Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Mixing freesurfer versions
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 08 Jun '20

08 Jun '20

Hi FS developers, I have a dataset that I am working on that has a mix of build stamps, including centos v6.0.0-2beb96c, centos dev-20190118, and dev-20180220 (a mess that was a little bit out of my control). I understand that these are all variations of FS6, and was wondering if its sufficient to leave them as is. Was there any meaningful changes in the recon-all steps that would warrant redoing some of these brains? Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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tkregisterfv -ss
by Boris Rauchmann 08 Jun '20

08 Jun '20

External Email - Use Caution Dear all, is there a way to use freeviews -ss command to obtain snapshots using tkregisterfv? I have a bunch of registrations to check and would prefer to do that using a bash script and snapshots. tkregisterfv --mov template.nii.gz --reg template.reg.lta --surfs -ss Gives back ERROR: Flag -ss unrecognized. Thanks, Boris

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mz3 for freesurfer brain render
by Kate Marvel 08 Jun '20

08 Jun '20

External Email - Use Caution Hi Freesurfer team, I would like to do a brain render using freesurfer ROIs. Is there .mz3 file for freesurfer brain atlas? Thanks, -- kate

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statement on recent events
by Fischl, Bruce R, 08 Jun '20

08 Jun '20

Not everything that is faced can be changed. But nothing can be changed until it is faced" -- James Baldwin. In these troubling times, it is increasingly obvious that silence is tantamount to complicity. If we do not object to objectionable events, we are tacitly condoning them, and as such we have an obligation to use platforms that are available to us. It is the responsibility of those in privilege to speak up. In that light we would like to express our horror and dismay at the recent, and not-so-recent, brutal attacks on George Floyd, Breonna Taylor, Ahmaud Arbery, Sandra Bland, Trayvon Martin, Freddie Gray, Eric Garner, Michael Brown, Tamir Rice, Philando Castile, Amadou Diallo, and so many others, many of whom we will never hear about. While some of us in the ivory tower like to think of ourselves as far-removed from this type of racism, we are of course not, as we all have biases both large and small. As such, it behooves us to consider these events and our own actions, and how we can work to create a more just, equitable and safe society. The global outrage generated by these horrific events is an opportunity to effect change. Racism remains after media coverage ceases, and it is our responsibility to ensure equality and respect are provided to those around us. We are committed to building an equitable and diverse workplace and progressing towards a fairer world. A non-exhaustive set of resources for advancing diversity can be found at: http://wis.martinos.org/black-lives-matter<http://wis.martinos.org/black-lives-matter/> Bruce Fischl Allison Stevens Lilla Zollei Caroline Magnain Chiara Maffei Anastasia Yendiki Brian Edlow Aina Frau-Pascual Matthew Vera Kimberly Nestor Holly Freeman Robert Jones Viviana Siless Andrew Hoopes Eugenio Iglesias Douglas Greve Ruopeng Wang André van der Kouwe Natalya Slepneva David Salat Divya Varadarajan Iman Aganj Hui Wang Robert Frost Matt Larrabee Jean Augustinack Leah Morgan Adrian Dalca Malte Hoffmann Martin Reuter Emily Williams Devani Cordero Paul Wighton Hamid Behjat Danielle Pace

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Freesurfer 7.1.0 - mris_flatten distortions
by Devavrat Vartak 07 Jun '20

07 Jun '20

External Email - Use Caution Hi Freesurfer community, OS: MacOS 10.14.6 I am cutting surfaces to make flat patches in freeview (Freesurfer 7.1.0) on and flatten them. The flat patches appear to have distortions ( https://imgur.com/a/KwG3iTa) This process worked well in FS6. I use mris_flatten -w 10 <input_file.3d> <output_file.flat> to flatten them. Additionally, when I use mri_surf2vol to convert the patch to a 3D nifti volume, I get an error. mri_surf2vol --ribbon <mri/ribbon.mgz> --o /<roi_patch/oc_full_patch.nii.gz> --subject <sub> --so </lh.inflated> </lh.occipital.patch.flat> ERROR: MRISreadCurvAsMRI: <path/to/freesurfer/recon_all/surf/lh.occipital.patch.flat, vals/vertex -12428437 unsupported Any idea why this is happening? Thank you, Dev

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Freesurfer statement
by Juranek, Jenifer 07 Jun '20

07 Jun '20

External Email - Use Caution I pledge to do better. I pledge to pursue systemic change as passionately as I pursue research questions. Thank you Freesurfer Team for speaking up so eloquently with your signed statement. Jenifer Juranek

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flirt.fsl error (NEWMAT::SingularException) when running bbregister in Freesurfer 7.0.0
by julienbesle 06 Jun '20

06 Jun '20

External Email - Use Caution Hi, I just installed freesurfer v7 and I'm getting an error in a script that calls bbregister with the --fslmat and --init-fsl options. This error does not occur in freesurfer v6 even when using exactly the same data, but it does also occur with a development version of freesurfer I downloaded in Sept 2019 (exact same error). The call is: DEBUG : 2020-05-06 12:07:12,816 : runCmd : Running: bbregister --s HLOSS_p5 --mov /home/julien/data/HLOSS/pilot05_B/DWI/B0_corrected_mean_resampled_MPRAGE.nii --reg /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/b0-TO-orig.dat --fslmat /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/b0-TO-orig.mat --init-fsl --dti The error occurs when bbregister calls fsl.flirt: INFO : 2020-05-06 12:08:24,560 : main : flirt.fsl -ref /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/refvol.fslregister.nii -in /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/reg.init.dat.fsl.mat0 INFO : 2020-05-06 12:08:55,102 : main : Wed May 6 12:08:54 EEST 2020 INFO : 2020-05-06 12:08:55,603 : main : /mnt/f/data/HLOSS INFO : 2020-05-06 12:08:56,105 : main : flirt.fsl -ref /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/refvol.fslregister.nii -in /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/reg.init.dat.fsl.mat -init /home/julien/data/HLOSS/pilot05_B/DWI/easy_lausanne_test/tmp.bbregister.8331/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch INFO : 2020-05-06 12:09:15,632 : main : terminate called after throwing an instance of 'NEWMAT::SingularException' INFO : 2020-05-06 12:09:15,633 : main : Abort (core dumped) INFO : 2020-05-06 12:09:15,634 : main : ERROR: flirt CRITICAL : 2020-05-06 12:09:15,634 : runCmd : Return Value: 1 It looks like the first time flirt.fsl is called everything goes fine, but the second time, the error occurs. Unfortunately this is not a script I wrote myself, so I'm not sure what this particular call to bbregister is supposed to achieve. I'm not sure the call to fsl.flirt depends on which version of FSL I have installed, but just in case, I used the FSL v6 and didn't change anything to the FSL installation between trying Freesurfer v6, dev or v7. I run everything on Ubuntu 16.04 running on WSL on Windows 10. Any idea what could be going wrong? Thanks Julien -- ------------------------------------- Julien Besle Lagos Center, Apt 9A Sadat Street Beirut Lebanon tel: +961 78 980 317 -------------------------------------

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Permutation simulation cluster include vertices below cluster-forming threshold
by Fengdan Ye 05 Jun '20

05 Jun '20

External Email - Use Caution Hello Freesurfers, I am using mri_glmfit-sim to find significant clusters using permutation simulation. My command is as follows: mri_glmfit-sim \ --glmdir lh.cn_ad.glmdir \ --perm 1000 3.0 pos \ --cwp 0.05 \ --2spaces \ --bg 1 When I opened the *.sig.masked.mgh, I noticed that some vertices below the cluster forming threshold (3.0) were also included (the lowest value I found in the cluster was around 2.5). These vertices also seem to be on the edge of the cluster. Based on the FsTutorial, the permutation simulation should exclude all vertices below the cluster forming threshold. Is there any sort of smoothing done on the clusters that could have caused the vertices below CFT to be included? I checked the mail archive and found this thread that have exactly the same question, but with no answer: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15375.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15375.html> Thank you, Fengdan

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mri_watershed
by Edoardo Pinzuti 05 Jun '20

05 Jun '20

External Email - Use Caution Dear Freesurfer community, I have a question regarding the mri_watershed. Is the inner_skull extracted from the brain.mgz which gets masked by the brainmask.mgz automatically? Thanks

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dura edits .mgz~ file?
by KennethSPrice 05 Jun '20

05 Jun '20

External Email - Use Caution Hello Freesurfers, I edited the brainmask.mgz file after running recon-all but no changes were saved. Instead I have a mysterious 'brainmask.mgz~' file that I cannot open with freeview. What is this file and does it contain my edits? If so how do I convert it? Already tried mri_convert. Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

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