Freesurfer June 2020

freesurfer@nmr.mgh.harvard.edu

91 participants
130 discussions

New option to run (Freeview) under Windows 10
by fsbuild 03 Jun '20

03 Jun '20

External Email - Use Caution Hello Freesurfer List Subscribers, Please be aware we have added another option to enable Freeview to run under Windows 10. In addition to the VirtualBox Ubuntu disk image you can download, there is now documentation about how to run Freeview in a Linux image using the Windows Subsystem for Linux (WSL).  The new web page is https://surfer.nmr..mgh.harvard.edu/fswiki//FS7_wsl.  We would be happy to receive feedback from users who try this option (the example is for how to run CentOS7 under WSL).   I recommend you first read through the web pages before trying the procedure. The disk image for the Ubuntu 18 VM has been updated to contain the freesurfer 7.1.0 release out of the box.  The wiki pages for running the VM on Windows (https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67_win) and the Mac (https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67_mac) have both been updated.  There is a new link on those pages to the updated disk image. Thank you in advance for your time, attention and any feedback you care to offer. - R.

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job add MR-Physicist/Engineer
by Michael Marxen 02 Jun '20

02 Jun '20

External Email - Use Caution Dear colleagues, we are currently looking for an MR-Physicist/Engineer at the post-doctoral level at the TU Dresden. Details can be found here: https://www.verw.tu-dresden.de/StellAus/download.asp?file=06-2020\Krug_WIMI… Please, distribute to your peers. Best regards, ------------------------------------------------------------------------------------ Michael Marxen, Ph.D., Dipl.-Phys. Group Leader Imaging Physics Department of Psychiatry and Neuroimaging Center Technische Universität Dresden Würzburger Str. 35 01187 Dresden Germany Phone: +49 (351) 46342212 Fax: +49 (351) 46342202 E-Mail: michael.marxen(a)tu-dresden.de<mailto:michael.marxen@tu-dresden.de> Web: https://tu-dresden.de/bereichsuebergreifendes/nic/forschung/grps_med/imagin… ------------------------------------------------------------------------------------?

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using freesurfer, Is it ok to compare cortical thickness for group-1 people from one scanner, while control group from another acanner
by John 02 Jun '20

02 Jun '20

External Email - Use Caution Hi friends, Using freesurfer, Is it ok to compare cortical thickness for group-1 people from one scanner, while control group from another acanner? Thanks.

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command not found: tksurfer
by ZhangBo 02 Jun '20

02 Jun '20

External Email - Use Caution Hi teams, After installing freesurfer-7.0.0 in MacOS 10.15.4, I followed the testing guid in https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer. It is ok for freeview, however for tksurfer and tkmedit, I get errors "zsh: command not found: tksurfer", "zsh: command not found: tkmedit". Could you please give some advice about how to solve this? Thanks. Bo

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Does freesurfer must use 3-D T1
by John 01 Jun '20

01 Jun '20

External Email - Use Caution Hi teams, Does freesurfer must use 3-D T1 to calculate cortical thickness? Thanks

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Compiling freesurfer 6.0 on centos 8.1
by Aaron Tanenbaum 01 Jun '20

01 Jun '20

External Email - Use Caution Hello All, I was wondering have any of you compiled FreeSurfer 6.0 on centos 8.1. And if so, have you had problem with it. Our lab got a new server, we are contemplating which operating system we should install. So I am going through the software to see what works and what does not on different versions of centos. Aaron Tanenbaum

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Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)
by Iglesias Gonzalez, Juan E. 01 Jun '20

01 Jun '20

Hi Elizabeth, segment_T1.sh uses a bunch of files in native space for initialization that you’d also have to deform, if you wanted to run it in MNI space. I think the easiest would be to run it in native space, and then warp the segmentation to MNI, using e.g., the registration given by CVS. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Elizabeth Haris <e.haris(a)unsw.edu.au> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, May 27, 2020 at 23:11 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152) External Email - Use Caution Hi guys, I’m wanting to run segmentHA_T1.sh on an MNI152 registered brain. On my subject, I have run recon-all, then run mri_cvs_register to obtain a brain image registered in MNI152 space. My questions are: 1. In recon-all, is there a way to specify registration to MNI152 space, or is it necessary to first run recon-all and then to run mri_cvs_register? 2. Is it possible to run the segmentHA script on the brain registered in MNI152 space? I’m unable to find where I would specify the use the cvs/norm.mgz (instead of the mri/norm.mgz file). And from what I can see in the script, the parameters set in lines 179/180/181 (below) point to fsaverage brain files, which don’t appear to be the correct targets for the new MNI152 brain; however, there are no corresponding output files in the cvs folder, so I am unsure how to define these parameters. 3. Is there anything I have missed and would also need to do to run the segmentHA script on an MNI152 brain? (I have previously run the script on the average brain and all went well.) 179 set ATLASMESH="$FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz"; 180 set ATLASDUMP="$FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz"; 181 set LUT="$FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt"; Thanks in advance, Elizabeth

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mri_vol2surf
by Nasr, Shahin,Ph.D. 01 Jun '20

01 Jun '20

Hi Surfers, Is there anyway to pass the full address of a surface to mri_vol2surf? To clarify, we are using surfaces that are saved outside <SBJ>/surf/ and we prefer not to relocate them every time that we want to use mri_vol2surf. Thanks

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Freesurfer 7 long -> cross surfaces
by Chris Adamson 01 Jun '20

01 Jun '20

External Email - Use Caution I had a script that transformed volumes and surfaces from long (base) space back to cross space for comparison. It doesn't work in Freesurfer 7 and I haven't been able to figure out why. Volumes work with the same code but surfaces are misaligned in cross space. The code is below, any thoughts on how to fix it? Cheers. SURFS="white pial inflated" HEMIS="lh rh" cd $SUBJECTS_DIR/$LONG/surf lta_convert --inlta $SUBJECTS_DIR/$BASE/mri/transforms/${CROSS}_to_${BASE}.lta --outreg register.native.dat --src $SUBJECTS_DIR/$CROSS/mri/rawavg.mgz for CURHEMI in $HEMIS do for CURSURF in $SURFS do mri_surf2surf --sval-xyz $CURSURF --reg-inv register.native.dat --tval $SUBJECTS_DIR/$OUTDIR/surf/$CURHEMI.$CURSURF --tval-xyz $SUBJECTS_DIR/$CROSS/mri/rawavg.mgz --hemi $CURHEMI --s $LONG done done Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT) Software Engineer, Cardiovascular Research (0.7 EFT) Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.

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Issues with bbregister
by Mason Wells 01 Jun '20

01 Jun '20

External Email - Use Caution Hi Experts, I am using bbregister to align functional data to anatomical space. I have been using the bbregister command with a combination of different flags. However, there appears to be varying levels of poor registration. The first command I used included flags for a whole brain reg image and the --init-header flag. As you can see in the attached image titled tkreg 1, there is a misalignment. bbregister --s PPT_1x --feat /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat/ --int Data/PMA_retinoScans/PPT_1x/WholeEPI.nii.gz --init-header I then removed the –int (whole brain reg image) flag. Again the registration is massively misaligned (image titles reg1) bbregister --s PPT_1x --feat /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat --init-header I then removed the –init-header flag. Again poor registration (image titled reg 2) Then I removed both flags. This was the best registration (see attached image titled reg 3), but even this still looks a little bit off to me. You can see that around the occipital lobe, there white matter isn't aligned very well. bbregister --s PPT_1x --feat /Data/PPT_1x/run1_pre_processed_functional.feat/ Can anyone give me any advice on this? I really am unsure as to which why these flags failed to aid registration. I have 3 other participants from a different dataset for which the bbregister pointing to the feat directory and the –init-header flag worked perfectly. Any advice would be great. 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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Freesurfer June 2020