Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Password Virtual Image file
by Brammie15 31 Oct '22

31 Oct '22

External Email - Use Caution Dear Freesurfer Team, I downloaded the Virtual Box image provided for windows computers. But was unable to extract the 7zip file. I read that I needed to send an e mail to this group. Can anybody help? Thank you Bart

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Neuroimaging Data Analyst Position Available at the Memory and Aging Program at Butler Hospital
by Elizabeth Sharp 28 Oct '22

28 Oct '22

External Email - Use Caution The Memory and Aging Program (MAP) at Butler Hospital is seeking a Neuroimaging Data Analyst to join the Neuroimaging Core Team (Director, Dr. Hwamee Oh) in the MAP. The MAP, one of the leading clinical research centers for Alzheimer’s disease (AD) in the United States, is conducting landmark studies that focus on preclinical and early AD such as ADNI, DIAN, LEADS, development of tau PET, tau-based treatments, deep brain stimulation and primary and secondary prevention trials for autosomal dominant and sporadic AD. The program performs extensive evaluations of study participants across the stages of AD from preclinical to dementia. The Neuroimaging Data Analyst will implement neuroimaging analysis pipelines of amyloid and tau PET as well as structural and functional MRI scans for ongoing studies. They will assist with neuroimaging data management, statistical analysis of imaging data, and preparing image data measures to be shared with MAP investigators as well as external collaborators. They will work closely with MAP investigators, 7-8 post-doctoral fellows, 5-7 undergraduate students and 3-5 research assistants. This position will also be responsible for providing supervision to trainees and research assistants. *Requirements:* Bachelor’s Degree in Computer Science, Bioinformatics, Biomedical Engineering, Electrical Engineering or related fields. A minimum of 3-5years of experience in neuroimaging data management or analysis, preferably of large dataset and clinical and brain imaging data and/or equivalent combination of skills and experience. Programming experience and proficiency in programming in Python (preferred) or Matlab. Demonstrable brain imaging data analysis skills (ideally PET and MRI) and solid working knowledge of Linux, MATLAB, python based neuroimaging analysis packages, and similar systems are required. Experience preprocessing and analyzing amyloid and tau PET and MRI imaging data using a variety of statistical packages, including SPM, FSL, and FreeSurfer are preferred. Must possess excellent communication and strong organizational skills. Must demonstrate an analytical mindset, excellent ability to attend to detail, superb problem-solving skills, and the ability to work independently as well as in a team setting. Knowledge in statistical analysis of neuroimaging data and experience using statistical packages e.g., R, SAS, SPSS.Possesses a willingness and ability to support a diverse and inclusive campus community. Applications can be submitted through this website: http://secure-web.cisco.com/1p9dusbzXfhud_haws8TdVK6yMNypE9bIi3p3TNwH7Qt9yH… opening.php?req=2195751&&cust_sort1=-1&cust_sort2=-1&cust_sort3=-1nohd&&internal=3932&nohd#job Schedule: Full Time -Days 40/wk -- Elizabeth Sharp Research Assistant Oh Lab Brown University

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Tracula path outputs quality checking
by Shanika Jayakody 28 Oct '22

28 Oct '22

External Email - Use Caution Dear FreeSurfer TRACULA team I have processed subjects using TRACULA on FS6.0 and 7.2. With both pipelines all the steps are completed without errors but for most subjects when I checked the pathstats.overall.txt file volume of the tract is almost equal to the length average. (unlike the example in Freesufer Wiki) I have attached pathstats for two people with (ID30720) and without (ID 30018) that problem (also attached one of my configuration files). Does this mean the tracts are not fully constructed? I was referring tracula freesurfer page and the following paper https://secure-web.cisco.com/1dIfxly6kRVrrbDgNkmQxrmTgb-DRd5cF1t7FkABP7tQos… I have done re-initializing of the tracts too without any luck of improving Even in freeview the tracts for 30720 looks like thin lines. I have been having this problem for a while and any suggestion to correct it will be much appreciated! Regrards Shanika

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conversion of .stats to .csv
by priya padma 27 Oct '22

27 Oct '22

External Email - Use Caution Dear Team, I would like to convert the .stats files that are being generated in the stats folder as an output from recon-all to csv file or excel file. Is there any way to convert .stats to .csv or .excel format? any help on this would be much appreciated. Thank you -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

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Trac-all -prep error with interreg
by Ashwati Vipin (Dr) 27 Oct '22

27 Oct '22

External Email - Use Caution Hello, I’ve been trying to run the first step of DTI processing for my subjects. In the config file I left the “interreg” option default as “5” but it gives me a “set variable name” error and prematurely stops the processing. When I set “interreg = 4” it gives “trctrain : at least one mean and/or Gaussian curvature file is missing (.H, .K)” error. I’m not sure if this is a problem with the ANTs installation which is why “interreg=5” doesn’t work but “interreg = 4” doesn’t work either. So I’m really not sure what’s happening. I’ve attached the log file and config file. For the ANTs installation I ran the following before running the trac-all command: export ANTSPATH=/Volumes/Macintosh\ HD/Applications/freesurfer/7.2.0/ants-2.4.1/bin/ export PATH=${ANTSPATH}:$PATH echo $ANTSPATH Could someone please help? Best, Ashwati -- Ashwati Vipin (PhD) Research Fellow – Dementia Research Centre (Singapore) Lee Kong Chian School of Medicine Nanyang Technological University, Singapore http://secure-web.cisco.com/1OSlDvqPJhl51Sc40lK71VUoqHNLymDzVOO62XWii17W08V…<http://secure-web.cisco.com/1OSlDvqPJhl51Sc40lK71VUoqHNLymDzVOO62XWii17W08V…> [signature_2362934844] ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

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overlay_threshold is ignored when using custom overlay
by Maya Yablonski 26 Oct '22

26 Oct '22

External Email - Use Caution Hello, I'm trying to use a custom colormap for an overlay in Freeview and I can't get the threshold option to work. Specifically, I want to display positive values with specific colors, and negative values with different colors, similarly to using the threshold with the default Heat colorscale ('Hot' for positive and 'cold' for negative, values outside the threshold do not appear at all). This is the code I've been using, and it seems to ignore the values provided by overlay_threshold: freeview -f <MYPATH>/sub-01/surf/lh.inflated:overlay=<MYPATH>tmap.curv:overlay_custom=-3,45,0,130,-9,220,210,250,3,255,70,0,9,255,255,0:overlay_threshold=3,9:overlay_color='clearlower','clearhigher' -colorscale This uses the right colors, but creates a continuous colorscale that spans -9 to 9, including the range [-3 3] which I want to threshold out of the map. I tried toggling the overlay_color='clearlower' and 'clearhigher', but couldn't find a combination that thresholded the low values around zero and not the extreme values (<-9 and >9). I also tested different values and seems like overlay_threshold is being completely ignored when overlay_custom is used. I couldn't get the right settings even when using the Freeview GUI. I tested this on Freesurfer versions 7.1.1 and 7.3.2 on MacOS Catalina (10.15.7). I'd appreciate any leads on this! Thanks, Maya

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Re: [Freesurfer] MRI recon-all failed at talairach
by fsbuild 26 Oct '22

26 Oct '22

External Email - Use Caution It looks like your terminal/character settings are messed up in the current terminal session.  That can happen from trying to look at a raw binary or image file in the terminal window or running something that outputs non-standard characters to the terminal (stdout).  I would open a new terminal window, source the freesurfer setup script, and try to identify if something you run corrupts the display of text in the new terminal window. - R. On 10/26/22 10:21, Douglas N. Greve (dgreve(a)mgh.harvard.edu) wrote: What is the error? The funny characters? Can you just send the entire logs (recon-all and avi.log)? On 10/25/2022 11:49 AM, Jonany, Vincent Joe wrote:         External Email - Use Caution         Dear FreeSurfer Developers, I am encountering a weird error in performing recon-all in my dicom directory. I believe the problem is here (snippet copied from talairach_avi.log. I have also attached here the recon-all.log, as well as the talaraich_avi.log. Does anyone know or have seen this problem before? I will appreciate any kind of help, please let me know if I need to provide anything else. FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: MacOS Monterey (apple silicon) $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ /Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 t4_read: talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4pupuÀþN èEÑ�àÔ�àÔ7SÎ0°þN #Öô>ÖxþN °þN �þN SÎðþN þN Ñ@ àþN � Ñ read error t4_read: transform initialized to I4 rotation matrix determinant 1.000000 Thank you in advance! I appreciate any help! Best, Vincent

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MRI recon-all failed at talairach
by Jonany, Vincent Joe 26 Oct '22

26 Oct '22

External Email - Use Caution Dear FreeSurfer Developers, I am encountering a weird error in performing recon-all in my dicom directory. I believe the problem is here (snippet copied from talairach_avi.log. I have also attached here the recon-all.log, as well as the talaraich_avi.log. Does anyone know or have seen this problem before? I will appreciate any kind of help, please let me know if I need to provide anything else. FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: MacOS Monterey (apple silicon) $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ /Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 t4_read: talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4pupuÀþN èEÑ�àÔ�àÔ7SÎ0°þN #Öô>ÖxþN °þN �þN SÎðþN þN Ñ@ àþN � Ñ read error t4_read: transform initialized to I4 rotation matrix determinant 1.000000 Thank you in advance! I appreciate any help! Best, Vincent

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dt_recon eddy correction fail and freeview errors
by Ward Deferm 26 Oct '22

26 Oct '22

External Email - Use Caution Dear Freesurfer Developers, I am trying to perform the dt_recon command for a single participant of my dataset. The original data comes from a philips scanner and was in the PAR/REC format. I converted these files to nifti’s using dcm2niix. This seemed to have worked as I got my nifti files and .bval and .bvec. However, when I run the dt_recon command it does not give me a hard error, but the output is not how it should be. Instead of taking 1-2 hours to complete the command, the command is done in about 3 minutes and I’m doubting if the eddy corrections are actually performed (fsl seems to be installed properly and is recognized when sourcing freesurfer. When trying to view the output with freeview I get 2 outcomes. Sometimes all of the file's work but there is no eddy correction performed and the FA volume is spread all over the brain when looking at this volume using freeview. But other times certain volumes either refuse to load or come up as a blank rectangle. In the freeview command line I then get the error: WARNING: 37103 NaNs found in volume /home/ward/freesurfer/subjects/testdtrecon/dti/ra.nii.gz In the attached files you can find the dt_recon log file. As for version and operating system I am running: 1) freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 2)Ubuntu 22.04.1 LTS Kind regards, Ward Deferm

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PostDoc (or qualified PhD) in Cognitive Computational Modeling (fMRI) in Copenhagen
by David Meder 26 Oct '22

26 Oct '22

External Email - Use Caution We are hiring a PostDoc (or qualified PhD student) on cognitive computational neuroimaging. This position is for you if you are interested in how the dopamine system works and like computational modeling. You would be part of a small and dynamic research project on the reward and motor systems in Parkinson’s Disease, embedded in the Movement Disorders research group at the Danish Research Centre for Magnetic Resonance. And all of that in the most liveable city in the world. For any inquiries or questions, write to davidm(a)drcmr.dk <mailto:davidm@drcmr.dk>. Follow this link for all details and for the application: https://secure-web.cisco.com/1P2UVw0p3pRPifdvgHBVRQ_b0Gh8fhcwt4AnFZTaVc0kpC… <https://secure-web.cisco.com/1P2UVw0p3pRPifdvgHBVRQ_b0Gh8fhcwt4AnFZTaVc0kpC…> Deadline is Nov. 13th David Meder Research Fellow Danish Research Centre for Magnetic Resonance DRCMR, Section 714 Copenhagen University Hospital Amager and Hvidovre Kettegaard Alle 30, 2650 Hvidovre, Denmark http://secure-web.cisco.com/15MpSS7cf-43ZjZWVO4wi088tGjgBnwHuBnw3d2e1b5falw…

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