Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

recon-all error
by cooperr1＠student.unimelb.edu.au 09 Apr '22

09 Apr '22

External Email - Use Caution Dear FreeSurfer developers, I'm attempting to run recon-all on a set of T1-weighted images acquired in the 1980s-1990s and am having trouble with the recon-all pipeline. I have used the original dicom files in the recon-all using the command below. Command: recon-all -s 1003156_dicom -i 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all Error message: /Applications/freesurfer_v6/bin/mri_convert: line 3: 8196 Segmentation fault: 11 mri_convert.bin "$@" The recon-all.log is also attached. I've also explored using dcmunpack and obtain the following result: Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 Message: cat: /tmp/dcmdir-all.89439: No such file or directory Found 0 unique series: Patient: Undefined variable. Do you have any idea what might be the problem? Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: Mac OS X 10.13.3 Recon-all.log: attached. With warm regards, Rebecca Cooper

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Re: [Freesurfer] mkheadsurf error: mris_smooth and mris_inflate synthesized bizarre output paths
by Megan Schendel 09 Apr '22

09 Apr '22

External Email - Use Caution Hello, I am also trying to use mkheadsurf and getting the same errors described in the January topic by user Yong-Jun Lin. https://secure-web.cisco.com/1gWrCRE26r6WP8WhRpdFnJDHSFKaCpEOt6y_UEivpQG5fG… 1. The first error message is "subjdir: Undefined variable.". I followed the thread and also manually defined subjdir 2. Same problems with mris_smooth -n 10 -b /.. resulting in error: MRISwriteCurvature: could not open lh./... and mris_inflate -n 10 -sulc /... resulting in error: MRISwriteCurvature: could not open /... Lastly, I followed the response from Douglas N. Greve <https://secure-web.cisco.com/1ahbUvtJEJ2YIzAb-v2Vq6dQ8vxhI4tzwwkf_H3Yz4GyLG…> to try the new mkheadsurf. When I tried that, the subjdir error went away, but the output paths errors with the mris_smooth and mris_inflate persisted. The end result output files that I need were created, however, so I can go on with my work. But I thought I'd reply to the list and let you know that I'm also getting these path errors. Thanks for any help, Megan MEG Technician Pronouns: she/her The Mind Research Network 1101 Yale Blvd. NE Albuquerque, New Mexico 87106

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Freesurfer stats output meaning
by Rafael Navarro 09 Apr '22

09 Apr '22

External Email - Use Caution Hello Freesurfer developers, I am attempting to build a brain age estimator with FreeSurfer output. However, I am having some problems disentangling Freesurfer stats output. I will be using only the Desikan-Killiany atlas cortical segmentation. I have identified these files as useful: aseg.stats -> subcortical segmentation features lhaparc.stats -> DK cortical segmentation left hemisphere features rhaparc.stats -> DK cortical segmentation right hemisphere features lh.w-g.pct.stats -> DK cortical segmentation left hemisphere grey matter - white matter contrast features rh.w-g.pct.stats -> DK cortical segmentation right hemisphere grey matter - white matter contrast features wmparc.stats -> white matter close to DK cortical segmentation areas features However, I checked these two files too: lh.curv.stats rh.curv.stats But I don't have a clear idea of the meaning of the features in those files. For what I understand the features are the mean and standard deviation of the white matter surface and the pial surface. However, these measurements would be redundant if I include the features from xhaparc.stats, wouldn't they? Thanks for your help! ___________________________________ ----------------------------------- || Rafael Navarro González || Ph.D. Student || ETSI Telecomunicación || Universidad de Valladolid || Campus Miguel Delibes || 47011 Valladolid, Spain || e-mail: rafael.navarro(a)uva.es || Phone: +34 672 394 294 ||_________________________________ -----------------------------------

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Medial prefrontal cortex
by Patricia Schwery 09 Apr '22

09 Apr '22

External Email - Use Caution Hi there, I would like to know if someone could tell me how i can measure the medial prefrontal cortex (mPFC) with freesurfer as i see it is displayed within the superior frontal but i would need only the mPFC. I thank you so much for your help. Patricia

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recon-all error in a specific data
by Lee, Jeungchan 09 Apr '22

09 Apr '22

Hi freesurfer team, I collected an MPRAGE in Bay2 scanner (0.75 x 0.75 x 0.75 mm resolution), and the recon-all procedures with freesurfer version 6.0.0 and 7.1.1 were both failed. I'm not sure if this is due to the participant's large CSF or motion or something else. I have attached the log files (recon-all.log and talairach.log from both versions), which I noticed a warning/error in the recon-all.log : (version6.0.0) WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. (version6.0.0 and 7.1.1) ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) mritotal -verbose -debug -clobber -modeldir /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.7133/src.mnc transforms/talairach.auto.xfm Can't locate shellwords.pl in @INC (@INC contains: /autofs/cluster/pubsw/1/pubsw/Linux2/packages/mni/1.4/bin/../lib/mni_autoreg /usr/local/freesurfer/stable6_0_0/mni/share/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/mritotal line 460. ERROR: mritotal failed, see transforms/talairach.log I have tested the recon-all with another Bay2 data (from different project in our group), and it worked perfectly (with version 6.0.0) with the same script. Thus, I did not think this is due to my script or FS version.. Thanks, Jeungchan

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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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