[Freesurfer] Issue with BBR and Applying CVS Warps to Diffusion Data
External Email - Use Caution Dear All, I have used CVS to align around 180 scans to a single, representative subject. I have then used BBR to align the mean b0 image to register the diffusion data to the native space T1 and then apply CVS warps; however, the resulting aligned images for calculated maps from the DWIs are very poor with a great deal of heterogeneity, especially at the boundary but also within white matter. The coefficient of variation of the mean b0 BB registered to the T1 is around 30% globally (excluding the edges of the brain) and 40% or greater for FA. I have reviewed the initial rigid registration of the b0s to the T1s for gross misalignment and found that FLIRT performed pretty well and didn’t fail for any of my subjects and didn’t require manual adjustment; however, the result of after applying the CVS warps is quite poor. The data T1s are 1mm (MPnRAGE) and the b0s are at 2mm. The DWIs were corrected for eddy currents, Gibbs’ ringing, rician noise, and B0 distortions and look pretty great. The DWIs are 70x180x180 at 2mm isotropic and the T1s are 256x256x256 at 1mm isotropic. Are there any suggestions for this issue? I have tried re-aligning the DTI parameter maps to the b0s before applying the CVS warps (although they should be in the same space) and I have tried using both the –t2 and –dti, as well as with/out the –fsl-init flag. Is bbregister shifting the origin for the images at all? Any help would be appreciated. Cheers, -Austin -- Austin M. Bazydlo, MS PhD Candidate Dept. of Medical Physics University of Wisconsin-Madison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Setting up Freeview on Ubuntu Linux 18.04: freeview can't find libpng12
External Email - Use Caution You also see a list of packages to install on the freesurfer wiki pages under, https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements - R. On Feb 26, 2020, at 12:03, Tim Schäfer ts...@rcmd.org wrote:External Email - Use Caution Hi Tim,try:wget http://mirrors.kernel.org/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.debsudo dpkg -i libpng12-0_1.2.54-1ubuntu1_amd64.debMore details at https://www.xsmd.org/brain/2019/06/19/freeview-libpng12-so-0-missing-under-lubuntu/Best,Tim--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, GermanyOn February 26, 2020 at 5:36 PM "Harrigan, Timothy P." timothy.harri...@jhuapl.edu wrote:External Email - Use Caution HI,I'm setting up freeview on a Linux 18..04 system and running through the instructions inhttps://surfer.nmr.mgh..harvard.edu/fswiki/DownloadAndInstallI got through to Example 4: "View the output volumes..." and got the error below.harritp1@TPHTVB:~/FSSubjects$ freeviewfreeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directoryIt looks like I need to either set up an environment variable, or install that specific graphics library. I did an install of the latest version of libpng: i. e. sudo apt-get install -y libpng-dev but that didn't fix the problem.Have you dealt with this?ThanksTimTimothy P. Harrigan ScDResearch and Exploratory Development DivisionJohns Hopkins University Applied Physics LaboratoryPhone: 240-228-5943Cell/Text: 240-280-9444___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] field inhomogeneities and eddy current correction evaluation
External Email - Use Caution Hello all, how can I evaluate the field inhomogeneities and eddy current correction I performed on my DWI images? Does any metric exist to do so? Thanks a lot in advance Regards Adam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Setting up Freeview on Ubuntu Linux 18.04: freeview can't find libpng12
External Email - Use Caution Hi Tim, try: wget http://mirrors.kernel.org/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb sudo dpkg -i libpng12-0_1.2.54-1ubuntu1_amd64.deb More details at https://www.xsmd.org/brain/2019/06/19/freeview-libpng12-so-0-missing-under-lubuntu/ Best, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > On February 26, 2020 at 5:36 PM "Harrigan, Timothy P." > wrote: > > > External Email - Use Caution > > HI, > I'm setting up freeview on a Linux 18.04 system and running through the > instructions in > https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall > > I got through to Example 4: "View the output volumes..." and got the error > below. > > harritp1@TPHTVB:~/FSSubjects$ freeview > freeview.bin: error while loading shared libraries: libpng12.so.0: cannot > open shared object file: No such file or directory > > It looks like I need to either set up an environment variable, or install > that specific graphics library. I did an install of the latest version of > libpng: i. e. sudo apt-get install -y libpng-dev but that didn't fix the > problem. > > Have you dealt with this? > > Thanks > Tim > > > Timothy P. Harrigan ScD > Research and Exploratory Development Division > Johns Hopkins University Applied Physics Laboratory > Phone: 240-228-5943 > Cell/Text: 240-280-9444 > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Setting up Freeview on Ubuntu Linux 18.04: freeview can't find libpng12
External Email - Use Caution HI, I'm setting up freeview on a Linux 18.04 system and running through the instructions in https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall I got through to Example 4: "View the output volumes..." and got the error below. harritp1@TPHTVB:~/FSSubjects$ freeview freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory It looks like I need to either set up an environment variable, or install that specific graphics library. I did an install of the latest version of libpng: i. e. sudo apt-get install -y libpng-dev but that didn't fix the problem. Have you dealt with this? Thanks Tim Timothy P. Harrigan ScD Research and Exploratory Development Division Johns Hopkins University Applied Physics Laboratory Phone: 240-228-5943 Cell/Text: 240-280-9444 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_subject
External Email - Use Caution As addendum to my message. The full terminal output: Reading surface /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/REMY001_M0//surf/lh.white Loading annotations from /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/REMY001_M0//label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) CTABwriteFileASCII(/Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.ctab): could not open for writing No such file or directory Seg base 0 mghWrite(/Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh, -1): could not open file Converting to a segmentation mri_surf2surf --mapmethod nnf --hemi lh --srcsubject REMY001_M0/ --srcsurfreg sphere.reg --sval /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh --trgsubject avgsubject --trgsurfreg sphere.reg --tval /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.std.mgh mghRead(/Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh, -1): could not open file Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output cd /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject mri_surf2surf --mapmethod nnf --hemi lh --srcsubject REMY001_M0/ --srcsurfreg sphere.reg --sval /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh --trgsubject avgsubject --trgsurfreg sphere.reg --tval /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.std.mgh sysname Darwin hostname K8WSBENINE machine x86_64 user benine srcsubject = REMY001_M0/ srcval = /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh srctype= trgsubject = avgsubject trgval = /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.std.mgh trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/REMY001_M0//surf/lh.sphere.reg Loading source data ERROR: could not read /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/avgsubject/label/tmpdir.annot2std.38242/seg.1.REMY001_M0/.mgh as type 3 ERROR: make_average_surface Thanks! Am Mi., 26. Feb. 2020 um 10:34 Uhr schrieb Benjamin Ineichen < bv.ineic...@gmail.com>: > Dear Freesurfer experts, > > I want to create a new standard template from my study population. For > this, I thought about using make_average_subject. Thus, I run: > make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003 > > I get an error message - ERROR: make_average_surface. Please find attached > the error.log. > > Would be very thankful for advice! > > Many thanks! > > /Ben > > -- > > Benjamin Victor Ineichen, MD PhD > Karolinska Institutet > Center for Molecular Medicine > Stockholm, Sweden > ineic...@protonmail.ch > +41 76 391 04 01 > > Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen > Karolinska Institutet > Center for Molecular Medicine > Stockholm, Sweden > ineic...@protonmail.ch > +41 76 391 04 01 > -- Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineic...@protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineic...@protonmail.ch +41 76 391 04 01 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average_subject
External Email - Use Caution Dear Freesurfer experts, I want to create a new standard template from my study population. For this, I thought about using make_average_subject. Thus, I run: make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003 I get an error message - ERROR: make_average_surface. Please find attached the error.log. Would be very thankful for advice! Many thanks! /Ben -- Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineic...@protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineic...@protonmail.ch +41 76 391 04 01 error.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
