Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Re: [Freesurfer] Does FS guarantee the same results if run several times?
by Xiaojiang Yang 17 Apr '20

17 Apr '20

External Email - Use Caution No. I just checked, they are not identical. Although some of numbers are the same, many are different. Xiaojiang Are the other results identical? Eg, lh.aparc.stats? On 4/17/2020 10:49 AM, Xiaojiang Yang wrote: External Email - Use Caution Dear Freeserfer developers, I have run recon-all for a bunch of subjects on the same machine for several times. When I use the "mris_anatomical_stats" to calculate the statistics (specifically, I am interested in average cortical thickness), I found that for the same subject I got different results, as shown below: $ mris_anatomical_stats -b QEN001 lh . 128449 86239 243375 2.588 0.876 0.123 0.026 1496 133.3 /xxx./subjects/QEN001/surf/lh.white $ $ mris_anatomical_stats -b QEN001_old lh . 128449 86241 229554 2.404 0.835 0.123 0.026 1496 133.3 /xxx./subjects/QEN001_old/surf/lh.white The results shows that some of the stats numbers ( such as the number of vertices) are the same, but the "average cortical thickness +- standard deviation (mm)" are different, and they differ quite a lot. I have tried several subjects; some of them get the all-the-same results, some of them not. I am sure the subjects and the corresponding images are the same. Are these expected results? Thanks! Xiaojiang

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Does FS guarantee the same results if run several times?
by Xiaojiang Yang 17 Apr '20

17 Apr '20

External Email - Use Caution Dear Freeserfer developers, I have run recon-all for a bunch of subjects on the same machine for several times. When I use the "mris_anatomical_stats" to calculate the statistics (specifically, I am interested in average cortical thickness), I found that for the same subject I got different results, as shown below: $ mris_anatomical_stats -b QEN001 lh . 128449 86239 243375 2.588 0.876 0.123 0.026 1496 133.3 /xxx./subjects/QEN001/surf/lh.white $ $ mris_anatomical_stats -b QEN001_old lh . 128449 86241 229554 2.404 0.835 0.123 0.026 1496 133.3 /xxx./subjects/QEN001_old/surf/lh.white The results shows that some of the stats numbers ( such as the number of vertices) are the same, but the "average cortical thickness +- standard deviation (mm)" are different, and they differ quite a lot. I have tried several subjects; some of them get the all-the-same results, some of them not. I am sure the subjects and the corresponding images are the same. Are these expected results? Thanks! Xiaojiang

2 1

concatenate transformations
by Sam W 17 Apr '20

17 Apr '20

External Email - Use Caution Hello! I performed two registrations: diffusion-to-orig.dat and orig-to-rawavg.dat. Now I would like to concatenate the two transformation matrices into a diffusion-to-rawavg.dat. Is there a command in freesurfer that allows me to do that? Best regards, Sam

2 1

BIDS v1.3.0 release and next focus
by Franklin Feingold 15 Apr '20

15 Apr '20

External Email - Use Caution The Brain Imaging Data Structure<https://bids.neuroimaging.io/> (BIDS) community is pleased to announce version 1.3.0 of the BIDS standard! This release includes the addition of genetic descriptors<https://bids-specification.readthedocs.io/en/v1.3.0/04-modality-specific-fi…> for linking BIDS datasets to genetic datasets. We would like to thank contributors to the Genetic Information BIDS Extension Proposal, led by Cyril Pernet, Clara Moreau with contributions from Tom Nichols and Jessica Turner. We’d also like to thank Arshitha Basavaraj and Tom Nichols for rendering the specification as a PDF<https://zenodo.org/record/3720628#.XpYUPNNKjFQ>. Our next priority will be finalizing the specification of BIDS-Derivatives<https://github.com/bids-standard/bids-specification/pull/265>. Please feel free to review the draft<https://bids-specification.readthedocs.io/en/common-derivatives/05-derivati…> and comment. The specification of spatial references, in particular composite surface/volume spaces, remains an open question<https://github.com/bids-standard/bids-specification/pull/301> with room for expert review.

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Data onto the Freesurfer surface
by Mason Wells 15 Apr '20

15 Apr '20

External Email - Use Caution Hi all, I apologise for cross-posting to both FSL and Freesurfer lists. I am trying to use an analysis package that works on surface based data (SamSrf). I have ran Feat and have a filtered_func file which is of course the motion corrected/unwarped version of my EPI. However, I need some advice on how to get these data onto the Freesurfer surface. I have found this page<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer>, but I wanted to double check this is the most up-to-date pipeline. On the page it suggests using the same DOF as used in Feat, I use BBR so this seems a little redundant. Has anyone on these lists got any experience of getting filtered_func onto the Freesurfer surface? Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Question on using T2 or FLAIR data to improve pial surfaces
by Tim Schäfer 15 Apr '20

15 Apr '20

External Email - Use Caution Dear FreeSurfer experts, I have both T2 and FLAIR images for the majority of the subjects in my study, and I want to use them to improve pial surface reconstruction during recon-all as explained in [1]. My questions are: 1) In general, should I prefer FLAIR over T2, or the other way around? 2) Some subjects (< 10%) do not have a FLAIR image, and others do not have a T2. Do you think that it is fine to use FLAIR for some subjects, and T2 for others, in the same study? We will perform manual QC after the recon-all run and exclude bad quality images, so I feel it should be fine, but I wanted to hear your opinion. Best, Tim [1] https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimp… -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Trac-All Error
by Hua, Jessica 15 Apr '20

15 Apr '20

External Email - Use Caution Attached are bvecs and bvals. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Freesurfer display resolution very low compared to other viewers
by Renner, Brian 14 Apr '20

14 Apr '20

External Email - Use Caution Hello all! Inaugural message to the list; I will attempt to be brief with the project description. The setup is consistent between both versions 6.0.0 and 7.0.0-beta, run on a high performance cluster, accessed through macOS terminal + Xquartz, most recent versions all. As it stands, our group is attempting to do subfield analysis of hippocampal analysis and lesion measurement in MS subjects. We have noticed that there is a major discrepancy of resolutions between files, which has irked some of our physicians undertaking the lesion measurement. We need to resolve the lesions down to 3mm and have noticed the quality between freeview and fsleyes of the same nifti files will yield much lower display resolution. This is true for most scans, though it has been compared using 1mm T2 FLAIR sequences as well as T2* sequences with 0.65mm voxel space. I have been attempting to find a workaround as the current solution for the physicians is to look at the files in fsleyes and then measure them with the ruler tool in freeview. I can send supporting pictures as necessary. Thank you in advance for any thoughts you may have! BR -- Brian Renner, MD Research Associate, Neurology brian.renner(a)cshs.org<mailto:brian.renner@cshs.org> Cedars-Sinai 127 S. San Vicente Blvd, Suite A6600 : Los Angeles CA 90048 office 310-423-1589 : mobile 310-658-3492 : cedars-sinai.org<https://www.cedars-sinai.org/> IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.

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Re: [Freesurfer] FreeSurfer UbuntuVM password
by fsbuild 14 Apr '20

14 Apr '20

External Email - Use Caution I will send it directly to your email in a minute. R. On Apr 14, 2020, at 16:53, sapere-aude(a)tuta.io wrote:        External Email - Use Caution        Hi,the FreeSurfer Ubuntu VirtualBox Virtual Machine asks for a password to log in (see the attached image).I can't find any information about what this password is on the tutorial page:https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_winCould anyone help me with the password to the VM?kind regards,Sapere-Aude<Ubuntu password.PNG>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer UbuntuVM password
by sapere-aude＠tuta.io 14 Apr '20

14 Apr '20

External Email - Use Caution Hi, the FreeSurfer Ubuntu VirtualBox Virtual Machine asks for a password to log in (see the attached image). I can't find any information about what this password is on the tutorial page: https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_win Could anyone help me with the password to the VM? kind regards, Sapere-Aude

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