Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

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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mri_vol2surf, error: mghRead(/mri/orig.mgz, -1)
by Wandschneider, Britta 16 Oct '22

16 Oct '22

External Email - Use Caution Hello, I am trying to map tumour+oedema lesion masks (generated with ITKSnap) to subjects' freesurfer surface (in native space) using mri_vol2surf. This is an example of the command I am using for a specific subject: mri_vol2surf --mov CI_01_t+oedema_corrected.nii \ --fwhm 0 \ --regheader CI_01 \ --hemi lh --surf pial \ --projdist-max 0 1 0.1 \ --interp trilinear \ --surfreg sphere.reg \ --icoorder 5 \ --out CI_01_t+oedema_corrected_lh.mgh However, I get this error message: IcoOrder = 5, nIcoVtxs = 10242 srcvol = CI_01_t+oedema_corrected.nii srcreg unspecified srcregold = 0 srcwarp unspecified surf = pial hemi = lh ProjDist = 0.5 reshape = 0 interp = trilinear float2int = round GetProjMax = 1 INFO: float2int code = 0 INFO: this is an unsiged short. I'll try to read it, but it might not work if there are values over 32k INFO: using NIfTI-1 qform INFO: changing type to float Done loading volume Computing registration from header. Using /subjects/CI_01/mri/orig.mgz as target reference. error: mghRead(/subjects/CI_01/mri/orig.mgz, -1): could not open file klp32e:7.1.1 Britta$ I have tried the same command with a different freesurfer version (6.0.0), which lead to the same problem. The /mri/orig.mgz loads in freeview and looks fine to me. I searched the mailing list but have not found a post with this error being reported. I am using version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 on MacOS Mojave version 10.14.6 I would be very grateful for any advice. Best wishes Britta

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Skullstripping
by priya padma 16 Oct '22

16 Oct '22

External Email - Use Caution Hello Team, I am trying to do only Skull stripping for my image and get the output. is there any command of freesurfer, when it executes only the first step- skull stripping. My objective is to get whole brain segmentation where only the brain tissues should remain and all the skull has to be removed. I searched through the internet but haven't got anything. Does anyone know any solution? Thank you -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

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somatosensory cortex (S1)
by Eszter Boros 16 Oct '22

16 Oct '22

External Email - Use Caution Dear FreeSurfer Team, I would like to do a ROI analysis focusing on the primary somatosensory cortex (S1) using Freesurfer and see the potential alterations after a (behavioral) treatment . I am wondering how I can do that? First, I picked and looked at the postcentral gyrus and sulcus, but I am specifically interested in the face area. Is there a way to make my analysis more accurate? I am using Freesufer 7.1.1 Thank you for your answer! I greatly appreciate it. All the best, Eszter Boros

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Pass code to unzip VM
by Allesha Eman 16 Oct '22

16 Oct '22

External Email - Use Caution Dear Researchers, I am emailing to request the pass code to unzip the FS_7_2_0_ubuntu_18_04_07.ova.7z file to use FreeSurfer on Windows. Thank you. Allesha Get Outlook for iOS<https://secure-web.cisco.com/1LtOdy3dE2mITbmcYnYqCazSDK21IfZF4a2GTuYxS23Zak…>

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Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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