Freesurfer

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30080 discussions

Tracula tracts do not display correctly and have large volume
by Goeckner, Bryna 29 Mar '22

29 Mar '22

External Email - Use Caution Hi Freesurfer Experts, I have run into a problem with several subjects ranging over several different tracts (usually just one tract per subject) where a tract will not display correctly in merged_avg16_syn_bbr.mgz or in the individual pathway (ex: lh.cbv_avg16_syn_bbr/path.pd.nii.gz) without first adjusting thresholds. I also discovered that the volume in pathstats.overall.txt in these cases is significantly higher than the average – on the order of 10 times bigger. I know there is mention of using “set reinit=1” to repair tracts that are too small or missing. Would this be recommended here as well or is there another better direction to take? I am including a link to the trac-all.log for a subject whose rh.ilf is problematic. Please let me know of there is any other information you need and thanks for your help! https://secure-web.cisco.com/1-H9YB7x0pcdABFBAqsjeogpPsh-50RChRNS5qTyoP0bcn… Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program

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Re: [Freesurfer] Seeking help:error in FreeSurfer license key and Freeview
by fsbuild 29 Mar '22

29 Mar '22

External Email - Use Caution Hello KC, You should try getting a new license.txt via,https://secure-web.cisco.com/1F7uoRb2K1btXJW51ulbB_sBWkHIL6Y-0iC-V12bpS… to use on the new system instead of your existing license.txt.  How licenses are read on your new system may no longer works with your old freesurfer license.txt file. The libpng12.so error may be because that is not installed on your new system.  If you let us know what operating system your new system is running, e.g., CentOS8, Ubuntu 20, etc. then maybe we can help you with that. - R. On Mar 29, 2022, at 09:52, Fischl, Bruce <BFISCHL(a)mgh.harvard.edu> wrote:Hi KC Where did you get the license.txt file originally? Can you try requesting another? I’ll leave the freeview question for Ruopeng. CheersBruce From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Koustav ChatterjeeSent: Monday, March 28, 2022 11:04 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Seeking help:error in FreeSurfer license key and Freeview         External Email - Use Caution        Dear FreeSurfer experts, I have reinstalled FreeSurfer 6 in my new system following the FreeSurferes. I saved  “license.txt” in /usr/local/freesurfer. I am getting the following error.  ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt  If you are outside the NMR-Martinos Center,  go to MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1tFW-ky57kTFY70H_r7AKEpl8R8xkyF6sTHkvP6… get a valid license file (it's free).  If you are inside the NMR-Martinos Center,  make sure to source the standard environment.   I am also getting another error while trying to run 'Freeview'. freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory. Please advise.Regards,KC_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] GLM analysis - volume and surface area
by Laura Willers de Souza 29 Mar '22

29 Mar '22

External Email - Use Caution Of course! To do GLM for volume and surface area analysis, is there any change in commands in relation to cortical thickness analysis? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies the measure to be analyzed) - I'm already using permutation in the correction of multiple comparisons. Many thanks! ------------------------------------------------------------------------------ On 3/09/2022 15:20 PM, Douglas N. Greve wrote: Can you just ask the question again so I don't have to sort it out myself? --------------------------------------------------------------------------------------- On 2/22/2022 9:15 AM, Laura Willers de Souza wrote: Thanks so much for the explanation! There is something different in the analysis of volume and surface area in relation to the analysis of cortical thickness? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies the measure to be analyzed) - I'm already using permutation in the correction of multiple comparisons. ------------------------------------------------------------------------------ On 2/21/2022 15:20 PM, Douglas N. Greve wrote: Yes, it is. It is confusing when you talk about area and volume since these are not point measures like thickness (ie, what is the volume or area of a vertex?). The area of a vertex is computed as the mean of the adjacent triangles of the vertex. The volume is the mean of the neighboring truncated tetrahedra. When you run mris_preproc, it will apply a jacobian correction (like VBM). Otherwise, it operates the same as if you had a thickness value at the vertex, ie, same GLM, etc. Make sure to use permutation for correction of multiple comparisons. ----------------------------------------------------------------------------------------- On 2/21/2022 12:13 PM, Laura Willers de Souza wrote: 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! Att, 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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[Moved to Europe Friendly Time Zone] DPABINet Brain Network Online Training Camp
by YAN Chao-Gan 29 Mar '22

29 Mar '22

External Email - Use Caution *[Given that most registered trainees are from Europe, the training time was moved to Europe friendly time zone]* The human brain is one of the most complex network systems in the universe, consisting of about 1011 neurons and about 1015 connections. Since the human brain is a highly integrated and cooperating complex system, studying the functional integration between different brain regions is crucial for understanding the information interaction between brain regions and the coordination between brain networks. In order to facilitate brain network research, Dr. Chao-Gan Yan’s team (The R-fMRI Lab <http://secure-web.cisco.com/14xnlK7Eei_sMSO3_q06ck_peQQ9l9mK7haGZZZlWLewMoB…>) developed a free and open source software DPABINet. DPABINet V1.1 has been released with DPABI <http://secure-web.cisco.com/1_qe887wfdc3X7xMhXFFxKI3dZeE4yMD6gK6oK8hJUqdJM0…> V6.1, which can construct brain network, calculate graph theory indices, perform statistical analyses and present brain network images. In addition, to better construct the brain network, we recommend using DPABISurf <http://secure-web.cisco.com/1SOajXUcJEucbuq3zxd8N5GctqwVz0Y0Xi5nyChupOjOeXQ…> for surface based preprocessing. DPABISurf is a surface-based resting-state fMRI data analysis toolbox evolved from DPABI/DPARSF, as easy-to-use as DPABI/DPARSF. DPABISurf is based on fMRIPrep, FreeSurfer, ANTs, FSL, AFNI, SPM, dcm2niix, PALM, GNU Parallel, Docker and DPABI. DPABISurf provides user-friendly graphical user interface (GUI) for pipeline surface-based preprocessing, statistical analyses and results viewing, while requiring no programming/scripting skills from the users. The use of DPABINet and DPABISurf is as simple as DPABI software, but hands-on practical training can make users proficient in DPABINet brain network analysis in the most correct and effective way. As there was no online English video course for DPABINet yet, here we are launching the DPABINet Brain Network online Training Camp (April 18th ~ 22nd, 2022, the teaching language is English). This DPABINet Brain Network online Training Camp <http://secure-web.cisco.com/1d8dz5C6fbHOk7tUc0T0Lt9q2Mf3Hh2_sNdSoujvhTLv5fN…> is lectured by Dr. Chao-Gan Yan, and is aimed at researchers and students in the fields of psychology, cognitive neuroscience, biomedical engineering, clinical medicine, etc. Because this training camp requires basic knowledge of brain imaging, we encourage the trainees first learn The R-fMRI Course <http://secure-web.cisco.com/1R8odPSiNAmJLVsOInsWj0xbQLHTWbYsgKlfqzm_YIL_bTh…> (freely available at http://secure-web.cisco.com/1R8odPSiNAmJLVsOInsWj0xbQLHTWbYsgKlfqzm_YIL_bTh…) In the training camp, trainees will first study DPABISurf for cortical reconstruction and data preprocessing, and then systematically learn brain network research, from the basic concepts of brain network to operations of DAPBINet software. More importantly, trainees are encouraged to come to study with their own projects and data, conduct in-depth research project discussions with the lecturer, process data with research questions, receive hands-on systematic scientific research training, get results and scientific interpretation for publication. We sincerely welcome your participation in this training camp and look forward to seeing you online! 1. Time: April 18th ~ 22nd, 2022 2. Language: English 3. Place: Online Camp This training camp is held in the form of cloud-based online small classes. Lectures and discussions will be held in the cloud conference Zoom room. One-on-one error-checking counseling by teaching assistants will also be held in the cloud small conference room. For trainees with insufficient local computing power, the cloud server will be opened for data processing exercises. 4. Lecturer Chao-Gan YAN, Ph.D. <http://secure-web.cisco.com/1igKvIBTP7egVAIAvbJj9df_8Qys2r-PtsZsZOksedvLKd2…> Dr. Chao-Gan Yan is a professor at the Institute of Psychology, Chinese Academy of Sciences (IPCAS). He is the Director of the Magnetic Resonance Imaging Research Center, the Director of International Big-Data Center for Depression Research, and the Principal Investigator of The R-fMRI Lab located at IPCAS. Before he joined the IPCAS in 2015, he worked as a Research Scientist at the Nathan Kline Institute for Psychiatric Research and a Research Assistant Professor at the Department of Child and Adolescent Psychiatry, New York University School of Medicine. Dr. Yan received his Ph.D. degree in Cognitive Neuroscience from State Key Laboratory of Cognitive Neuroscience and Learning at Beijing Normal University in 2011. His research mainly focuses on the resting-state fMRI (R-fMRI) computational methodology, mechanisms of spontaneous brain activity, and their applications in depression. He has addressed fundamental methodological issues (e.g., impact of head motion (ESI Top 1‰ of highly cited papers), standardization (ESI Top 1% of highly cited papers) and multiple comparison correction (ESI Top 1% of highly cited papers)) on the study of resting-state functional connectomics. He has also developed data processing and analysis toolbox for R-fMRI, DPABI (ESI Top 1‰ of highly cited papers) and DPARSF, with the latter has been cited over 2000 times. He initiated a Chinese consortium for big data of brain imaging of depression (REST-meta-MDD), performed big data study of depression neuroimaging (PNAS 2019, ESI Top 1% of highly cited papers), and studied the brain mechanisms of depression through a longitudinal study of animal model. He has published 70+ peer-reviewed articles (30+ as first or corresponding author) in prestigious journals including *PNAS, Molecular Psychiatry, NeuroImage, Human Brain Mapping*. His work has been widely cited in the scientific community (total citations > 14000, http://secure-web.cisco.com/1BdhQOQOjp_AE84wafciXjZyiVotVy2UuZEJtAj8iHMvSWM…) achieving an h-index of 37. Six of his first-author/corresponding author papers ranked as ESI Top 1% Highly Cited Papers, 2 of which were ESI Top 1‰. He has been ranked as 2019 and 2020 most cited Chinese Researchers by Elsevier. He was awarded the 2021 Early Career Investigator Award by The Organization for Human Brain Mapping (OHBM). Additionally, he currently serves as associate editor for *Neuroimage: Reports* and servers in the editorial boards of *NeuroImage* and *Journal of Neuroscience Methods*. 5. Schedule (Of note: the schedule is not optimized for the American time zone, we may launch another training camp optimized for the American time zone depending on the needs.) Time Course April 18th, 2022 Beijing: 14:30H~17:30H Rome: 08:30H~11:30H London: 07:30H~10:30H New York: 02:30H~05:30H Camp Opening Ceremony Brain Network: Current Research and Methodological Issues Brain Network: Applications Brain Network: Innovation Points April 19th, 2022 Beijing: 14:30H~17:30H Rome: 08:30H~11:30H London: 07:30H~10:30H New York: 02:30H~05:30H Introduction of Trainees and Projects Surface-Based Brain Imaging Analysis and DPABISurf Data Processing with DPABISurf Software Installation and Practice April 20th, 2022 Beijing: 14:30H~17:30H Rome: 08:30H~11:30H London: 07:30H~10:30H New York: 02:30H~05:30H DPABINet: Network Construction DPABINet: Statistical Analysis and Results Viewing DPABINet: Practice April 21st, 2022 Beijing: 14:30H~17:30H Rome: 08:30H~11:30H London: 07:30H~10:30H New York: 02:30H~05:30H Graph Theoretical Analysis: Current Research and Methodological Issues Graph Theoretical Analysis: Applications DPABINet for Graph Theoretical Analysis Graph Theoretical Analysis: Practice April 22nd, 2022 Beijing: 14:30H~17:30H Rome: 08:30H~11:30H London: 07:30H~10:30H New York: 02:30H~05:30H Brain Network Analysis: Example of Rumination DPABINet: Utilities Practice Camp Summary 6. Enroll Please visit http://secure-web.cisco.com/1d8dz5C6fbHOk7tUc0T0Lt9q2Mf3Hh2_sNdSoujvhTLv5fN… for more details. If you have any questions, please contact Dr. Yan’s team (The R-fMRI Lab) at rfmrilab#gmail.com <rfmrilab(a)gmail.com>. Best, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Principal Investigator Director, International Big-Data Center for Depression Research Director, Magnetic Resonance Imaging Research Center Institute of Psychology, Chinese Academy of Sciences 16 Lincui Road, Chaoyang District, Beijing 100101, China - Initiator <http://secure-web.cisco.com/1IJa9h3rPXrcu672dW8yhBstkZcNgntfCcHqymtNRs5z6CF…>DPABI <http://secure-web.cisco.com/1_qe887wfdc3X7xMhXFFxKI3dZeE4yMD6gK6oK8hJUqdJM0…> <http://secure-web.cisco.com/1IJa9h3rPXrcu672dW8yhBstkZcNgntfCcHqymtNRs5z6CF…>, DPABISurf, <http://secure-web.cisco.com/1SOajXUcJEucbuq3zxd8N5GctqwVz0Y0Xi5nyChupOjOeXQ…>DPARSF <http://secure-web.cisco.com/1IJa9h3rPXrcu672dW8yhBstkZcNgntfCcHqymtNRs5z6CF…>, and The R-fMRI Network <http://secure-web.cisco.com/1u2VyAjXQ0zUTB56mnBIg3mmMngLgRB5cZplMmJ7-AlKc8J…> ( RFMRI.ORG <http://secure-web.cisco.com/1E5Rpr5gcuDDO7em8KZWH4EvIrNlINTtEV-IK3UbeKpZ3MU…>) http://secure-web.cisco.com/1igKvIBTP7egVAIAvbJj9df_8Qys2r-PtsZsZOksedvLKd2… http://secure-web.cisco.com/1BdhQOQOjp_AE84wafciXjZyiVotVy2UuZEJtAj8iHMvSWM…

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Removal from Mailing list
by Haniya Saleh 28 Mar '22

28 Mar '22

External Email - Use Caution Hello, Can I please be removed from this mailing list? I no longer work in a position related to freesurfer. Thanks! Warm Regards, Haniya Saleh ________________________________________________ Haniya Saleh | OVC IT Technician - Client Productivity Ontario Veterinary College (OVC) | University of Guelph MacNabb House rm. 103 | 2 College Avenue West | Guelph, ON | N1G 2W1 519-824-4120 x54691 | hsaleh(a)uoguelph.ca

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Re: [Freesurfer] Pass code to expand the archive of Free surfer 7.2.0
by fsbuild 28 Mar '22

28 Mar '22

External Email - Use Caution Hello Krystaly, Sending the info to your email shortly. - R.On Mar 28, 2022, at 01:15, krystaly <krystaly(a)hku.hk> wrote:        External Email - Use Caution        Dear Free Surfer expert,Would you please send me the pass code for opening the archive of FS 7.2.0?Thanks for your attention!Yours sincerely,Krystal_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Pass code to expand the archive of Free surfer 7.2.0
by krystaly 28 Mar '22

28 Mar '22

External Email - Use Caution Dear Free Surfer expert, Would you please send me the pass code for opening the archive of FS 7.2.0? Thanks for your attention! Yours sincerely, Krystal

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lh.pial and rh.pial is 0Kb, I cannot open them by using freesurfer
by Muhammed Görünen 27 Mar '22

27 Mar '22

External Email - Use Caution Hi, I run recon-all process for a subject's T1 data. At the end, the pial files are 0Kb and I cannot open them from python. What would be the problem here? Also, is there any difference between pial file and pial.T1 file? I will be happy if you can answer. Best, --Muhammed

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classes for GLM analysis
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 27 Mar '22

27 Mar '22

External Email - Use Caution Hi all, I am doing an analysis and generating the FSGD. I understand sex and race are classes in this context, but something I was also hoping to regress out is the effects of scanner/sequences. We have a large participant size, so we have around 10+ scanner/sequences, which makes for a large amount of classes combinations, with some having just 1 (if not zero) fitting into a class. Would you proceed with this nonetheless? If not, should scanner/sequence be something that we consider? Should we find some other way to adjust site (I don't think we can z-score...). Or can we consider site/scanner as a continuous variable Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Question about calculation of pial area in DKatlas
by Dongyue Zhou 27 Mar '22

27 Mar '22

External Email - Use Caution Dear FreeSurfer experts: I want to calculate mean pial surface area in DKatlas in individual space.And I know the function read_annotation.m in $FREESURFER_HOME/matlab for loading this atlas.And if I can load sub/surf/?h.area.pial as the area in each vertice and calculate mean pial area by dividing sum PSA of all vertices in one ROI by the number of vertices in this ROI?But why my result is not the same as result in sub/stats/?h.aparc.stats ? Does the column named surface area represent mean PSA in each ROI?

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