Freesurfer May 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
208 discussions

Re: [Freesurfer] FreeSurfer 7.1 Matlab error, GLIBC_PRIVATE not defined {Disarmed}
by fsbuild 28 May '20

28 May '20

External Email - Use Caution Hello Alex, I would try unseting LD_LIBRARY_PATH altogether or at least take the matlab paths out of it.  My understanding is freesurfer commands don't need matlab paths in LD_LIBRARY_PATH to use matlab after you have setup the freesurfer environment (set FREESURFER_HOME, and source’d the freesurfer setup script).   It looks like the matlab libraries in LD_LIBRARY_PATH are overriding other binaries trying to find the system libc with the symbols they need (and are instead finding the matlab copy of the system libraries). - R. On May 27, 2020, at 23:22, Alexandru Hanganu <hanganu.alexandru(a)gmail.com> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I attemting to run brainstem/ hippocampus/ thalamus segmentation with FS 7.1 and there seems to be a problem with environment variables. Based on comments on other forums, I cannot install GlibC (if this is the case) since it's a cluster. Are there any methods that can be used to avoid this limitation?FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0Platform: CentOS Linux 7 (Core)uname -a: Linux cedar5.cedar.computecanada.ca 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 GNU/Linuxerror:Setting up environment variables---grep: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referenceLD_LIBRARY_PATH is .:/lib64:/home/user/freesurfer/MCRv84//runtime/glnxa64:/home/user/freesurfer/MCRv84//bin/glnxa64:/home/user/freesurfer/MCRv84//sys/os/glnxa64:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/opt/software/slurm/libod: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referencetr: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referenceRegistering imageDump.mgz to mask from ASEGcp: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referencegzip: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time referenceERROR: problem reading fnameSWITCH expression must be a scalar or string constant.Error in myMRIread>load_mgh (line 550)Error in myMRIread>myMRIread_aux (line 92)Error in myMRIread (line 63)Error in SegmentThalamicNuclei (line 278)MATLAB:badSwitchExpressionrm: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference255Best regards,Alex_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)
by Elizabeth Haris 27 May '20

27 May '20

External Email - Use Caution Hi guys, I’m wanting to run segmentHA_T1.sh on an MNI152 registered brain. On my subject, I have run recon-all, then run mri_cvs_register to obtain a brain image registered in MNI152 space. My questions are: 1. In recon-all, is there a way to specify registration to MNI152 space, or is it necessary to first run recon-all and then to run mri_cvs_register? 2. Is it possible to run the segmentHA script on the brain registered in MNI152 space? I’m unable to find where I would specify the use the cvs/norm.mgz (instead of the mri/norm.mgz file). And from what I can see in the script, the parameters set in lines 179/180/181 (below) point to fsaverage brain files, which don’t appear to be the correct targets for the new MNI152 brain; however, there are no corresponding output files in the cvs folder, so I am unsure how to define these parameters. 3. Is there anything I have missed and would also need to do to run the segmentHA script on an MNI152 brain? (I have previously run the script on the average brain and all went well.) 179 set ATLASMESH="$FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz"; 180 set ATLASDUMP="$FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz"; 181 set LUT="$FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt"; Thanks in advance, Elizabeth

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FreeSurfer 7.1 Matlab error, GLIBC_PRIVATE not defined
by Alexandru Hanganu 27 May '20

27 May '20

External Email - Use Caution Hello FreeSurfer Developers, I attemting to run brainstem/ hippocampus/ thalamus segmentation with FS 7.1 and there seems to be a problem with environment variables. Based on comments on other forums, I cannot install GlibC (if this is the case) since it's a cluster. Are there any methods that can be used to avoid this limitation? FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0 Platform: CentOS Linux 7 (Core) uname -a: Linux cedar5.cedar.computecanada.ca 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 GNU/Linux error: Setting up environment variables --- grep: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference LD_LIBRARY_PATH is .:/lib64:/home/user/freesurfer/MCRv84//runtime/glnxa64:/home/user/freesurfer/MCRv84//bin/glnxa64:/home/user/freesurfer/MCRv84//sys/os/glnxa64:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/opt/software/slurm/lib od: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference tr: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference Registering imageDump.mgz to mask from ASEG cp: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference gzip: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in SegmentThalamicNuclei (line 278) MATLAB:badSwitchExpression rm: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference 255 Best regards, Alex

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Circular/cyclic color map for polar data and threshold-ing question in freeview
by Devavrat Vartak 27 May '20

27 May '20

External Email - Use Caution Hello freesurfer community, I had asked this question before, however I am unable to reply to that thread. The question still remains unsolved. I am trying to setup a retinotopy pipeline. I have analysed population receptive field data that generates polar angle and eccentricity maps which I project onto an inflated surface / flattened surface in freeview (Freesurfer 6). MacOS 10.14.6 Freesurfer 6 Nipype (nipype version 1.5.0-rc1 (latest: 1.4.2) I have two queries, which I think are connected. 1) Is there a way to display a circular/cyclic colour map (for the polar angle data) in the overlay screen? The existing 'color wheel' option seems linear(?) (i.e it doesn't not warp around). 2) The distribution of data overlayed changes/shifts compared to the RAW data distribution. I have linked the raw theta values generated from the pRF analysis (in radians) as a histogram and a polarmap - (the figures depict values for both hemispheres) and the distribution when I overlay it on the LH (the distribution for RH is similar) See here for images: imgur[dot]com/a/Wo42DLd This is my processing stream: > The raw theta values based on their voxel coordinates are affined to the functional image and saved as a NIFTI volume. The NIFTI volume in functional space is transformed to the anatomical space and is converted to a surface using > > ! mri_vol2surf --src (input_file_theta.nii.gz) --o theta.mgh --hemi lh --regheader sub-03/freesurfer/recon_all --projfrac 0.5 Any help will be appreciated :-) --- From the old thread, there was this comment: "*Hi!* *Jumping in on this, since it has come up many times but is without a solution so far: the issue is that the color code is now mapped onto a straight color bar, not a circle. At the same time, it is not documented what color refers to which angle. That makes it very difficult to work with this kind of color bar. It would be very helpful to reintroduce the circle, and to explicitly document how angles are mapped to colors. Thank you! - Caspar (**Caspar M. Schwiedrzik)* " Thank you . Cheers, Dev

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Registering Mean Diffusivity to Anatomical Space
by Nillo, Ryan Michael R 27 May '20

27 May '20

Hello FreeSurfer users, I have a mean diffusivity map that exists in MNI152 space that I want to register to a subject’s anatomical space. In the end, I want to display the diffusivity on the subject’s surface. I want to ask if this is the correct way to do this: 1) bbregister --s sub-01 --mov ./MD.mni152.nii --reg $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti #create registration matrix 2) mri_vol2vol --mov ./MD.mni152.nii --targ $SUBJECTS_DIR/sub-01/mri/brain.mgz --reg $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii #register mean diffusivity map to subject space Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging External Email - Use Caution

2 3

mris_register using manual label(s) as guides
by Danny Kim 27 May '20

27 May '20

External Email - Use Caution Hi FreeSurfer experts, I'm currently working on a brain with a bit of atypical morphology and was wanting to parcellate through the DKT labels, but by using manually drawn labels as guides. The intent here is to fix specific labels to be where they are on the surface by drawing them manually and then automatically classify other labels around them (e.g. fix precentral and superiortemporal using manual labels). However, it seems like during the mris_register step, I'm able to use one of my manual label to guide the registration to the sphere, but not more than one. e.g. mris_register -L label/manual_precentral.label DKTatlas40.gcs precentral -curv sphere folding.atlas.acfb40.noaparc.tif surf/sphere.reg (WORKS, after mris_ca_label, precentral is where the manual label was. Superior temporal label is not where the manual label is) e.g. mris_register -L label/manual_precentral.label DKTatlas40.gcs precentral -L label/manual_superiortemporal.label DKTatlas40.gcs superiortemporal -curv sphere folding.atlas.acfb40.noaparc.tif surf/sphere.reg (Runs but output looks exactly the same as before, i.e. superiortemporal label is not where the manual label was specified) Is there a trick to specifying multiple manual labels in guiding mris_register? I am not sure if the -L flag can be specified multiple times and there's no information on that on the mris_register manual. I'm using the following FreeSurfer on my MAC: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 Thanks for your time in this experts! Danny Kim

2 1

Citation of hard and soft failures
by Monereo Sanchez, Jennifer (RAD) 27 May '20

27 May '20

External Email - Use Caution Dear all, I am writing a paper for which I need to introduce the concepts of "hard" and "soft failures", and I am wondering what is the proper way of citing them. I am aware there is plenty of material online (see for example https://fscph.nru.dk/slides/Allison/freesurfer.failure_modes.pdf) but I am wondering if there is a citable paper in which these are described or discussed. Best wishes, ?Jennifer Monereo

2 1

recon-all misses part of occipital cortex
by Isaac Adanyeguh 27 May '20

27 May '20

External Email - Use Caution Dear Freesurfer Development Team, I am having some issues with recon-all where it misses a huge chunk of the occipital cortex in several of my subjects. I have searched the archive and have not found any report of similar issues. Could you please help me figure out how to solve this issue. I have attached a screenshot showing the missing occipital cortex segmentation and a copy of the recon-all.log. I performed the analysis using: - Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20150828 - Platform: Linux 3.10.0-1127.el7.x86_64 Thank you and hope you will be able to help me resolve the issue. Isaac

2 1

Problem_mri_watershed
by Edoardo Pinzuti 27 May '20

27 May '20

External Email - Use Caution Dear Freesurfer community, using the mri_watershed and -surf to crate inner_skull, outer_skin and outer_skull I get a incorrect inner_skull segmentation, probably due to an erroneous skullstrip. I tried to modify the parameters available but it does not help. Is there a way to correct this, manually correct or with a mask ? Any other suggestions will be really appreciated Thanks Edoardo

2 1

PETsurfer: --usf in gtmseg
by Julie Ottoy 27 May '20

27 May '20

External Email - Use Caution Hi, In PETsurfer gtmseg, there is the --usf (upsampling factor) which is by default 2, corresponding to 0.5 mm voxelsize. I was wondering if the usf is recommended to be chosen depending on your mri voxelsize (eg, usf 1 for 1mm voxelsize of the mri), or will it just depend on how "accurate" you want your segmentation to be? Can you safely use --usf 2 for an mri with 1mm voxelsize? Thank you! best regards Julie

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Freesurfer May 2020