Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

Corresponding coordinate in fsaverage?
by Dorian P. 25 Jan '17

25 Jan '17

Hi, I am trying to find the corresponding coordinate of a vertex in lh.pial in fsaverage space. I manage to transform lh.pial in fsaverage space but this does not give corresponding points or a way to do point by point transformation. I want to do the same with some vertices from lh.pial-outer-smoother. Trying to transform this with mri_surf2surf gives an error because obviously there is no registration of that mesh. Any idea if this can be achieved at all? Last question: am I correct assuming that the surface to surface registration (sphere.reg) does a better job at matching gyri and sulci on fsaverage than the simple conversion in MNI305 (aka fsaverage): MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' Thank you. Dorian

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Registration: Variable Must Begin with a Letter Error <Repost>
by Anderson Napolitano 25 Jan '17

25 Jan '17

Hello Experts! I am having trouble checking the registration per step 2 of the pet surfer tutorial: http://freesurfer.net/fswiki/PetSurfer. The line: mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta worked just fine but when checking the registration using the line: tkregisterfv --mov template.nii.gz --reg template.reg.lta --surfs I get the following output: set: Variable name must begin with a letter As suggested by Dr. Greve, I've attached a text file documenting the input, the output and the output with the debug flag on. Please let me know if I can provide you any further details and I will get to it as soon as I can. Thank you very much for your time. Warmest Regards, Anderson

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Freeview v6.0 Draw ROI Bug - Only Brush Size of 1 Saved?
by Douglas Merkitch 25 Jan '17

25 Jan '17

Hello, I think I have encountered a bug in freeview on freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c. When I attempt to draw and save an ROI label, I get the following error in the terminal: QFileInfo::absolutePath: Constructed with empty filename The ROI label does save, but when I open it, it's as if only the voxels that my cursor had touched during the drawing process are saved and those that were added by any brush size greater than 1 are not saved (see attached screenshots). Also, the fill all "paint bucket" seems to work and save correctly. When I revert to freeview v5.3 (freesurfer-Darwin-lion-stable-pub-v5.3.0) the ROI draw and save function works without issue. Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu> [cid:9CA11EAB-FC31-47E2-BA5D-0352FC446845][cid:6D9024DF-9ABB-4C56-AE5C-BF8007F5648C]

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autorecon2-cp vs autorecon2-wm
by Alex Cohen 25 Jan '17

25 Jan '17

Just out of curiosity, digging through recon-all finds this section quoted below, however I thought -cp and -wm started at different spots?: case "-autorecon2-cp": case "-autorecon2-noaseg": case "-autorecon2-wm": set DoNormalization2 = 1; set DoSegmentation = 1; set DoFill = 1; set DoTessellate = 1; set DoSmooth1 = 1; set DoInflate1 = 1; set DoQSphere = 1; set DoFix = 1; set DoMaskBFS = 1; set DoWhiteSurfs = 1; set DoSmooth2 = 1; set DoInflate2 = 1; set DoSegStats = 0; set DoCurvHK = 1; set DoCurvStats = 1; breaksw echo " -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg)" echo " -autorecon2-wm : process stages 15-23" echo " -autorecon2-inflate1 : 6-18" echo " -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon" echo " -autorecon3 : process stages 24-34" echo " if edits made to correct pial, then run -autorecon-pial" -Alex ---------------------------------------------------------------- Alexander Li Cohen, M.D., Ph.D. E-mail: Alexander.Cohen2(a)childrens.harvard.edu (Medical/Science Email) E-mail: alexcohen(a)gmail.com (Lifetime Email) ----------------------------------------------------------------

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Freeview in 6.0 - editing labels
by Trisanna Sprung-Much 25 Jan '17

25 Jan '17

Hi there Does the 6.0 version of Freeview have a way to edit labels on surfaces similar to how tksurfer allowed us to do this? Thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Freesurfer 6.0 link
by Aziz Nanthaamornphong 25 Jan '17

25 Jan '17

Hi experts, How can I download Freesurfer version 6.0? Is there an available URL link? Thank you, Aziz -- Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz

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More freeview feature requests
by Chris Adamson 25 Jan '17

25 Jan '17

Freesurfer devs, Freeview is really nice to use. I have a few more suggestions: It would be good to have keyboard shortcuts to change the brush size ala. Tkmedit. A clone feature ala tkmedit that would be needed to fill in brainmask or brain.finalsurfs.manedit.mgz When you are saving control points you have to manually change to the tmp directory and save as control.dat. It would be good to have an option that would automatically create this file. Thanks in advance, Chris Adamson. ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Parcellation using recon-all
by Katarzyna Anna Kazimierczak 25 Jan '17

25 Jan '17

Hi, I wanted to do the brain parcellation using Destrieux atlas on quite big dataset, however it will take too much time. I thought that maybe there is a way to restrict the number of regions used for parcellation (for me the most interesting are areas in the temporal lobe), so it will shorten the processing time? Do you have any experience with that? Is it possible? Best regards, Katarzyna

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cuda 7.5 and new ver6
by Jeff Stevenson 25 Jan '17

25 Jan '17

hi freesufer folks, has your new version 6 run a successful cuda7.5 gpu on ubuntu 16.04? i'm getting a core dump. jeff here is the cmd: recon-all -all -use-gpu -s ${filenames_arr[$i]}_freesurf -i ${sesnum_arr[$i]}/anat/${filenames_arr[$i]}.nii first output gave: Testing for CUDA device: /home/toddr/Software/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Linux redshirt 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux thinking its a missing link i did: sudo ln -s /usr/lib/x86_64-linux-gnu/libcudart.so.7.5.18 /usr/lib/x86_64-linux-gnu/libcudart.so.5.0 and then got: Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 8.0 Runtime : 7.50 Acquiring CUDA device Using default device CUDA device: GeForce GTX TITAN Black Segmentation fault (core dumped) Linux redshirt 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-bbc101_ses-1_mpr_3_freesurf exited with ERRORS at Tue Jan 24 13:21:33 PST 2017 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] Freesurfer 6.0
by John Papatriantafyllou 25 Jan '17

25 Jan '17

Please do not forget windows people!!!! John On Jan 25, 2017 12:45 PM, "Aziz Nanthaamornphong" <aziz.n(a)phuket.psu.ac.th> wrote: > Hi experts, > > How can I download Freesurfer version 6.0? Is there an available URL link? > > Thank you, > Aziz > -- > > Aziz Nanthaamornphong, Ph.D., > Chair of Master of Science Program in Information Technology > Department of ICT > Faculty of Technology and Environment > Prince of Songkla University, Phuket Campus > +66 7627 6716 (v) > http://research.te.psu.ac.th/aziz > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

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Freesurfer January 2017