Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

DenoiseImage shifting scan orientation
by Nathan Kindred (PGR) 09 Apr '22

09 Apr '22

External Email - Use Caution Hi, I have been using DenoiseImage from ANTs during pre-processing (DenoiseImage -i T1.nii -o denoised.nii.gz -v), however for some scans I am having an issue where this step is changing the scan orientation. The scans appear shifted so they now no longer match the orientation of my T2 scans. Does anyone know why this is happening and how to prevent it? Thank you, Nathan

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Advice: changing Freeview light source?
by Sam Buck Johnson 08 Apr '22

08 Apr '22

External Email - Use Caution Dear Freesurfer Community, I use Freeview to render 3D views of overlays on cortical surfaces. For my current processing, the absolute scale of the overlay map is important, and this absolute scale is distorted / marred by the shading that Freeview adds due to its default light source. (E.g., the top of the image is lighter than the bottom.) My question is this: is there any way to change the default light source of Freeview? I would prefer to use a uniform ambient light that did not cast any shadow, such that each pixel’s rendered intensity was exactly correlated with the absolute value of the visualized overlay in that pixel. If this is not possible, a point light source “at infinity” pointing directly into the plane of view might also suffice, since I believe it would produce a uniform illumination on a spherical base hemisphere. (I could be wrong here.) One final note: ideally this method would be possible to achieve by the command line, or failing that, to manually change in the GUI such that the setting would be preserved upon quitting and restarting Freeview. As always, any help is much appreciated. If someone happens to know that this functionality is absolutely not available, I would certainly like to know that, too. Thanks in advance. Sincerely, Sam Johnson Postdoctoral Scholar Brain and Education Lab, Stanford University GSE

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Re: [Freesurfer] Request for the pass code to expand the archive
by fsbuild 08 Apr '22

08 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 8, 2022, at 09:34, 李莹莹 <liyu_1104(a)yeah.net> wrote:        External Email - Use Caution        I understand and accept the riskAt 2022-04-08 21:22:22, "李莹莹" <liyu_1104(a)yeah.net> wrote:        External Email - Use Caution        Hi!Following the instructions on your wiki page, I would like to request the pass code to expand the archive of the file: FS_7_2_0_Ubuntu_18_04_06.ova.7z (Freesurfer 7.2.0 release in Ubuntu 18.04.06).. Thank you for your help!  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freesurfer 7.2.0 release in Ubuntu 18d // .ova.7z password
by fsbuild 08 Apr '22

08 Apr '22

External Email - Use Caution Sending the info to your email shortly. -R. On Apr 8, 2022, at 07:54, Anouck Matthijs <anouck.matthijs(a)student.kuleuven.be> wrote:        External Email - Use Caution        Hi!Following the instructions on your wiki page, I would like to request the pass code to expand the archive of the file:FS_7_2_0_Ubuntu_18_04_06.ova.7z (Freesurfer 7.2.0 release in Ubuntu 18.04.06).Thank you for your help!Anouck Matthijs, Phd-studentMotor control & Neuroplasticity research groupKU Leuven, Belgium_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FW: Announcing Neuromatch Academy courses for 2022!
by Fischl, Bruce 08 Apr '22

08 Apr '22

FYI ----------------------- Dear colleagues, We are excited to announce that Neuromatch Academy (NMA) is offering two courses this year from July 11th to July 29th 2022 which will run in parallel online. Applications for students and teaching assistants are now open until April 20th, 2022. NMA-Computational Neuroscience Flagship course covering contemporary computational neuroscience modeling and analysis techniques. Content: https://compneuro.neuromatch.io<https://secure-web.cisco.com/1WyCiMNQsY2EbX-OhP2xnE-8AIEBntEQUfSqtImZzbBlmv…> NMA-Deep Learning: In-depth advanced materials, ideal for graduate students and postdocs wishing to add computational techniques to their neuroscience research, or for individuals looking to dive into the Deep Learning world. Content: https://deeplearning.neuromatch.io<https://secure-web.cisco.com/1p8ODjCiUqGkTgPX1ZTtH4V7XoIaXZsCq2-2785Fcu0CWW…> Application Form: https://portal.neuromatchacademy.org/<https://secure-web.cisco.com/1qQc6w9pR8HHcsHhhmElXV8hJBJptrSQP8DPBxJhKmoOSX…> What is Neuromatch Academy? Neuromatch Academy (NMA) launched in 2020 as a response to the COVID-19 pandemic. Our aim is to provide globally-accessible, high-quality, TA-supported training in computational techniques related to neuroscience. In 2020 and 2021, NMA designed and ran a fully online 3-week Computational Neuroscience and a Deep Learning course for over 3000 students with more than 350 teaching assistants (TAs) working in virtual inverted (or flipped) classrooms and on small group projects. Fourteen languages, active community management, and low cost allowed for an unprecedented level of inclusivity and universal accessibility. What’s in a course? Our courses are intensive 3-week programs involving hands-on tutorials developed by experts in the field. Accepted students are placed into TA-led pods (groups) using the Neuromatch algorithm, which matches students with common interests who are in the same timezone and their preferred language for instruction. Students also receive personalized support as they work through hands-on tutorials and collaborate on course projects. [Please note that course participation requires active attendance and attention of the students for 3 weeks.] What does it cost? Neuromatch Academy’s mission is to make education affordable to everybody, no matter their financial background. We do this by pricing our courses significantly lower than other summer schools, adjusting for national economic factors, and allowing students to pay what they can when those adjustments are insufficient. Please see the website (https://academy.neuromatch.io/<https://secure-web.cisco.com/183dkl-QPcyXbhKRZXZt5et66_kZi_v87aZEvPXoNj8qW6…>) for additional information, and volunteer opportunities![https://secure-web.cisco.com/1zTmFqcfdC0LDKwMW7sdDxwITDoPV9h… Warm Regards, Neuromatch Academy team Stay in touch with us via these platforms: Website: https://academy.neuromatch.io/<https://secure-web.cisco.com/183dkl-QPcyXbhKRZXZt5et66_kZi_v87aZEvPXoNj8qW6…> LinkedIn: https://www.linkedin.com/company/neuromatch-academy<https://secure-web.cisco.com/1H8G1rXJWv4HcLUDF6fEm3vQug9Tb_ChwmDf3_8plqF6O4…> Instagram: https://www.instagram.com/neuromatch/<https://secure-web.cisco.com/1wMJSFlf9L3UBL-eTl_vSJ3lMtjd8T0C5waS1k833fdkmt…> Facebook: https://www.facebook.com/NeuromatchAcademy<https://secure-web.cisco.com/1jOxLH18FsNL2SVAeaSes23LMmAVfmexePMdVrjhui3umV…> Reddit: https://www.reddit.com/r/neuromatch/<https://secure-web.cisco.com/1FnME7knYQkBeMq8GcIOWUCRvbdw-3aMJMvAANvhj7YjHo…>

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Request for the pass code to expand the archive
by 李莹莹 08 Apr '22

08 Apr '22

External Email - Use Caution Hi! Following the instructions on your wiki page, I would like to request the pass code to expand the archive of the file: FS_7_2_0_Ubuntu_18_04_06.ova.7z (Freesurfer 7.2.0 release in Ubuntu 18.04.06). Thank you for your help!

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Freesurfer 7.2.0 release in Ubuntu 18d // .ova.7z password
by Anouck Matthijs 08 Apr '22

08 Apr '22

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FW: Postdoc positions
by Fischl, Bruce 07 Apr '22

07 Apr '22

FYI From: Irene Costantini <costantini(a)lens.unifi.it> Sent: Wednesday, April 6, 2022 4:08 AM To: Fischl, Bruce <BFISCHL(a)mgh.harvard.edu>; Boas, David <dboas(a)bu.edu>; Hof, Patrick <patrick.hof(a)mssm.edu> Cc: Mora, Jocelyn S. <JSMORA(a)mgh.harvard.edu> Subject: Postdoc positions External Email - Use Caution Dear all, we are currently trying to recruit two Postdocs to work on advanced microscopy and on software development. Would you be able to share the attached job ads to your department/any potential people who you think might be interested? The full job ads can be found here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://titulus.unifi.it/albo/viewer?view=files%2F004431997-UNFICLE-598a3c3…<https://secure-web.cisco.com/1kPhHLMBhUu-vS1faq6vimMDhXv3PtcQFBtc5k2peEW6yT…> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://titulus.unifi.it/albo/viewer?view=files%2F004427588-UNFICLE-c354f42…<https://secure-web.cisco.com/1JBNr871Fgprip5XORZ2gZWpsLO-VnaqUfVFqgp0Q3jkGP…> Please do not hesitate to get in touch if you would like any further information. Best wishes, -- Irene Costantini LENS - European Laboratory for Non-linear Spectroscopy Department of Biology, University of Florence Via Nello Carrara 1 50019 Sesto Fiorentino (FI) Italy Tel: +39 055 4572514 Lab: +39 055 4572018 Fax: +39 055 4572451 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.lens.unifi.it <http://secure-web.cisco.com/1w_0GSbPHOhggn34U8KRMYqYHJDBT7ccvhpkiJAoMX4lTHh…> <http://secure-web.cisco.com/1w_0GSbPHOhggn34U8KRMYqYHJDBT7ccvhpkiJAoMX4lTHh…> Topic Editor of "The Human Brain Multiscale Imaging Challenge", an ongoing research topic in "Frontiers in Neuroanatomy". More information about the project can be found here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.frontiersin.org/research-topics/18963<https://secure-web.cisco.com/1g6AJLqbnosx-2r4RmfYffqDh7QEgP9Y48I7h-ySN448Il…>

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Using Glaser Atlas (HCP-MMP1) on Standard Recon-All
by Ruben sn:: RMO2cmZlbA== 07 Apr '22

07 Apr '22

External Email - Use Caution Hi all, I'm trying to use the Glaser atlas (HCP-MMP1) to get thickness, volume, and area measures for an existing fs-subject, meaning that the standard recon-all was already performed. I was able to extract some measures, but it would be nice to get verified that my approach is valid. I'm using FreeSurfer 7.1 and have already applied standard recon-all to all my subjects. The following variables are used: $subjid = folder name of the recon-all output for a specific subject $hcpdir = the directory where I stored the annotation files for the hcp-atlas I got annotation files with the atlas projected onto fsaverage from here https://secure-web.cisco.com/1I7iKyRV6ybWIIhCzcBweKSPq9s7w7SmrhQN_FfL8XYj8j…. Then I applied the annotation files to get the statistics file using: mris_anatomical_stats -th3 -mgz -cortex $subjid/label/lh.cortex.label -f lh.hcp.stats -b -a $hcpdir/lh.HCP-MMP1.annot f475 lh white Subsequently, I used the following commands to extract measures in CSV files. aparcstats2table --delimiter comma --subjects $subjid --parc hcp --hemi lh --meas area --transpose --tablefile lh_hpc_area_stats.csv aparcstats2table --delimiter comma --subjects $subjid --parc hcp --hemi lh --meas volume --transpose --tablefile lh_hpc_volume_stats.csv aparcstats2table --delimiter comma --subjects $subjid --parc hcp --hemi lh --meas thickness --transpose --tablefile lh_hpc_thickness_stats.csv Is this a valid approach, and would I get meaningful values, or would I have to run some other additional steps? Kind regards, Ruben Dörfel.

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Hippocampal Segmentation issue on Freesurfer 7.2.0 on MacOS Monterey 12.2
by Ashwati Vipin (Dr) 06 Apr '22

06 Apr '22

External Email - Use Caution Dear Freesurfer developers, The hip segmentation starts running and the matlab icon pops up as well but it stops abruptly and shows this error instead: #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Wed Apr 6 13:44:29 +08 2022 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0/MCRv84//bin/maci64:/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0/lib/gcc/lib: Registering imageDump.mgz to hippocampal mask from ASEG Error using images.internal.morphmex Invalid MEX-file '/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/morphmex.mexmaci64': dlopen(/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/morphmex.mexmaci64, 0x0006): Library not loaded: @rpath/libmwimages_res.dylib Referenced from: /private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/morphmex.mexmaci64 Reason: tried: './libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64/libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64/libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/lib/gcc/lib/libmwimages_res.dylib' (no such file), '/libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/./libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/../../../../../bin/maci64/libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/../../../../../sys/os/maci64/libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/./libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/../../../../../bin/maci64/libmwimages_res.dylib' (no such file), '/private/tmp/MCR_3070620170/.mcrCache8.4/segmen0/toolbox/images/images/+images/+internal/../../../../../sys/os/maci64/libmwimages_res.dylib' (no such file), '/Applications/MATLAB_R2014b.app/bin/maci64/libmwimages_res.dylib' (no such file), '/Applications/MATLAB_R2014b.app/bin/maci64/./libmwimages_res.dylib' (no such file), '/Applications/MATLAB_R2014b.app/bin/maci64/../../sys/os/maci64/libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/./libmwimages_res.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/../../sys/os/maci64/libmwimages_res.dylib' (no such file), '/usr/local/lib/libmwimages_res.dylib' (no such file), '/usr/lib/libmwimages_res.dylib' (no such file) Error in images.internal.morphop (line 99) Error in imerode (line 122) Error in segmentSubjectT1_autoEstimateAlveusML (line 188) MATLAB:invalidMEXFile Darwin Ashwatis-MacBook-Pro.local 21.3.0 Darwin Kernel Version 21.3.0: Wed Jan 5 21:37:58 PST 2022; root:xnu-8019.80.24~20/RELEASE_ARM64_T8101 arm64 T1 hippocampal subfields exited with ERRORS at Wed Apr 6 13:44:48 +08 2022 For more details, see the log file /Users/ashwativipin/Desktop/Freesurfer/Stats//BIOC_0001_v01_T1_FS/scripts/hippocampal-subfields-T1.log I’ve attached the logfile as well. ls /Applications/freesurfer/7.2.0/MCRv84/ gives me the following output: [cid2539829440*image001.png(a)01D849BC.F5AB1960] Please help. Best, Ashwati -- Ashwati Vipin (PhD) Research Fellow - Dementia Research Centre Lee Kong Chian School of Medicine Nanyang Technological University, Singapore [signature_1222593402] ________________________________ 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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