Freesurfer August 2019

freesurfer@nmr.mgh.harvard.edu

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144 discussions

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Substancia-Nigra ROI
by Gwang-Won Kim 30 Aug '19

30 Aug '19

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PETsurf kinetic modeling with MRTM
by Chanmi Kim 30 Aug '19

30 Aug '19

External Email - Use Caution Hello, I'd like to perform MRTM2 approach in ADNI3 tau PET data for partial volume correction (PVC). So, I've tried to do a command line as below. mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz The 'mri_glmfit' required 'time.dat' which is an information of the time activity curve (TAC), however, I don't know how to get this information. Can you please let me know how to get this information? Please share any examples of 'time.dat' If there is anyone who has experience in PetSurf PVC, Chan

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Corresponding structures to an ROI
by Wang, Lily 30 Aug '19

30 Aug '19

Hi All, I have several white matter ROI masks unique to each subject that were made using the subjects' T2 scans and I would like to use wmparc to find out what brain structures those ROI's correspond to. I'm guessing that I will need to either register T1 to T2 or T2 to T1 at one point, which I have done by using mri_robust_register to register T1 to T2 (and it seemed to turn out ok, but how do I check other than by eye? And is there a better way to register?), and apply that transformation to wmparc. But other than figuring out the registration, what else do I do? Thank you, Lily

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recon_all cuda 9.1
by Dev vasu 30 Aug '19

30 Aug '19

External Email - Use Caution Dear all, Does recon_all -use-gpu only works for CUDA 5.0, is there any way to make it work for CUDA 9.1. Thanks Vasudev

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I have a question for subthalamic nucleus ROI.
by Gwang-Won Kim 30 Aug '19

30 Aug '19

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Problem with install freesurfer
by 余文豪 30 Aug '19

30 Aug '19

External Email - Use Caution Dear MR/MS: I have a problem with installation as the following. Could anyone help me with that. Thanks a lot

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T2 flair as additional scan in hippocampal subfields segmentation
by Rovai Antonin 30 Aug '19

30 Aug '19

External Email - Use Caution Hello I’d like to know if there is any advantage in having a T2 FLAIR as additional scan (in addition to our 1mm isotropic T1 scans) when using the hippocampal subfield segmentation tool. We do not have T2 nor PD available. Thanks for you help Antonin Rovai Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

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viewport does not affect snapshots for --slice option in cmd mode
by Hoke, Harris 29 Aug '19

29 Aug '19

Freeview does not update in the viewer window to the correct slice position when calling on viewport. This means instead of taking snapshots of N slices of the brain from N specified slice coordinates, it takes the same snapshot over and over again. Originally, we found a workaround by disabling qt_setup in the freeview tcsh script: #source $FREESURFER_HOME/bin/qt_setup. After this, it worked perfectly. Since then, it has stopped working well. The error occurs for saggital and coronal views. (Axial works fine, for some reason). I am using the stable release of freesurfer 6.0.0. The problem still happens if I interleave axial/coronal/saggital viewport commands, instead of running them together as below. The problem also occurs using the development version of freesurfer from august 27th, CentOS7 build (but only for sagittal and coronal; Axial works fine). freeview -cmd minimalcmd.txt minimalcmd.txt: freeview -v SUBDIR/mri/orig/001.mgz -layout 1 -cc -nocursor -viewport sagittal -slice 80 127 127 -ss OUTDIR/T1_sag_1.jpg -noquit -viewport sagittal -slice 90 127 127 -ss OUTDIR/T1_sag_2.jpg -noquit -viewport axial -slice 127 80 127 -ss OUTDIR/T1_ax_1.jpg -noquit -viewport axial -slice 127 90 127 -ss OUTDIR/T1_ax_2.jpg -noquit -viewport coronal -slice 127 127 80 -ss OUTDIR/T1_cor_1.jpg -noquit -viewport coronal -slice 127 127 90 -ss OUTDIR/T1_cor_2.jpg -noquit -quit In case it's useful: uname -a Linux ncfservice02 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux I'm unsure what else I can try or what other information I can provide. Please let me know.

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how to get the displacement from template to the linearly registered image
by ping cao 29 Aug '19

29 Aug '19

External Email - Use Caution Dear expert， I saw a paper mentioned this ： By using the *deformation field* from nonlinear registration, we can > build the correspondence between voxels in the template and each > linearly-aligned image. For instance, for each voxel (x, y, z) in the > template image, we can find its corresponding voxel (x + dx, y + dy, z + > dz) in each linearly-aligned image, where (dx, dy, dz) is the > *displacement* from the template image to the linearly-aligned image > defined by the deformation field. So, I want to get the deformation field from the template to the linearly registered image(flirt_T1). Can Freesurfer do this? Which file is a linearly registered image that does not contain an affine transformation? How can I get this deformation field? Your help is greatly appreciated. Best, ping

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New fsaverage
by Westeneng, H.J. 29 Aug '19

29 Aug '19

External Email - Use Caution Dear FreeSurfer experts, It has previously been reported that vertex 40969 is the same as vertex 0, which creates a very large triangle in fsaverage (appearing as a defect in freeview) and is fixed in the development version. For our research we would very much appreciate to use the new fixed version of fsaverage. In the release notes (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) it has been mentioned that a post to this list is needed to get the new fsaverage version. I hope anyone can help me to get this new version. Kind regards, Henk-Jan ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Freesurfer August 2019