Freesurfer October 2022

freesurfer@nmr.mgh.harvard.edu

89 participants
132 discussions

Re: [Freesurfer] matlab 2019b and brainstem substructures analysis
by fsbuild 18 Oct '22

18 Oct '22

External Email - Use Caution Hello Jung, You can try either matlab R2014b or R2019b with the commands below. You should have already set FREESURFER_HOME in your Environment to point to where it is installed …. I will list a default location here for a linux install but what you set for FREESURFER_HOME should not matter (as long as it is a valid path). $ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0 … then you should run the provided script to install one of the above Matlab environment with either the argument R2014b or R2019b.   You can run the script multiple times to switch between the distributions, but you can only install and use one at a time. $ cd $FREESURFER_HOME/bin$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr  R2014b … switch to R2019b ... $ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr  R2019b I can’t comment on which might be a better choice, but I believe the 7.2..0 release was tested with R2014b, and subsequently the current 7.3.2 release was updated to use and tested with R2019b.   Since you are running 7.2.0, I would try installing R2014b as listed above and running with that. You can find all the 7.X releases under, https://secure-web.cisco.com/1RxNv9aW1kS9fevrfjvWAkwbIG9pgzvcCv… - R. -------- Forwarded Message --------Subject:[Freesurfer] matlab 2019b and brainstem substructures analysisDate: Sat, 8 Oct 2022 17:26:14 +0800From: tulu@ms36.hinet.netReply-To:Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>To: freesurfer@nmr.mgh.harvard.edu        External Email - Use Caution        Dear Freesurfer experts,I will analysis brainstem structure and I use Freesurfer 7.2 version and maltab 2019b.I wonder if I need to install Matlab R2014b runtime or how to run hippocampal subfield/brainstem module by matlab2019b Thanks your helpJung Lung Hsu<Attached Message Part.txt>

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Re: [Freesurfer] 7.2.0 CentOS7 and Ubuntu 18.04
by fsbuild 18 Oct '22

18 Oct '22

External Email - Use Caution Hello Jim, We do post this caveat on the download page, Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). So I suspect the answer is it depends upon what you are running and, e.g., how statistics are subsequently computed using the (floating point) output.   Running on a different OS with a different release of Freesurfer means floating point results will not be identical to the output produced with your previous systems and (older) FS releases at some position to the r.h.s of the decimal point. - R. On Oct 18, 2022, at 11:22, Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl..edu> wrote:        External Email - Use Caution        We’ve made system software upgrades recently and of some our data was run using the FS 7.2.0 CentOS 7 build but on Ubuntu 18.04 servers. The outputs look good and there no output errors. Should these data be rerun? Jim     The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Tracula - Preproc
by Alan Francis 18 Oct '22

18 Oct '22

External Email - Use Caution Hi Anastasia, King Wei: I did as you suggested with the config file and the preprocessing ran for a bit but then an error occurred. I have attached the run script. It says BET not found. Is this the Brain Extraction tool? Could you please shed some light on this? thanks so much, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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Freeview: missing voxels in reconstructed surfaces
by Sarah Lavelle 18 Oct '22

18 Oct '22

External Email - Use Caution Dear Freesurfer, I have an issue when viewing my reconstructed surfaces on Freeview my linux version : freesurfer-linux-ubuntu18_x86_64-dev freesurfer 7-dev The surfaces have a large number of *empty voxels*. This is not a problem with the recon-all function as I can see the same surface file perfectly on my Mac with the fully working mac version. It seems to be a problem with my Freeview. Some additional information that may help finding the cause: When I open Freeview from Ubuntu, I get the following errors: QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-lavells1' QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20 QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20 There are no other errors in ubuntu after I load Freeview i.e. No errors in Ubuntu when I then load the surface. I hope you can help me fix this issue as soon as possible. Many thanks, Sarah [image: image.png] [image: Empty_Voxels_PialSurface_CloseUp.PNG] [image: Empty_Voxels_PialSurface.PNG]

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mris_make_surfaces error: MRISedges(): too many faces
by Arcaro, Michael 18 Oct '22

18 Oct '22

External Email - Use Caution Hey FreeSurfer Devs! I’m trying to do a surface reconstruction on a rodent-sized animal (tree shrew). I have a good segmentation of the white matter and have been able to generate reasonable looking orig / smoothwm surfaces. I’m running into an error with mris_make_surfaces: MRISedges(): too many faces: 9578 9599 n=9, m=4, k=2. I am running this command manually: mris_make_surfaces -noaseg -orig_white lh.smoothwm.nofix -white white.preaparc -noaparc -mgz -T1 brain shrewsurf lh I also hit this error when running autorecon2: recon-all -autorecon2-wm -subjid shrewsurf -hires -nonormalization2 -nofill -noaseg -nosegmentation -nocortribbon -notessellate -no-isrunning Some details on the MRIs I’m trying to do this recon on: 0.05mm^3 T2. No T1s (poor contrast on 9.4T). I’m trying to recon on the native resolution: mris_convert T2.nii T2.mgz -cs 0.05. I dummied a T1 by segmenting the grey/white matter, assigned voxels values of 90 and 110, respectively, then blurred the image a little so there is a gradient across the grey matter from white matter to out of brain. I’ve had no issues running mri_tessellate, mris_extract_main_component, mris_smooth, mris_inflate. Any advice would be greatly appreciated! Mike

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Don't find libquadmath.so.0
by Pål Gunnar Larsson 18 Oct '22

18 Oct '22

External Email - Use Caution I am reinstalling Freesurfer on an offline system. Run Ubuntu 21.10 and has installed Freesurfer 7.3.2 from a tar-ball and have installed tcsh. However, the run stopes with: libquadmath.so.0 cannot open shared library : No such file. How do I solve this? Best Pål G. Larsson M.D., PhD. Senior Medical Officer Department of Neurosurgery Division of Surgery and Clinical Neuroscience Oslo University Hospital Po.box 4950 Nydalen 0424 Oslo Norway Tel: (+47) 23074407 Mobile: (+47) 93429791 E-mail: pall(a)ous-hf.no<mailto:pall@ous-hf.no> not sensitive

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Freesurfer Virtual Box 7zip file password
by Şiyar Bahadır 18 Oct '22

18 Oct '22

External Email - Use Caution Hello everyone, I downloaded the Virtual Box image provided for windows computers. But was unable to extract the 7zip file. I read that I needed to send an e mail to this group. Can anybody help? Cheers. -- Şiyar BAHADIR, MD. Neurosurgery Resident Hacettepe Üniversitesi Tıp Fakültesi, Nöroşirürji Kliniği/Ankara Hacettepe University Medical Faculty, Neurosurgery Clinic/Ankara

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VirtualBox Password Request
by Andrew Augustine 17 Oct '22

17 Oct '22

External Email - Use Caution Good afternoon, everyone! My name's Andrew Augustine and I'm a systems group member within Florida State University's Mathematics department. I'm emailing on behalf of Claire Hickey, one of our grad students who has been instructed to learn to use your software. We're installing FreeSurfer on her computer via the VirtualBox route, but the image archive requires a password that we don't have. Can we receive this information? Thank you in advance for your help. --- Andrew Augustine Math System Group aaugusti(a)math.fsu.edu

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mris_transform with flirt transformation wrong result
by Chris Adamson 16 Oct '22

16 Oct '22

External Email - Use Caution Freesurfer experts, I'm trying to put some subject surfaces into a template space. I have performed the following flirt registration per subject: flirt -in $SUBJECTS_DIR/$CURSUBJECT/mri/T2.nii.gz -ref template0.nii.gz -omat $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.fslmat -out $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.nii.gz -dof 12 -searchrx -$D $D -searchry -$D $D -searchrz -$D $D Then apply the flirt transform mris_transform --trx-src $SUBJECTS_DIR/$CURSUBJECT/mri/T2.nii.gz --trx-dst template0.nii.gz $SUBJECTS_DIR/$CURSUBJECT/surf/${CURHEMI}.${CURSURFTYPE} $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.fslmat $SUBJECTS_DIR/$CURSUBJECT/surf/${CURHEMI}.${CURSURFTYPE}.flirt When I overlay the output surface $SUBJECTS_DIR/$CURSUBJECT/surf/${CURHEMI}.${CURSURFTYPE}.flirt over the template template0.nii.gz the surface is in the wrong orientation and in the wrong position, i.e. not correct. I have tried using lta_convert to make a lta transform and I get the same result. Any thoughts? Thanks, Chris. 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> http://secure-web.cisco.com/1xyTfBzNnFowZ_Fne30rgRiCxmIVmOJ_-BycsOHrk_XaYht…<http://secure-web.cisco.com/1qlMpfQw8j0R3pB1zfzODqkjLHdA5pw_AMVxM9hBQD5XAjo…> 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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NoPVC PET
by Marina Fernández 16 Oct '22

16 Oct '22

External Email - Use Caution Dear experts, I would like to get a noPVC PET volume scaled by the intensity of the pons, then project it and apply standard surface-based analysis. On the PetSurfer website it says: ** If you do not want to perform PVC, you can just run mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --seg gtmseg.mgz --default-seg-merge --auto-mask 1.01 --no-tfe --o gtmpvc.output ** If I do this, I cannot find any output in the folder which I can project on the surface corresponding to the non-PVC PET volume referenced to the pons. The idea is to have comparable PET-PVC vs. PET-noPVC data scaled to the pons in both cases. In order to do this, should I divide (externally to the mri_gtmpvc function) each voxel of the PET image by the average of the pons? Thank you very much in advance. Best regards, Marina

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Freesurfer October 2022