Freesurfer April 2022

freesurfer@nmr.mgh.harvard.edu

97 participants
155 discussions

Resampling of surface-based bivariate data
by Burke Rosen 27 Apr '22

27 Apr '22

External Email - Use Caution Is there a way to resample a vertex-by-vertex matrix of data from one subject to another or to ico? For example, I have calculated the Euclidean distance matrix for all the vertices of lh.white for my subjects and wish to find the average distance matrix. Another example might be functional connectivity values. If the data were univariate (i.e. vectors not matrices), I could save my measure as a .w file for each subject and use mri_surf2surf to morph each vector to ico and then average across the resulting ico vectors. One idea is to use make_average_subject to morph each subject’s surface to ico and then calculate bivariate measures on these surfaces. This might be ok for the functional connectivity case. However, this morphing distorts the absolute size of the surface, so the Euclidean distance matrix would be untenably distorted. In other words, is there an extension of mri_surf2surf (or maybe mris_convert) that operates on v(i,j) measures rather than v(i) measures? Thank you, -Burke

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Re: [Freesurfer] pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by fsbuild 27 Apr '22

27 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 23, 2022, at 20:56, Peng, Shichun <speng(a)northwell.edu> wrote:        External Email - Use Caution        Could you please send me the pass code to unzip the file?Thanks,ShichunThe information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Beta values (resubmitting)
by Laura Willers de Souza 27 Apr '22

27 Apr '22

External Email - Use Caution Thanks so much! I would also like to confirm that I am interpreting the beta values correctly for a second model. Model 2: Two Groups, One Covariate Contrasts (DOSS): difference between the group intercepts; covariate effect. The fsgd file looks like this: GroupDescriptorFile 1 Title CU_CI_CSF MeasurementName thickness Class CU Class CI Variables cortisolCSF Input 011_S_0003_S9128 CI 2.397895273 Input 022_S_0004_S9233 CI 2.772588722 Input 011_S_0005_S9137 CU 3.044522438 Input 011_S_0008_S9196 CU 2.397895273 Input 011_S_0010_S8800 CI 2.151762203 ... (n=300) The file with the beta values contains 3 lines (image below). [cid:image003.png@01D858C5.3392CD10] * The first line would be the beta value for the intercept of the 1st group; the second line for the intercept of the 2nd group; and the third line for the slope of the covariate? * Thus the glm equation for the 1st cluster would be: * 1st group ---- cortical thickness = 2.64 - 0.12X + n * 2nd group --- cortical thickness = 2.54 – 0.12X + n Am I interpreting correctly? Thank you very much for all the help! 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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Permission denied error from -localGI
by Billah, Tashrif 27 Apr '22

27 Apr '22

Sorry about missing your earlier question--our FreeSurfer is 7.1.0 We still need your help with this issue. Thank you, Tashrif Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700 =================== What version of FS are you running? On 3/20/2022 8:47 PM, Billah, Tashrif wrote: It does not exist and cannot be created in a shared cluster. Is there a way to define a different folder for /scratch/tp24093955057547375.load_mgh.m.mgh? =============== Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800 Do you have permission to /scratch? Does it exist? =============== Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800 Hi all, We are trying to run recon-all with -localGI but running into an unknown permission denied error: $ recon-all -s sub-1001 -localGI ``` make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 >> reading filled volume... /bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for reading ERROR: loading /path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz as MGH Struct contents reference from a non-struct array object. Error in make_outer_surface (line 25) volume=vol.vol; >> ERROR: make_outer_surface did not create output file '/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022 ``` Our MATLAB environment is properly setup and we regularly run other FreeSurfer-MATLAB commands. So I do not think that is causing the issue. Best, Tashrif

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(no subject)
by Jabeur Mouna 27 Apr '22

27 Apr '22

External Email - Use Caution Hello, How can i import an image.nii from a folder different from /usr/local/freesurfer/7.2.0/subjects to visualise it with freeview ? Please!

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Opening for PhD position based in Tours (Loire Valley, France)
by briend 27 Apr '22

27 Apr '22

External Email - Use Caution Dear colleagues, The INSERM-U1253 & University of Tours research unit based in Tours (Loire Valley, France) invites applications for a PhD position to begin in the Fall of 2022 on the reward and interoceptive systems in autism. The main objective of the current PhD proposal is to identify impaired social processing in autism and AD across the last two dimensions. To do that, first, this project will explore the neural activity of the reward system in these patients via functional magnetic resonance imaging. Then, we will probe the deficit of interoception present in these disorders. This sensory modality will also be examined in relation to social processes, within an innovative device of immersive reality (the CAVE: computer automatic virtual environments). Applicants should hold a Master's degree (or equivalent) in one of the following disciplines: computational or cognitive neuroscience, computer science, mathematics, physics, cognitive science or related. Prior experience in the field of computational neuroscience and/or neuroimaging are of advantage. Sound knowledge of statistics and programming are essential. The candidate’s main missions will be to program, run and analyze behavioral and neuroimaging tests with individual with autism and healthy controls, involving interoceptive tasks and cognitive tests. A good command of written and spoken English is requested of all applicants. Knowledge of French language is beneficial. Prospective candidates should also contact directly Frederic Briend (frederic.briend(a)univ-tours.fr) and/or Marianne Latinus (marianne.latinus(a)univ-tours.fr) by June 2, 2022. Please include the following documents in your application (as a single PDF-file): Cover letter, curriculum vitae, at least one recommendation letter. The position should start in October 2022. Frederic Briend

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Postdoctoral studies in Neuroimaging at Karolinska Institute - Last Days to Apply
by Joana Braga Pereira 27 Apr '22

27 Apr '22

External Email - Use Caution Dear all, We are looking for a Postdoc to work in an interdisciplinary and internationally competitive environment at Karolinska Institute, one of the top medical universities in the world and the home for the Nobel Prize in Medicine. We combine imaging analyses, statistical tools, machine learning algorithms, biofluid assays and genetics to study brain aging and the earliest signs of Alzheimer’s and Parkinson’s diseases. This project will be carried out under the supervision of Associate Professor Joana B. Pereira and it will involve analyzing cross-sectional and longitudinal imaging data, combining clinical measures and cerebrospinal fluid biomarkers, as well as writing manuscripts and presenting results in international conferences. The fellow is expected to be independent, develop his or her own projects, supervise students and show an interest in approaches based on graph theory. In addition, he/she will have the opportunity to develop new skills, analyze large datasets, apply for grants and develop a wide network of collaborations. The ideal candidate should have the following qualities: - A PhD in neuroimaging, computational science, neuropsychology, physics, statistics or a related field; - Experience in statistical techniques, programming, or scripting; - Experience with structural MRI, DTI, fMRI or PET imaging analyses; - Clinical or research experience with aging and/or neurodegenerative disorders. - Excellent record of scientific publications. The Postdoctoral studies will be performed for 1 year, with possible extension for an additional year. To apply please go to: https://secure-web.cisco.com/17Z5BFWVOFKkgw67dU4BS_mGuivQTiYdB22cHmKJrEgcp1… (Deadline: 29/04/2022) For further information or general inquires, please contact Joana B. Pereira at jbragapereira(a)gmail.com or joana.pereira(a)ki.se. Best wishes, Joana

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Item shared with you: "Downloads.zip"
by Rebecca Elizabeth Cooper (via Google Drive) 26 Apr '22

26 Apr '22

External Email - Use Caution I've shared an item with you: Downloads.zip https://secure-web.cisco.com/1-oSwFXMVhHr2jh63UZQla8uWiUfbTDQCL-8u9LcpMsdv4… It's not an attachment -- it's stored online. To open this item, just click the link above.

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Request for 7Zip Archive passcode
by Logan Tate 26 Apr '22

26 Apr '22

External Email - Use Caution Hi, I made a prior request but believe the passcode was sent to someone who posted under my request, and not myself. I just need a passcode to archive the zip folder for file FS_7_2_0_Ubuntu_18_04_06.ova.7z Sorry for the spam! Thank you.

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Re: [Freesurfer] FreeSurfer 7Zip archive passcode
by fsbuild 26 Apr '22

26 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 25, 2022, at 04:59, Katharina Hense <Katharina.Hense(a)klinik.uni-regensburg.de> wrote:        External Email - Use Caution        Hello, I'm trying to expand the 7Zip archive for FreeSurfer on the VirtualBox. Can I get the passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z? Sincerely,Katharina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer April 2022