Freesurfer April 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
170 discussions

Data onto the Freesurfer surface
by Mason Wells 15 Apr '20

15 Apr '20

External Email - Use Caution Hi all, I apologise for cross-posting to both FSL and Freesurfer lists. I am trying to use an analysis package that works on surface based data (SamSrf). I have ran Feat and have a filtered_func file which is of course the motion corrected/unwarped version of my EPI. However, I need some advice on how to get these data onto the Freesurfer surface. I have found this page<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer>, but I wanted to double check this is the most up-to-date pipeline. On the page it suggests using the same DOF as used in Feat, I use BBR so this seems a little redundant. Has anyone on these lists got any experience of getting filtered_func onto the Freesurfer surface? Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Question on using T2 or FLAIR data to improve pial surfaces
by Tim Schäfer 15 Apr '20

15 Apr '20

External Email - Use Caution Dear FreeSurfer experts, I have both T2 and FLAIR images for the majority of the subjects in my study, and I want to use them to improve pial surface reconstruction during recon-all as explained in [1]. My questions are: 1) In general, should I prefer FLAIR over T2, or the other way around? 2) Some subjects (< 10%) do not have a FLAIR image, and others do not have a T2. Do you think that it is fine to use FLAIR for some subjects, and T2 for others, in the same study? We will perform manual QC after the recon-all run and exclude bad quality images, so I feel it should be fine, but I wanted to hear your opinion. Best, Tim [1] https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimp… -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Trac-All Error
by Hua, Jessica 15 Apr '20

15 Apr '20

External Email - Use Caution Attached are bvecs and bvals. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Freesurfer display resolution very low compared to other viewers
by Renner, Brian 14 Apr '20

14 Apr '20

External Email - Use Caution Hello all! Inaugural message to the list; I will attempt to be brief with the project description. The setup is consistent between both versions 6.0.0 and 7.0.0-beta, run on a high performance cluster, accessed through macOS terminal + Xquartz, most recent versions all. As it stands, our group is attempting to do subfield analysis of hippocampal analysis and lesion measurement in MS subjects. We have noticed that there is a major discrepancy of resolutions between files, which has irked some of our physicians undertaking the lesion measurement. We need to resolve the lesions down to 3mm and have noticed the quality between freeview and fsleyes of the same nifti files will yield much lower display resolution. This is true for most scans, though it has been compared using 1mm T2 FLAIR sequences as well as T2* sequences with 0.65mm voxel space. I have been attempting to find a workaround as the current solution for the physicians is to look at the files in fsleyes and then measure them with the ruler tool in freeview. I can send supporting pictures as necessary. Thank you in advance for any thoughts you may have! BR -- Brian Renner, MD Research Associate, Neurology brian.renner(a)cshs.org<mailto:brian.renner@cshs.org> Cedars-Sinai 127 S. San Vicente Blvd, Suite A6600 : Los Angeles CA 90048 office 310-423-1589 : mobile 310-658-3492 : cedars-sinai.org<https://www.cedars-sinai.org/> IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.

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Re: [Freesurfer] FreeSurfer UbuntuVM password
by fsbuild 14 Apr '20

14 Apr '20

External Email - Use Caution I will send it directly to your email in a minute. R. On Apr 14, 2020, at 16:53, sapere-aude(a)tuta.io wrote:        External Email - Use Caution        Hi,the FreeSurfer Ubuntu VirtualBox Virtual Machine asks for a password to log in (see the attached image).I can't find any information about what this password is on the tutorial page:https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_winCould anyone help me with the password to the VM?kind regards,Sapere-Aude<Ubuntu password.PNG>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer UbuntuVM password
by sapere-aude＠tuta.io 14 Apr '20

14 Apr '20

External Email - Use Caution Hi, the FreeSurfer Ubuntu VirtualBox Virtual Machine asks for a password to log in (see the attached image). I can't find any information about what this password is on the tutorial page: https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_win Could anyone help me with the password to the VM? kind regards, Sapere-Aude

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Compiling Freesurfer 6 on Centos7 Install not working due to annex files missing
by Jorge Naranjo 14 Apr '20

14 Apr '20

External Email - Use Caution Hi all I’m building Freesurfer version 6 (stable6 branch) in a fresh centos7 OS git clone https://github.com/freesurfer/freesurfer.git cd freesurfer git checkout stable6 git remote add datasrc https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/annex.git git fetch datasrc git annex get --metadata fstags=makeinstall . I do this since the options in the wiki using CMAKE and everything don’t work for this version and BTW I can’t find the instruction to build it in Linux anymore. I don’t know if this instructions were removed or what After some small tweaks in the configure and packages I do: ./setup_configure ./configure --with-cuda=/usr/local/cuda/lib64 --enable-openmp --disable-Wall --disable-Werror --enable-emu LDFLAGS=-lQt5X11Extras CFLAGS=-fpermissive CXXFLAGS=-fpermissive --disable-Werror --with-pkgs-dir=/opt/freesurfer/packages --prefix=/share/apps/NYUAD4/freesurfer/6/ --with-cppunit-dir=/usr --with-itk-dir=/opt/freesurfer/packages/itk/3.16.0/ --with-vtk-dir=/opt/freesurfer/packages/vtk/5.6.0/ --with-gts-dir=/opt/freesurfer/packages/gts/0.7.6/ --with-ann-dir=/opt/freesurfer/packages/ann/1.1.2/ --with-petsc-dir=/opt/freesurfer/packages/petsc/2.3.3/ --with-mni-dir=/opt/freesurfer/packages/mni/current/ --with-mpi-dir=/usr/lib64/openmpi/ --with-vxl-dir=/opt/freesurfer/packages/vxl/1.14.0 --with-kwwidgets-dir=/opt/freesurfer/packages/KWWidgets/5.6.0 make Up to this point, everything goes OK! Now the "make install" fails: /bin/install: cannot stat ‘face.gca’: No such file or directory /bin/install: cannot stat ‘talairach_mixed_with_skull.gca’: No such file or directory /bin/install: cannot stat ‘wmsa_new_eesmith.gca’: No such file or directory /bin/install: cannot stat ‘aseg+spmhead.ixi.gca’: No such file or directory /bin/install: cannot stat ‘aseg+spmhead+vermis+pons.ixi.gca’: No such file or directory /bin/install: cannot stat ‘pons.mni152.2mm.mgz’: No such file or directory /bin/install: cannot stat ‘lh.atlas2002_simple.gcs’: No such file or directory /bin/install: cannot stat ‘lh.atlas2005_simple.gcs’: No such file or directory /bin/install: cannot stat ‘lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs’: No such file or directory /bin/install: cannot stat ‘lh_trans_toSulc.gcs’: No such file or directory /bin/install: cannot stat ‘lh.destrieux.simple.2009-07-29.gcs’: No such file or directory /bin/install: cannot stat ‘rh.atlas2002_simple.gcs’: No such file or directory /bin/install: cannot stat ‘rh.atlas2005_simple.gcs’: No such file or directory /bin/install: cannot stat ‘rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs’: No such file or directory /bin/install: cannot stat ‘rh_trans_toSulc.gcs’: No such file or directory /bin/install: cannot stat ‘rh.destrieux.simple.2009-07-29.gcs’: No such file or directory /bin/install: cannot stat ‘rh.DKTatlas40.gcs’: No such file or directory /bin/install: cannot stat ‘lh.DKTatlas40.gcs’: No such file or directory /bin/install: cannot stat ‘rh.DKTatlas100.gcs’: No such file or directory /bin/install: cannot stat ‘lh.DKTatlas100.gcs’: No such file or directory /bin/install: cannot stat ‘lh.average.curvature.filled.buckner40.tif’: No such file or directory /bin/install: cannot stat ‘lh.average.CURVATURE.tif’: No such file or directory /bin/install: cannot stat ‘lh.average.tif’: No such file or directory /bin/install: cannot stat ‘rh.average.curvature.filled.buckner40.tif’: No such file or directory /bin/install: cannot stat ‘rh.average.CURVATURE.tif’: No such file or directory /bin/install: cannot stat ‘rh.average.tif’: No such file or directory /bin/install: cannot stat ‘rigidly_aligned_brain_template.tif’: No such file or directory /bin/install: cannot stat ‘label_scales.dat’: No such file or directory /bin/install: cannot stat ‘mni305.cor.mgz’: No such file or directory /bin/install: cannot stat ‘mni305.mask.cor.mgz’: No such file or directory /bin/install: cannot stat ‘mni305.cor.subfov1.mgz’: No such file or directory /bin/install: cannot stat ‘mni305.cor.subfov2.mgz’: No such file or directory /bin/install: cannot stat ‘mni305.cor.subfov1.reg’: No such file or directory /bin/install: cannot stat ‘mni305.cor.subfov2.reg’: No such file or directory /bin/install: cannot stat ‘mni152.register.dat’: No such file or directory /bin/install: cannot stat ‘mni152.mni305.cor.subfov1.dat’: No such file or directory /bin/install: cannot stat ‘mni152.mni305.cor.subfov2.dat’: No such file or directory make[2]: *** [install] Error 1 The problem arises when moving to the stable6 branch, and I need that one. I tried what suggested here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51895.html $> git annex get distribution/average/mult-comp-cor.tar.gz $> make install But didn’t work either Any help?? Thanks in advance Jorge A. Naranjo Senior HPC Computational Specialist NYU Abu Dhabi Office Tel (UAE): +971 2 628 4750 Mobile (UAE): +971 56 319 2814 New York University - Abu Dhabi (NYUAD) Saadiyat Campus - A2, Room-131 P.O. Box 129188 Abu Dhabi, United Arab Emirates http://nyuad.nyu.edu Please consider the environment before printing this email.

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T2 values from segmented areas
by Agnieszka Sabisz 14 Apr '20

14 Apr '20

External Email - Use Caution Dear All, I would like to ask you a question. I'm trying to extract values from T2 maps from few brain areas. In my pipeline I miss something and I have a problem to figure out what I'm doing wrong. In the first step, I register my T2w image to T1 (that has got recon-all) 2nd I orient T2_map by registration transformation that is made by bbregister and target it to aparc+aseg.mgz. (T2_map was created from T2w images.) 3rd mri_segstats with a calculation of T2 values My script looks like that: bbregister --s HTN_Con_083 --mov /users/work/asabisz/HTN_dane/T2/HTN_Con_083_T2calc__TE60.nii.gz --t2 --reg /users/work/asabisz/HTN_dane/T2/HTN_Con_083_reg.dat mri_vol2vol --mov /users/work/asabisz/HTN_dane/T2/HTN_Con_083_T2calc__map.nii.gz --targ /users/work/asabisz/subjects/HTN_Con_083/mri/aparc+aseg.mgz --reg /users/work/asabisz/HTN_dane/T2/HTN_Con_083_reg.dat --inv --interp nearest --o /users/work/asabisz/subjects/HTN_Con_083/mri/aparc+aseg2t2.mgz mri_segstats --seg /users/work/asabisz/subjects/HTN_Con_083/mri/aparc+aseg2t2.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --id 192 --id 3 --id 42 --id 4 --id 5 --id 7 --id 8 --id 10 --id 11 --id 12 --id 13 --id 17 --id 18 --id 24 --id 26 --id 46 --id 47 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --id 77 --id 85 --id 251 --id 252 --id 253 --id 254 --id 255 --id 2 --id 41 --i /users/work/asabisz/HTN_dane/T2/HTN_Con_083_T2calc__map.nii.gz --sum /users/work/asabisz/HTN_analizy/T2/HTN_Con_083_t2.stats The problem that I have is: I don't get values from --id 192 (corpus callosum) --id 3 and --id 42 - Cerebral Cortex. What I should add to my script? All the best Agnieszka Sabisz

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PETSurfer / Questions
by Ferraro, Pilar 14 Apr '20

14 Apr '20

External Email - Use Caution Dear Freesurfer experts, I see below that Message number 10 should be the reply to my email, but I can’t see this message in the thread. Would you be able to send it again, please? Many thanks, Pilar Maria Ferraro > Il giorno 14 apr 2020, alle ore 4:43 PM, freesurfer-request(a)nmr.mgh.harvard.edu ha scritto: > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Trac-All Error (Hua, Jessica) > 2. Re: Queries on the Function of Freesurfer (Koustav Chatterjee) > 3. Re: Queries on the Function of Freesurfer (Douglas N. Greve) > 4. Re: Queries on the Function of Freesurfer (Koustav Chatterjee) > 5. Re: Queries on the Function of Freesurfer (Bruce Fischl) > 6. Freesurfer display resolution very low compared to other > viewers (Renner, Brian) > 7. Re: Trac-All Error (Yendiki, Anastasia) > 8. Re: Overlap of vertices in downsampled data (Ersin Ers?zl?) > 9. Re: PETSurfer / Questions (Ferraro, Pilar) > 10. Re: PETSurfer / Questions (Douglas N. Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Apr 2020 16:10:32 +0000 > From: "Hua, Jessica" <jphc55(a)mail.missouri.edu> > Subject: Re: [Freesurfer] Trac-All Error > To: "AYENDIKI(a)mgh.harvard.edu" <AYENDIKI(a)mgh.harvard.edu>, > "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <BY5PR01MB5652D061831FADB2BB1F032593DD0(a)BY5PR01MB5652.prod.exchangelabs.com> > > Content-Type: text/plain; charset="iso-8859-1" > > External Email - Use Caution > > Hi Dr. Yendiki, > > I wasn't sure if I could attach files to the FreeSurfer, so I have also emailed your work email. Attached is my full configuration file as well as my error log. > > Best, > > Jessica > > --- > > Jessica Hua, M.A. > Cognitive and Emotional Control Lab > Doctoral Candidate Clinical Psychology > University of Missouri >

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Issue with tkregister command
by Tiffany Bell 14 Apr '20

14 Apr '20

External Email - Use Caution Hello I am trying to transform a free surfer segmentation to functional space using reg-feat2anat but I get the error tkregister2_cmdl_cmdl: Command not found. I am running freesufer on linux through a virtual machine. See below for the full command and output. Any help would be greatly appreciated. reg-feat2anat --feat LTFI_FEAT_PE_FB_R1/LTFI_02.feat --subject LTFI_02 FeatDir is LTFI_FEAT_PE_FB_R1/LTFI_02.feat template volume is LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz log file is LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/reg-feat2anat.log Thu 26 Mar 17:17:56 GMT 2020 /storage/gold/cinn/2013/neuroade/LTFI_Analysis /usr/local/freesurfer7/freesurfer/bin/reg-feat2anat --feat LTFI_FEAT_PE_FB_R1/LTFI_02.feat --subject LTFI_02 Linux neurodebian-1022 4.4.0-165-generic #193-Ubuntu SMP Tue Sep 17 17:42:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux example_func ras_good_flag 1 ------------------------------------------------------- Initializing exf2anat with header tkregister2_cmdl_cmdl --targ /storage/gold/cinn/2013/neuroade/LTFI_Analysis/Freesurfer_output/LTFI_02/mri/brainmask.mgz --mov LTFI_FEAT_PE_FB_R1/LTFI_02.feat/example_func.nii.gz --reg LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout LTFI_FEAT_PE_FB_R1/LTFI_02.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit tkregister2_cmdl_cmdl: Command not found. Many Thanks Tiffany ------------------------------------------------------ Tiffany Bell, PhD Postdoctoral Associate Cumming School of Medicine University of Calgary Alberta Children’s Hospital 2888 Shaganappi Trail, NW Calgary, AB T3B 6A8 (E) tiffany.bell(a)ucalgary.ca<mailto:tiffany.bell@ucalgary.ca> (T) 403-955-2970 www.kidsmigraine.info<http://www.kidsmigraine.info>

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Freesurfer April 2020