics
by X K 09 May '24

09 May '24

External Email - Use Caution Postdoc positions are available at Zhejiang University (Hangzhou, China). The successful candidates are expected to work on multi-disciplinary projects in cognitive neuroscience, neuroimaging and computational modelling related to individual differences in language/spatial navigation, relevant brain networks, aging and disorders. The Cognomics Lab is led by Dr. Xiangzhen Kong, who has extensive experience in cognitive neuroscience and the application of computational modelling and neuroimaging genetics to investigate functional architecture of the human brain and how it supports human-defining cognition. We conduct large-scale studies using a variety of data sources including in-house datasets (e.g., fMRI, SEEG), and open data from UK Biobank and ENIGMA. We seek highly motivated candidates with a Ph.D. degree in cognitive neuroscience, psychology, bioinformatics, or computer science with biomedical applications, etc. The ideal candidates should be highly motivated to publish first-author papers and present at conferences, and are expected to have strong quantitative skills and experiences in programming and machine learning. Interested applicants should submit a CV, a letter briefing current research interests, and contact information for two individuals who can provide letters of recommendation to Dr. Xiangzhen Kong (*xiangzhen.kong(a)zju.edu.cn <xiangzhen.kong(a)zju.edu.cn>*). Positions will remain open until filled.

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Incorporating hi-res T2w image in longitudinal pipeline
by Raikes, Adam C - (adamraikes) 08 May '24

08 May '24

External Email - Use Caution Good afternoon, We are collecting hi-resolution T1w and T2w images (0.8mm3) in a pre-/post- design. I am using Freesurfer 7.4.1 to process the data and have been successful in ingressing the T2w images in the cross-sectional recon-all runs with -T2 <path> and -T2pial. Two questions: 1. When creating the base image, is there any value to using the T2s and, if so, is there a way to do that? 2. When running the -long step, I know that -T2pial is an option but do I need to pass -T2 <path> with it? If I need the path, should it point to the original image or something from the cross/mri folder? Thanks Adam C. Raikes, PhD Imaging Projects Manager Center for Innovation in Brain Science University of Arizona

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outcome directions of longitudinal two stage model
by L 08 May '24

08 May '24

External Email - Use Caution Dear exports, I am wondering whether the outcomes of the longitudinal two stage model is tp1 - tp2 or tp2 - tp1. Thank you, Lihong Wang -- - Lihong

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surface and cortical thickness normalization
by yunus soleymani 08 May '24

08 May '24

External Email - Use Caution Hello, I hope you are doing well. Yesterday, I had some questions regarding normalization in Freesurfer. Thanks to Dr. Douglas N. Greve, I received answers for all of them. However, I still have one more question. When I normalize brain surfaces to eTIV, they appear to be in two different units (mm2 and mm3). Will this be a problem? Additionally, I would like to know your thoughts on normalizing cortical thicknesses. Do you think they should be normalized to eTIV, or would it be better to normalize them to the mean cortical thickness of each subject? I would greatly appreciate your response. Thank you, Yunus --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------

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Difference between 2 ways to set up fsgd file and contrasts
by Lydia Chung 08 May '24

08 May '24

External Email - Use Caution Hi FS support team, I am going to be using mri_glmfit to test 1) main effects (which regions show differences in cortical thickness between group 1 and group 2) and 2) interaction effects (does the relationship between IV and DV depend on moderator). Depending on the model, the IV is sometimes a binary categorical variable and sometimes a continuous variable. The moderator is always continuous. So, interaction effects are either continuous x continuous OR categorical x continuous. One thing I'm trying to understand is whether the two examples below are basically two different approaches that answer the SAME question: Do people in Group 1 differ from Group 2 on cortical thickness? Version 1 is the one provided by FS and Version 2 is an analog of another setup I have been provided by colleagues. Are these models answering the same or different questions? The freesurfer link below also shows an example of how to do an interaction (Group x Age) using Version 1 setup; for Version 2 setup of an interaction, I know I would multiply the IV and Moderator before this step so that I would have an additional "interaction variable" column to add as one of the 'Variables' listed in the fsgd code. So, I'm also curious if the two different methods of testing an interaction (in addition to the first question about the main effect) will get you the identical answer OR if there is something conceptually different? Do the nuances of this setup have to do with the difference between using DODS or DOSS? *Main effect of Group on cortical thickness Version 1 (copied from FS example. link here <https://secure-web.cisco.com/1cgzre8FgLw0c17s9QNhmU_14vQ714XlLV20U4K14P96Af…>)* GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Variables Age Weight Input subject1 Group1 30 100 Input subject2 Group2 40 120 Contrasts: 1 -1 0 0 0 0 (to test main effect of group; this feels like an anova approach?) *Main effect of Group on cortical thickness Version 2* GroupDescriptorFile 1 Title OSGM Class Subjects Variables Group Age Weight Input subject1 Subjects 0.5 30 100 Input subject2 Subjects -.5 40 120 contrasts: 0 1 0 0 (to test main effect of group; this feels like a linear regression approach?) Thank you in advance for your help! Lydia -- Lydia Wu-Chung, M.A. Doctoral candidate BMED Lab Department of Psychological Sciences Rice University 6500 Main St - MS201 Houston, TX 77030 Lab Phone: 713-348-8126 Email: lydia.wu(a)rice.edu <lw50(a)rice.edu> *Confidentiality Text:* The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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recon-all process still not finishing properly
by Dong, Yilei 08 May '24

08 May '24

External Email - Use Caution Hi Freesurfer Support, The past few weeks, I've emailed about my recon-all processing stream never completely finishing. We are still encountering the same problem. For context, our recon-all job submission script runs recon-all for 1 image. Given a folder of 100 MRI images, we have another script that calls upon the recon-all script for each image within the folder via a for loop. The result is 100 jobs running in parallel on the cluster. I have attached a screenshot of the parameters we set whenever we submit each recon-all job for each image by SLURM to UCSD's cluster. The maximum time we are allowed for each job is 48 hours. Our jobs are shared-node jobs, which means we run more than 1 job on a single node. This time, we increased RAM from 8GB to 16GB in hopes the entire recon-all processing stream can fully run through for each image, but it still stops at "mri_pretess done" and does not go on to the -fill step. Each job submitted to the cluster took around 4 hours and 20 minutes each to run in our most recent attempt. If increasing the RAM did not change anything for us, how else can we get more verbose error messages? What other reasons could be why our recon-all aborts before finishing? I have attached a recon-all.log from one of our subjects for reference and a screenshot of the parameters we set for submitting jobs in our cluster for reference. Freesurfer version: 7.2.0, but already available as module on UCSD's cluster system Platform: Rocky Linux release 8.8 (Green Obsidian) uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Recon-all log: see attached Thank you! Sincerely, Yilei

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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis
by Dan Levitas 08 May '24

08 May '24

External Email - Use Caution Hi Kersten, If that's alright with you then that would be great. I completely accept if my threshold is accurate and leaves no significant findings, I just can't find a comparable threshold on this forum or elsewhere with such an elevated threshold value. I can touch base next week to see what you need from me. Thanks again, Dan On Tue, May 7, 2024 at 3:09 PM Diers, Kersten /DZNE <Kersten.Diers(a)dzne.de> wrote: > Hi Dan, > > I can see no obvious issues at the moment, but am happy to take a closer > look when I am back in office next week. > > The fslmer tool ist just an R Implementation of the Matlab scripts, so I > don't see any need to use them in your case. > > Best, > > Kersten > > Gesendet von Outlook für Android <https://secure-web.cisco.com/1KzII-MfH6rTxaOnzZUTUvJp9x_boMj6aQnEUUoTp8Re7R…> > > ------------------------------ > *Von:* Dan Levitas <djlevitas208(a)gmail.com> > *Gesendet:* Dienstag, Mai 7, 2024 7:11:58 PM > *An:* djlevitas208(a)gmail.com <djlevitas208(a)gmail.com> > *Cc:* Kersten.Diers(a)dzne.de <Kersten.Diers(a)dzne.de>; > MREUTER(a)mgh.harvard.edu <MREUTER(a)mgh.harvard.edu>; > freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > *Betreff:* Re: [Freesurfer] Lingering questions for Longitudinal > spatiotemporal LME analysis > > CAUTION: This email originated from outside of DZNE. Do not click links > or open attachments unless you recognize the sender and know the content is > safe. > ACHTUNG: Dies ist eine externe E-Mail, bitte seien Sie vorsichtig beim > Anklicken von Links oder Öffnen von Anhängen > > Hi Kersten & Martin, > > I just wanted to ping this thread again, as I'm still unsure about my pcor > value (4.4) that I'm getting. I've seen other posts where the threshold > (thmin) value specified in functions such as *mri_surfcluster* are around > 2 (corresponding to a p-value of 0.01) when threshold *sig.mgh file(s). > Given that I'm interested in both right and left hemispheres, I'm surprised > that my single threshold value to account for both hemispheres is so high > relative to others posts I've come across in the forum. I seem to have > followed the LME approach correctly ( > https://secure-web.cisco.com/1SQ58WEznZe-ibw3QO19omrHSeej1iX-z28jkMlUtsQ61n…) but > I'm unsure if I've done something that has resulted in an elevated pcor > value. > > Martin had recommended the *fslmer* tool ( > https://secure-web.cisco.com/1k8MMiLU-B44BypnewP6obBaoWvRatpcAdkGjbKYO0VGEe…) I'd be happy to use that instead if > it's more current and the preferred tool for this kind of analysis. > > Thanks again, > > Dan > >

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ERROR: cannot find AntsN4BiasFieldCorrectionFs in path
by Christine Farrugia 07 May '24

07 May '24

External Email - Use Caution Hi, I have installed FreeSurfer (freesurfer-linux-centos7_x86_64-7.4.1) into my research group's directory on the University cluster, using the tar archive. I source it with GROUPDIR=<path_to_group_directory> export FREESURFER_HOME=$GROUPDIR/software/freesurfer . $FREESURFER_HOME/SetUpFreeSurfer.sh export PATH=$FREESURFER_HOME/bin:${PATH} and am trying to run recon-all like so: recon-all -s <subj_id> -i <path_to_T1_data> -T2 <path_to_T2_data> -T2pial -autorecon-all However, FreeSurfer keeps giving the error: ERROR: cannot find AntsN4BiasFieldCorrectionFs in path when AntsN4BiasFieldCorrectionFs is definitely in freesurfer/bin Any insight into the matter would be greatly appreciated 🙂 Regards, Christine The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis
by Dan Levitas 07 May '24

07 May '24

External Email - Use Caution Hi Kersten & Martin, I just wanted to ping this thread again, as I'm still unsure about my pcor value (4.4) that I'm getting. I've seen other posts where the threshold (thmin) value specified in functions such as mri_surfcluster are around 2 (corresponding to a p-value of 0.01) when threshold *sig.mgh file(s). Given that I'm interested in both right and left hemispheres, I'm surprised that my single threshold value to account for both hemispheres is so high relative to others posts I've come across in the forum. I seem to have followed the LME approach correctly (https://secure-web.cisco.com/1P1DqCgATuRJ8Gb_Cv23uM_tkjhG63bDl2SmrFrqCZVQtv… <https://secure-web.cisco.com/1P1DqCgATuRJ8Gb_Cv23uM_tkjhG63bDl2SmrFrqCZVQtv…>) but I'm unsure if I've done something that has resulted in an elevated pcor value. Martin had recommended the fslmer tool (https://secure-web.cisco.com/1f2ZYTXcSbFY4HqsjtbVZ5WFtQdhPr_P5UgrBHbi4cv6tX… <https://secure-web.cisco.com/1f2ZYTXcSbFY4HqsjtbVZ5WFtQdhPr_P5UgrBHbi4cv6tX…>), I'd be happy to use that instead if it's more current and the preferred tool for this kind of analysis. Thanks again, Dan

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