Freesurfer

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30132 discussions

problem with mri_label2vol
by Mareike Grotheer 06 Dec '18

06 Dec '18

External Email - Use Caution Hello FreeSurfer Developers, I am trying to bring functional ROIs defined in a different program into FreeSurfer, so that I can dilate them into the white matter with –proj abs, but I am running into a problem I was hoping you could help me with. Here are the steps I am taking: 1)I am converting my ROIs, which are in nifti format, to FreeSurfer labels using: cmd = ['mri_vol2label --c ' outFile{1} ' --id ' num2str(roiVal(roi)) ' --l ' saveLabel{1} ' --surf ' subject ' ' hemi ]; unix(cmd); 2)Next, I want to dilate the labels using this: cmd = sprintf('!mri_label2vol --subject %s --label %s --o %s.nii.gz --hemi %s --reg %s.dat --temp %s --proj abs -7 0 .1 --fillthresh .001', fs_subject,labelFileName,niftiRoiName,hemisphere, tmpRegFile, regMgzFile); eval(cmd); This does not work, I get the following Error Message: ERROR: label my_label.label is not a surface label. I can circumvent this error by manually opening the label in tksurfer and saving it again. After that mri_label2vol runs without error. I assume that tksurfer automatically converts the label to a surface label. While this solves my problem in principle, I have many labels and am hoping that there may be a better way. Do you have any ideas how one could do this automatically? I am running the above code in Matlab R2015a. I am using FreeSurfer version 6.0.0 on Ubuntu 12.04 LTS. Thank you very much, Mareike

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Registering Anatomical Parcellation to DWI
by Maedeh Khalilian 06 Dec '18

06 Dec '18

External Email - Use Caution Dear FreeSurfer experts, I have a parcellation and a whole brain white matter files which are the outputs of FreeSurfer. I want to register them to my DWI. I mean I want my parcellation and white matter to be in the physical space of my DWI. Can FreeSurfer do it for me? If not , can you suggest me a toolbox that can do it fast? I would be grateful if u could help me. Cheers, Maedeh,

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Fwd: fcseedcor output
by Sara Jafakesh 06 Dec '18

06 Dec '18

External Email - Use Caution Dear freesurfer experts, I want to calculate corrolation between two seeds with freesurfer-linux-centos6_x86_64_stable_pub-v6 .after using fcseed-config and fseed-sess , I used fcseedcor. the command that I trying to run is as follow: fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat but the output of fcseedcor is not .dat file ( the connectivity matrix for my result 2*2 matrix) as it has been explained in the fcssedcor help. the output is just the .log file named seedcor2.dat.log. although it has been done without error. I really dont know what is the problem. I would be grateful if you could help me. best regards, sara

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Direction of significant group comparison
by Backhausen, Lea 06 Dec '18

06 Dec '18

External Email - Use Caution Dear FreeSurfer experts, I am running whole-brain based group comparisons of cortical measures between a patient group and a control group using glm-fit and Monte-Carlo correction for multiple comparisons. It works fine but I am not sure where to find information on which group has more or less volume, for example, in a significant cluster. I use the xxx.sig.cluster.summary files which give me something like this: ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 3.806 82573 3279.56 44.3 22.8 29.5 0.00020 0.00000 0.00040 5510 11256.20 rostralmiddlefrontal 2 2.099 122283 806.53 38.4 -69.6 44.6 0.68055 0.67327 0.68774 1654 2759.09 inferiorparietal Is the direction hidden somewhere or in another file? Do I have to run additional commands to get to the information? Thank you so much for any advice! Best Lea ------------------------------ Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>

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Re: [Freesurfer] mris_preproc paired diff outputs 0 values
by Sims, Sara A 06 Dec '18

06 Dec '18

External Email - Use Caution I have now gotten this to run on 3 subjects. However I have 786 subjects and need to find the bad apple. Is there a way I can do quality checks on each subject’s difference map in fsaverage space that mris_preproc has made? Basically I want to cycle through the concatenated file in a systematic way that hopefully doesn’t involve me opening them one at a time in freeview. How could I do this? Sara Sims From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Sara Sims <snolin(a)uab.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, December 3, 2018 at 10:56 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] mris_preproc paired diff outputs 0 values External Email - Use Caution Hello, I am trying to do a paired difference analysis of two runs of probtrackx (I have already put them on the surface). The two conditions are “central” and “far” for each subject. I have already checked the individual subjects data and it does indeed have values. Here is a sample of my subject list: 100206.central 100206.far 100307.central 100307.far 100408.central 100408.far …etc. Here is my mris_preproc script: mris_preproc --target fsaverage --hemi lh --isp $in/FP/100206.central/lhsurf.mgh --isp $in/FP/100206.far/lhsurf.mgh --isp $in/FP/100307.central/lhsurf.mgh --isp $in/FP/100307.far/lhsurf.mgh --isp $in/FP/100408.central/lhsurf.mgh --isp $in/FP/100408.far/lhsurf.mgh … --out $out/preproc_FP_cf_lh/lh.paired-diff.FP_cf.mgh --f $sublist --paired-diff The output log shows no errors, the number of inputs equals the number in the subject list and it creates a file but it’s all zeros. I just have no idea as to why this would happen? Thanks, Sara Sims

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visual cortex {Disarmed}
by 郑凤莲 06 Dec '18

06 Dec '18

External Email - Use Caution Hi experts, I want to do some research on the cortical thickness of visual cortex using FS 6.0. Is there specified or associated cortex model for the segmentation of visual cortex? Thanks for your reply in advance. I need your help. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

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Re: [Freesurfer] Freeview command not found {Disarmed}
by fsbuild 05 Dec '18

05 Dec '18

External Email - Use Caution It should be OK to use qt4 on Ubuntu 16, though I think qt5 would work as well. Please test to see if you can freeview from where it was installed.  Your output below says that FREESURFER_HOME is /usr/local/freesurfer, so you should have a /usr/local/freesurfer/bin/freeview.  Or I am assuming that if you built freesurfer, then after you did the “make” command to build it, you did “make install” with the install prefix set to to /usr/local/freesurfer After you are in the freesurfer shell with FREESURFER_HOME and the other environment variables set, the which command can verify the location of freeview,$ which freeview/usr/local/freesurfer/bin/freeview You can check what libraries freeview cannot find with the following,$ ldd `which freeview` | grep not If all the libraries are found, you will get no output from the ldd command, and you should be able to test just running freeview from the command line.  They GUI should come up with no volume loaded. $ freeview But if the ldd command reports some libraries are not found, then freeview will not run. Does the ldd command report that libvtkverdict.so.5.6 (or any other libraries) are not found ? - R. On Dec 5, 2018, at 18:24, Maeve Barrett <barretm2(a)tcd.ie> wrote:        External Email - Use Caution        Thanks so much!I installed the qt4 library but I received another error the 'freeview: command not found error'When I attempted it again, I received the following error:freeview.bin $argvfreeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directoryI then tried to install the libvtkverdict.so.5.6: package but received the following error:sudo apt install libvtkverdict.so.5.6Reading package lists... DoneBuilding dependency tree       Reading state information.... DoneE: Unable to locate package libvtkverdict.so.5.6E: Couldn't find any package by glob 'libvtkverdict.so.5.6'E: Couldn't find any package by regex 'libvtkverdict.so.5.6'I then installed the qt5 library and tried to start freeview again but I received this error:freeview: error while loading shared libraries: libQt5X11Extras.so.5: cannot open shared object file: No such file or directoryI tried to install this package but then I received this error:Reading package lists... DoneBuilding dependency tree       Reading state information... DoneE: Unable to locate package libQt5X11Extras.so.5E: Couldn't find any package by glob 'libQt5X11Extras.so.5'E: Couldn't find any package by regex 'libQt5X11Extras.so.5'Am I missing another library? Thanks in advance!Best,M.On Wed, 5 Dec 2018 at 15:32, fsbuild <fsbuild@contbay..com> wrote:        External Email - Use Caution        Hello Maeve,You can search for the package to install with apt-file, but you may need to install that first, so try,$ sudo apt install apt-file$ sudo apt update… now search for the package with that library name using apt-file$ sudo apt-file search libQtScriptTools.so.4I think it will come back with something like,libqt4-scripttools:  /usr/lib/x86_64-linux-gnu/libQtScriptTools.so.4…..- but the name of the package to the left hand side of the colon is what you want to install, so try$ sudo apt install libqt4-scripttoolsIf that does not fix the libqt references, then you could also try$ sudo apt install qt4-default- R.On Dec 5, 2018, at 13:32, Maeve Barrett <barretm2(a)tcd.ie> wrote:        External Email - Use Caution        Hello,I've been trying to resolve this issue but I haven't found a fix on the mailing lists. I downloaded and installed the most recent version of Freesurfer for Linux. I am running Ubuntu 16.04 LTS as guest on Virtualbox 5.2.22 on a windows 10 host. My tcsh version is 6.18.01 (Astron). When I type the commands $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.cshI get the following output: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurferFSFAST_HOME       /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /home/maevebarrett/Documents/AM8750_Structural/MNI_DIR           /usr/local/freesurfer/mniI have been able to run recon-all with no errors. However, when I try to open freeview, I receive the error message 'freeview: command not found.'I ensured I have permissions on the requisite folders. When I navigate to freesurfer/bin and type freeview.bin $argv I get the following error:/usr/local/freesurfer/bin> freeview.bin $argvfreeview..bin: error while loading shared libraries: libQtScriptTools.so.4: cannot open shared object file: No such file or directoryI tried downloading the libQtScriptTools.so.4 but when I attempt to install it I get the following error:sudo apt-get install libQtScriptTools.so.4Reading package lists... DoneBuilding dependency tree       Reading state information... DoneE: Unable to locate package libQtScriptTools.so.4E: Couldn't find any package by glob 'libQtScriptTools.so.4'E: Couldn't find any package by regex 'libQtScriptTools.so.4'I'm at a loss. Any help would be greatly appreciated.Best,M._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freeview command not found
by fsbuild 05 Dec '18

05 Dec '18

External Email - Use Caution Hello Maeve, You can search for the package to install with apt-file, but you may need to install that first, so try, $ sudo apt install apt-file $ sudo apt update … now search for the package with that library name using apt-file $ sudo apt-file search libQtScriptTools.so.4 I think it will come back with something like, libqt4-scripttools:  /usr/lib/x86_64-linux-gnu/libQtScriptTools.so.4….. - but the name of the package to the left hand side of the colon is what you want to install, so try $ sudo apt install libqt4-scripttools If that does not fix the libqt references, then you could also try $ sudo apt install qt4-default - R. On Dec 5, 2018, at 13:32, Maeve Barrett <barretm2(a)tcd.ie> wrote:        External Email - Use Caution        Hello,I've been trying to resolve this issue but I haven't found a fix on the mailing lists. I downloaded and installed the most recent version of Freesurfer for Linux.. I am running Ubuntu 16.04 LTS as guest on Virtualbox 5.2.22 on a windows 10 host. My tcsh version is 6.18.01 (Astron). When I type the commands $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.cshI get the following output: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurferFSFAST_HOME       /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /home/maevebarrett/Documents/AM8750_Structural/MNI_DIR           /usr/local/freesurfer/mniI have been able to run recon-all with no errors. However, when I try to open freeview, I receive the error message 'freeview: command not found.'I ensured I have permissions on the requisite folders. When I navigate to freesurfer/bin and type freeview..bin $argv I get the following error:/usr/local/freesurfer/bin> freeview.bin $argvfreeview.bin: error while loading shared libraries: libQtScriptTools.so.4: cannot open shared object file: No such file or directoryI tried downloading the libQtScriptTools.so.4 but when I attempt to install it I get the following error:sudo apt-get install libQtScriptTools.so.4Reading package lists... DoneBuilding dependency tree       Reading state information... DoneE: Unable to locate package libQtScriptTools.so.4E: Couldn't find any package by glob 'libQtScriptTools.so.4'E: Couldn't find any package by regex 'libQtScriptTools.so.4'I'm at a loss. Any help would be greatly appreciated.Best,M._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview command not found
by Maeve Barrett 05 Dec '18

05 Dec '18

External Email - Use Caution *Hello,* *I've been trying to resolve this issue but I haven't found a fix on the mailing lists. I downloaded and installed the most recent version of Freesurfer for Linux. I am running Ubuntu 16.04 LTS as guest on Virtualbox 5.2.22 on a windows 10 host. My tcsh version is 6.18.01 (Astron). When I type the commands * $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.csh *I get the following output: * -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/maevebarrett/Documents/AM8750_Structural/ MNI_DIR /usr/local/freesurfer/mni *I have been able to run recon-all with no errors. However, when I try to open freeview, I receive the error message* 'freeview: command not found.' *I ensured I have permissions on the requisite folders. * *When I navigate to freesurfer/bin and type freeview.bin $argv I get the following error:* /usr/local/freesurfer/bin> freeview.bin $argv freeview.bin: error while loading shared libraries: libQtScriptTools.so.4: cannot open shared object file: No such file or directory *I tried downloading the libQtScriptTools.so.4 but when I attempt to install it I get the following error:* sudo apt-get install libQtScriptTools.so.4 Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package libQtScriptTools.so.4 E: Couldn't find any package by glob 'libQtScriptTools.so.4' E: Couldn't find any package by regex 'libQtScriptTools.so.4' *I'm at a loss. Any help would be greatly appreciated.* *Best,* *M.*

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Lab manager position in Perception & Brain Dynamics Laboratory at NYU Medical Center
by Max Levinson 05 Dec '18

05 Dec '18

External Email - Use Caution The Perception & Brain Dynamics Laboratory (http://www.med.nyu.edu/helab/) at Langone Medical Center, New York University is looking for a lab manager to start in summer 2019. The Laboratory is within the Neuroscience Institute at NYU Langone Health (http://www.med.nyu.edu/neuroscience) affiliated with Departments of Neurology, Neuroscience and Physiology, and Radiology. Our research focus is on understanding the neural bases of perceptual awareness using multimodal imaging (fMRI, MEG, EEG, ECoG) and stimulation (tDCS, TMS) techniques in humans, combined with computational neuroscience approaches. We are looking for a bright and driven candidate with a Bachelor’s or Master’s degree who is dedicated to neuroscience research. A variety of backgrounds, including neuroscience, biology, psychology, and computer science is possible, and experience with programming is highly desirable. In addition, the ideal candidate has high responsibility and dependability, as well as excellent critical thinking, organizational and leadership skills. Performing independent research is an important aspect of the position, in addition to lab management duties. A minimal commitment of 2 years is required. Interested candidates please send a cover letter, a CV, undergraduate and/or graduate transcript, and names and contacts of two to three referees, to Prof. Biyu J. He at biyu.jade.he(a)gmail.com, with the subject line “Lab manager application 2019”.

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