Freesurfer

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30086 discussions

freeview Inflated image with mosaic
by Wei Shao 08 Sep '20

08 Sep '20

External Email - Use Caution Hi, Freesurfer Team My name is Wei Shao, as you can see, whenever I tried to Freeview Inflated image , it gives me the picture with mosaic. I was wondering this is because of hardware or the setting? Thanks Best, Wei [image: 3D freesurfer.PNG]

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lobe annotation and stats file
by Marina Fernández 08 Sep '20

08 Sep '20

External Email - Use Caution Dear experts, I would like to get a .stats file this the volume and thickness of lobe annotation, so I am following the steps indicated in this link https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation. Specifically, I used these commands: mri_annotation2label --subject s_001 --hemi lh --lobesStrict lobe.annot cd /usr/local/freesurfer/subjects/; mris_anatomical_stats -a s_001/label/lh.lobe.annot -f s_001/stats/lh.lobe.stats -b s_001 lh The output file that I get (lh.lobe.stats) seems normal and contains the measurements that I need (volume and thickness). The problem is that the terminal output contains this error message: ERROR: stating file /usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot (below you can find the full terminal output) What I have to do to obtain the lh.lobe.stats file (with the same or similar stucture) without the error message? Best regards, Marina % *TERMINAL OUTPUT * % *subject = s_001annotation = aparchemi = rhsurface = whiteReading surface /usr/local/freesurfer/subjects/s_001/surf/rh.whiteLoading annotations from /usr/local/freesurfer/subjects/s_001/label/rh.aparc.annotreading colortable from annotation file...colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)Seg base 2000MRISmergeAnnotations: parcCount=11, newparcname=frontalmri_annotation2 supposed to be reproducible but seed not setMRISmergeAnnotations: parcCount=9, newparcname=temporalMRISmergeAnnotations: parcCount=5, newparcname=parietalMRISmergeAnnotations: parcCount=4, newparcname=occipitalMRISmergeAnnotations: parcCount=4, newparcname=cingulatecomputing statistics for each annotation in s_001/label/rh.lobe.annot.reading volume /usr/local/freesurfer/subjects/s_001/mri/wm.mgz...reading input surface /usr/local/freesurfer/subjects/s_001/surf/rh.white...Using TH3 vertex volume calcTotal face volume 176610Total vertex volume 173305 (mask=0)reading input pial surface /usr/local/freesurfer/subjects/s_001/surf/rh.pial...reading input white surface /usr/local/freesurfer/subjects/s_001/surf/rh.white...reading colortable from annotation file...colortable with 8 entries read (originally none)table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure nameERROR: stating file /usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annotatlas_icv (eTIV) = 1198953 mm^3 (det: 1.624839 )37262 24668 63218 2.363 0.474 0.124 0.029 414 43.8 frontal 3602 2412 6370 2.374 0.615 0.137 0.027 54 3.8 cingulate12917 8443 18251 2.024 0.428 0.134 0.030 171 15.6 occipital19235 12890 36112 2.488 0.535 0.119 0.028 211 21.0 temporal26568 17417 41499 2.204 0.466 0.119 0.024 287 25.6 parietal 2510 1617 4741 3.018 0.820 0.126 0.036 28 3.9 insula*

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mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999
by Paul 08 Sep '20

08 Sep '20

2 1

MEMPRAGE vs. MP2RAGE
by Caspar M. Schwiedrzik 08 Sep '20

08 Sep '20

External Email - Use Caution Hi! I was wondering whether the issues with surface reconstruction from MP2RAGE data that were reported for Freesurfer v5.1 in Fujimoto et al., 2014 still persist in more recent releases of Freesurfer, and whether there is information to what extent they apply to 3T data? Thank you! Caspar

3 4

Results summary in QDEC
by Steve Petersen 08 Sep '20

08 Sep '20

External Email - Use Caution Dear Freesurfer experts, I performed group analysis in QDEC in order to compare cortical thickness between two groups using the Monte Carlo Z simulation correction. My question is, where is located the z-score of each significant cluster? Maybe in the second column named as Max?. Below you can find an example. In this case z-scores of the precuneus and the inferior parietal would be 3.422 and 3.926 respectively? Input /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-HC-ad_plus-Intercept-thickness/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # group_avg_surface_area 82220 # group_avg_vtxarea_loaded 1 # annot aparc # SUBJECTS_DIR /usr/local/freesurfer/subjects # SearchSpace_mm2 75146 # SearchSpace_vtx 146493 # Bonferroni 0 # Minimum Threshold 2.3 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.300000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 4.16102 at vertex 61133 # Overall min -1.24867 at vertex 155746 # NClusters 2 # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 3.422 78695 820.44 -11.2 -54.8 49.4 0.00250 0.00190 0.00310 1664 4553.35 precuneus 2 3.926 52042 733.99 -30.8 -66.6 40.7 0.00410 0.00330 0.00490 1190 3620.13 inferiorparietal Simulation complete. Thanks in advance. Best regards, Steve.

2 1

recon-all error
by Jie Zhao 08 Sep '20

08 Sep '20

External Email - Use Caution Dear freesurfer developer: I am using Freesurfer 7.1.1 and encounter an error like this when using recon-all : zhao@zhao-VirtualBox:~$ export SUBJECTS_DIR=/usr/local/freesurfer/subjects zhao@zhao-VirtualBox:~$ recon-all -s test4 -i sample-002.nii.gz -autorecon1 Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 24 06:16:15 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Segmentation fault ERROR: Executable 'mri_ca_label -all-info failed! Is it missing from the distribution?' What can I do to fix this? Thanks Best regards Jie Zhao

7 26

Piriform gyrus and other regions of the olfactory pathway
by Diógenes Bispo 08 Sep '20

08 Sep '20

External Email - Use Caution Dear, I would like to know how do I get thickness and cortical volume measurements of the piriform gyrus in Freesurfer version 7, as well as other regions of the olfactory pathway. Thanks. Diógenes Bispo Neuroradiologist diogenesdiego(a)gmail.com

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Re: [Freesurfer] Freeview not starting on Ubuntu 16.04: "failed to initialize XRandr"
by fsbuild 08 Sep '20

08 Sep '20

External Email - Use Caution Hi Alex, I see via a search for, ubuntu 16 Failed to initialize XRandr - that what you report happens when trying to connect remotely, e.g., via VNC, to something running X windows/graphics (for other flavors of linux as well).  This thread,https://serverfault.com/questions/788503/xrandr-error-when-accessing… seems to indicate the version of libGL.so could be an issue.  One take away is if you are trying do run X remotely, then you can test to see if a simple X program like glxgears can be run remotely (before trying to run freeview). I don’t think this one is much help as it reads like you already have these installed,https://askubuntu.com/questions/1039129/randr-extension-missing There could be interactions going on w.r.t what you have installed, and then having to set/configure some things so X can work remotely thru the google cloud.  I don’t know how/if Goggle cloud supports X forwarding etc., but I do know that other ways of doing cloud virtualization, e.g., thru docker containers, needs some work to run X applications remotely.   Maybe google cloud taking your virtual machine image and turning it into some kind of “container” to run (which can be done with docker I believe). If possible, I would first test the Ubuntu 16 virtual machine by running it directly on a local machine and check that glxgears and freeview work..  Then I would try running it in the cloud and see what happens with respect to trying to run those programs remotely.   If you don’t have to use Ubuntu 16, we have an Ubuntu 18 virtual disk image you can download and run that already has everything installed to run 7.1.0 (and you could update it to 7.1.1), https://drive.google.com/file/d/1bPvF9m2z4yRDIOv51B5bihU1VN_o2… - R. On Sep 7, 2020, at 14:22, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hi Thanks for the quit reply. I followed those instructions, it seemed that all those libraries were already installed. Freeview still won’t launch (even after rebooting). Here’s the output of the second command you suggested: alexlw@alexs:~$ sudo apt-get install libx11-dev  libxext-dev  libxrandr2  libxrender-devReading package lists... DoneBuilding dependency tree       Reading state information... Donelibxext-dev is already the newest version (2:1.3.3-1).libxext-dev set to manually installed.libxrandr2 is already the newest version (2:1.5.0-1).libxrender-dev is already the newest version (1:0.9.9-0ubuntu1).libxrender-dev set to manually installed.libx11-dev is already the newest version (2:1.6.3-1ubuntu2.2).The following packages were automatically installed and are no longer required:  guile-2.0-libs hdf5-helpers libaec-dev libavcodec-dev libavformat-dev  libavutil-dev libfontconfig1-dev libgc1c2 libgl2ps-dev libgsasl7  libhwloc-dev libibverbs-dev libjbig-dev libkyotocabinet16v5 libllvm5.0  liblzma-dev libmailutils4 libnetcdf-cxx-legacy-dev libntlm0 libnuma-dev  libopenjp2-7 libopenmpi-dev libswresample-dev libswscale-dev libtiffxx5  libxft-dev libxss-dev mailutils-common mpi-default-dev python3-boto tcl-dev  tcl8.6-dev tk-dev tk8.6-devUse 'sudo apt autoremove' to remove them.0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.Any other ideas? Thanks a million AlexOn Sep 7, 2020, at 12:21 AM, fsbuild <fsbuild(a)contbay.com> wrote:Hello Alex,I’m not sure Ubuntu 16.04 LTS has everything installed by default that the Qt graphics framework is looking to run in the X windows server.  You could try installing, $ sudo apt-get update$ sudo apt-get install libx11-dev  libxext-dev  libxrandr2  libxrender-dev- R.On Sep 7, 2020, at 01:52, Alex White <alexander.l.white(a)gmail.com> wrote:Qt: XKEYBOARD_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Fwd: Whole Thalamus Volume
by Al Qadi, Ameen 07 Sep '20

07 Sep '20

External Email - Use Caution ---------- Forwarded message --------- From: Al Qadi, Ameen <ameen.alqadi(a)icahn.mssm.edu> Date: Fri, Sep 4, 2020 at 6:09 PM Subject: Whole Thalamus Volume To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Dear Freesurfer Developers, I noticed a significant disparity in the left and right whole thalamus volumes between *aseg.stats *generated from recon-all and *ThalamicNuclei.v12.T1.volumes.txt *generated from the thalamic nuclei segmentation. Which set of volumes is the correct one to use? Best, Ameen -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi(a)icahn.mssm.edu -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi(a)icahn.mssm.edu

2 1

Extracting hierarchical hippocampal segmentation volumes
by Kelsey Leigh Canada 07 Sep '20

07 Sep '20

External Email - Use Caution Hello, I am newer to Freesurfer and have been unable to find a reference on how to extract the volumes/voxels of the hierarchical segmentations using FS 7.1 (e.g, from rh.hippoAmygLabels-T1-T2.v21.CA.mgz). I am trying to compare manual segmentations to those generated by Freesurfer and the closest hierarchical segmentation is "CA". However, because the volume output (i.e., from quantifyHAsubregions.sh) does not seem specific to a given hierarchical segmentation, I am unsure how the molecular layer is being assigned for the "CA" segmentation given these voxels are assigned to the nearest voxel that isn't the molecular layer or background. Any guidance on how to extract volumes that reflect the "CA" segmentation would be greatly appreciated. Best regards, Kelsey Canada

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