Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Infant Atlas
by li ki 06 Dec '17

06 Dec '17

Hi experts, We are presently involved in a project for analyzing MRI data of 1-3 year old children using FreeSurfer. We cannot find a correct infant atlas. From online search, I know that an infant atlas is being developed which will be integrated into FreeSurfer in the future. （link https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/ [https://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcgifs/pmc-logo-share.png]<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/> A FreeSurfer-compliant consistent manual segmentation of ...<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/> www.ncbi.nlm.nih.gov We present a detailed description of a set of FreeSurfer compatible segmentation guidelines tailored to infant MRI scans, and a unique data set of manually segmented ... ） Can I know when this will be available? If not soon, is there any other methods for us to generate an infant(kid) atlas? Also I know there are infant atlas from UNC(http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-a…, how can I use this atlas in Freesurfer? Free Softwares ― IDEAgroup<http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlas…)> www.med.unc.edu Free Softwares developed by IDEA lab are collected here for research use. Best, Lemon

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freeview abort
by ~永夜~ 05 Dec '17

05 Dec '17

Hi experts, When I use xshell to connect our Ubuntu system，freeview aborts without any other complaint.wade@DL:/$ freeview Abort (core dumped) after dealed with suggestion on https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-September/05399… still cannot work. wade@DL:/$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so /sbin/ldconfig.real: Can't stat /lib/i686-linux-gnu: No such file or directory /sbin/ldconfig.real: Can't stat /usr/lib/i686-linux-gnu: No such file or directory /sbin/ldconfig.real: Path `/usr/lib/nvidia-367' given more than once /sbin/ldconfig.real: Path `/usr/lib32/nvidia-367' given more than once /sbin/ldconfig.real: Path `/lib/x86_64-linux-gnu' given more than once /sbin/ldconfig.real: Path `/usr/lib/x86_64-linux-gnu' given more than once /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libMapReduceMPI.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a symbolic link libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/cuda-8.0/targets/x86_64-linux/lib/libcudnn.so.5 is not a symbolic link /sbin/ldconfig.real: /lib/i386-linux-gnu/ld-2.19.so is the dynamic linker, ignoring /sbin/ldconfig.real: /lib/x86_64-linux-gnu/ld-2.19.so is the dynamic linker, ignoring /sbin/ldconfig.real: Cannot stat /usr/lib32/nvidia-367/libOpenGL.so: No such file or directory /sbin/ldconfig.real: /lib32/ld-2.19.so is the dynamic linker, ignoring /sbin/ldconfig.real: /libx32/ld-2.19.so is the dynamic linker, ignoring libvtkverdict.so.5.8 -> libvtkverdict.so.5.8. Can I get the tar of the vtk library or any help is highly appreciated! Thanks you! Wade

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subcortical structures volume
by 郑凤莲 04 Dec '17

04 Dec '17

Hi professor, I am using Freesurfer 6.0 and get the volume of subcortical structures. I want to get the relationship between age and volume. I only have one group, is it necessary to take gender and eTIV as a covariate? If it is necessary, Which statistical analysis should be used? I really appreciate your help. Thanks a lot. Sincerely, Zheng

3 7

(no subject)
by Myriam Oliver 04 Dec '17

04 Dec '17

help unsubscribe

1 0

recon edit error
by Nicole Orme 04 Dec '17

04 Dec '17

Hello FreeSurfer Developers, I have been editing my MRI images using the recon edit tool. I have been editing the white matter so it does not include grey matter. When I click shift to remove the extra voxels included in white matter they are removed, which is what supposed to happen. Where I’m encountering a problem is sometimes I’ll have clicked the shift but are not holding the mouse down so it seems as if the entire image gets selected. I’ve attached a screenshot. I don’t know how to reverse this. It then will have all the images selected. If you could help me that would be great! Nicole

2 1

Make binary ROIs appear 3d in Freeview
by Anna Mynick 04 Dec '17

04 Dec '17

Hi all, I’m using Tracula and would like to display some regions of interest (ROIs) along with the tracts produced by Tracula. I’m wondering whether there’s a way to visualize these ROIs with 3d texture in the same way that Tracula applies this 3d effect to its tracts. At present, my region of interest (see lower lefthand corner of image below, in yellow) can be viewed in concert with Tracula but doesn’t assume the same 3d texture. Is there a way to make it appear 3d like the tracts? For reference, the ROI is an .nii.gz file containing only 0s and 1s. Thanks for any help! Best, Anna

2 1

Overlaying multiple results onto one surface
by Nguyen, Tin 04 Dec '17

04 Dec '17

Hello, I have been running different analyses through QDEC GUI for different covariates that describe a similar construct, for instance: * Model A: (cortical thickness) ~ (covariate 1) + (nuisance factors) * Model B: (cortical thickness) ~ (covariate 2) + (nuisance factors) * Model C: (cortical thickness) ~ (covariate 3) + (nuisance factors) * Model D: (cortical thickness) ~ (covariate 4) + (nuisance factors) * Model E: (cortical thickness) ~ (covariate 5) + (nuisance factors) As a result, I have 5 different brain images to illustrate each of the 5 models for their corresponding covariates. Is there way to overlay all 5 of the images onto a common space to have 1 representative brain image? This is to show overlapping effects, or the lack thereof, of the covariates. Thank you. -Tin

2 1

Combining parcellated regions within an atlas?
by Michiko H. 04 Dec '17

04 Dec '17

Hi Freesurfer Experts, I was wondering what the best way of combining regions within a parcellation? For example, in the Schaefer 2017 functional atlas, there are regions such as: 7Networks_LH_DorsAttn_FEF_1 0 118 22 0 7Networks_LH_DorsAttn_FEF_2 0 119 17 0 7Networks_LH_DorsAttn_FEF_3 0 119 18 0 7Networks_LH_DorsAttn_FEF_4 0 119 19 0 7Networks_LH_DorsAttn_PrCv_1 0 119 20 0 7Networks_LH_DorsAttn_PrCv_2 0 119 21 0 If I would like to combine all the DorsAttn_FEF areas into 1 node and DorsAttn_PRCv areas into another, what is the best way to do this? I currently have an image that has been parcellated using this atlas that was brought into volumetric space. I would need to have a transformed re-parcellated file and a corresponding color LUT file. Would appreciate any help, thank you! Best, Michiko

2 1

QDEC and comparing two conditions
by Rizvi, Batool 04 Dec '17

04 Dec '17

Hi FreeSurfer experts, We calculated the correlation between thickness two different behavioral conditions using QDEC. We now want to compare the spatial overlap and difference in thickness-correlation between the two behavioral conditions. We would like to do this both visually as well as statistically. Is there an option to do this either in QDEC or in the command line? Thanks for your time! Batool

3 3

Concatenating .mgh surface space functional MRI runs
by Abisan - 04 Dec '17

04 Dec '17

Hi Freesurfer experts, I want to concatenate multiple preprocessed fMRI runs in the form of .mgh freesurfer surface space files (2-D matrices vertexes * time_frames). Is there a tool that can do this easily, or do you have other recommendations how to do this? Thank you!

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