Freesurfer July 2018

freesurfer@nmr.mgh.harvard.edu

112 participants
165 discussions

Regenerate Qcache without Recon-ALL
by Mr. Tass 12 Jul '18

12 Jul '18

External Email - Use Caution Hello just a quick question i didn't run recon-all using the -qcache do i have to start all over ? 😢 the initial run took a week Please advise if there is a way to fix that without having to restart recon-all again thank you

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lazy symbol binding errors
by Davide Momi 12 Jul '18

12 Jul '18

External Email - Use Caution Dear experts, I was running mri2mesh command and I got this error: mris_convert /Users/davidemomi/Desktop/DAVE/sim_fem/fs_subj60/surf/rh.white /Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/tmp/wm.rh.stl dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib So I've tried to source Freesurfer and run sudo -E fs_update But I got another error rsync -zbrlv --progress --suffix=.1531384527_bak rsync:// surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OS… /Applications/freesurfer rsync: failed to connect to surfer.nmr.mgh.harvard.edu: Operation timed out (60) rsync error: error in socket IO (code 10) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52/rsync/clientserver.c(106) [receiver=2.6.9] Could you please help me with both errors? Thanks in advance Davide

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FreeSurfer - Lateral Ventricle Definition
by AKUDJEDU, THEOPHILUS 12 Jul '18

12 Jul '18

External Email - Use Caution Dear FreeSurfer Experts, Can you confirm whether, the volume of the choroid plexus has automatically been added to the laterel ventricle volume or not. Thanks Theo _______________________________ Theophilus Akudjedu BSc, MSc, PhD Candidate Room 202 Comerford Suite, Clinical Science Institute, Department of Psychiatry, National University of Ireland, Galway Phone: +353 838329602 Email: t.akudjedu1(a)nuigalway.ie<mailto:t.akudjedu1@nuigalway.ie> rasningo(a)gmail.com<mailto:rasningo@gmail.com> [https://ci6.googleusercontent.com/proxy/b9-AoNc-V0v85TZ_pj6puJTgX7uWBNlZdoh…]

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make_average_subject error
by Wang, Xiaoyu 12 Jul '18

12 Jul '18

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to perform group analysis on a group of subjects. However, When I am trying to create an average subject I get the following error. mghRead(mri/norm.mgz, -1) could not open file I went into the average folder but I could not find norm.mgz anywhere. Looking further up on the log, it would seem that norm.mgz is supposed to be relabled from aseg.presurf.hypos However, said file is still there. I have looked in the wiki and found a few others who have had similar issues to me however, I can't see the solution or a reply. Does anyone have any Idea what I'm doing wrong? I have attached the recon-all.error as well as the recon-all log if it will be of any help Sincerely Xiaoyu Wang

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Putting results from probabilistic tractography on the surface
by Sims, Sara A 11 Jul '18

11 Jul '18

External Email - Use Caution Hello, I have outputs from FSL probtrackx that I would like to display on Freesurfer surfaces. If I put the volume into freesurfer space how can I get it to sample onto a surface when the values are in white matter and not grey matter? To rephrase, how can I pull data from white matter (just below the grey matter) and display it on a surface? Many thanks, Sara

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Custom color map in Freeview
by Anna Mynick 11 Jul '18

11 Jul '18

Hi all, I’m wondering whether there’s a way to create a custom color map in Freeview that would operate as a alternative to the preset Greyscale, Heatmap, NIH, PET, Jet and GE Color options. Ideally, I could assign each number value a given color, e.g. every “0” value in an .nii file is black, every “1” value is red, every “2” value is blue, every “3" is green and so on. I already have the RGB values worked out for each number value; I just need to know how to format this information and where to put it so that I can my custom colormap as an option in Freeview. For my purposes, there would be no need to adjust the assigned colors based on the overall range of values. For instance, there would be no need to assign a different color value to a “1” value depending on whether the highest value in the overall .nii file is 1 or 100. I did try reading the related conversation here<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051277.ht…> but I can’t seem to find the file it references, annotval2surfoverlay.m, in the Freesurfer directory. Thanks very much for your help! Anna

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Errors preprocess
by Lee, Seonjoo 11 Jul '18

11 Jul '18

External Email - Use Caution Dear Freesurfer experts, I tried to run preproc-sess but did not have much luck to make it work. I converted resting fmri file into .nii, and I created the following directory structure and it’s stored under /data/sub1/rest/001/fMRI.nii: /data /data/sub1 /data/sub1/rest /data/sub1/rest/001/ /data/sub1/rest/001/fMRI.nii Then I ran preproc-sess -s sub1 -fsd rest -surface $FSAVERAGE_DIR/fsaverage lhrh -mni305 -fwhm 5 -per-run And I kept getting the following error message: ERROR: cound not find session sub1 To run freesurfer I specified SUBEJCTS_DIR as /data (I don’t think it matters, though…) export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh SUBJECTS_DIR=/data Any suggestion to make it work? Thanks. -Seonjoo

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mris_ca_label seed
by Rosemary Nicholas 11 Jul '18

11 Jul '18

External Email - Use Caution Hello, I am running a dataset through version 6.0 of Freesurfer on Linux, extracting results for both the Desikan atlas and our own atlas. When extracting the stats for our atlas, the results were varying considerably (sometimes up to 10%) in test-retest runs. The release notes for 4.5 indicate that the default setting for mris_ca_label should use the same number as a seed, and therefore give the same results, but it doesn't. "The binaries in the recon-all stream which are subject to variability due to usage of a random number generator (mris_smooth, mris_sphere, mris_topology_fixer, mris_topo_fixer and mris_ca_label) are now seeded with the same number, with the result being that repeated runs of the recon-all stream on a subject on the same platform will always give identical results." The issue seems to be resolved by adding -seed 1234 as a flag to mris_ca_label. I would like to understand what this is actually doing though, before applying it to all my data. What is the random number generator used for? What does setting it to 1234 actually do? It isn't listed in the optional flagged arguments. Is it just deciding which vertex is labeled first? Here is how we are running it (in two independent scripts): FIRST: # autorecon1 including data conversion recon-all -i $mprage/001 -autorecon1 -subjid $s # autorecon2 with threshold adjustments recon-all -seg-wlo 60 -seg-ghi 70 -autorecon2 -subjid $s # autorecon3 recon-all -autorecon3 -subjid $s THEN: mris_ca_label $s $h sphere.reg /g5/dcn/freesurfer_testing/subjects/"$h".rantaFL.gcs rantaFL.annot modified to: mris_ca_label -seed 1234 $s $h sphere.reg /g5/dcn/freesurfer_testing/subjects/"$h".rantaFL.gcs rantaFL.annot Thank you, Rosemary Nicholas Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute

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/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
by Jasmin Alves 11 Jul '18

11 Jul '18

External Email - Use Caution Hello FreeSurfer Developers, I am trying to analyze the subfields of the hippocampus using FreeSurfer 6.0 based on the tutorial, "Segmentation of hippocampal subfields". However, several errors come up when I run: recon-all -s 102 -hippocampal-subfields-T1 #@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18 PDT 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18 PDT 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. I have searched through the list to see if anyone else has had this issue but to no avail. Version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c OS: X V 10.9.5 Thanks! Jasmin -- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

2 5

recon-all fatal error
by Daniel Kimmel 11 Jul '18

11 Jul '18

External Email - Use Caution Hello, I'm attempting to run basic preprocessing with reconstruction using fmriprep-docker.py and freesurfer. The fmriprep process completes when excluding freesurfer, but encounters a fatal error when including freesurfer. There error is: recon-all -s sub-18042401 exited with ERRORS at Wed Jul 11 01:39:47 UTC 2018 For more details, see the log file /out/freesurfer/sub-18042401/scripts/recon-all-rh.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> Standard error: ln: failed to create symbolic link 'rh.white.H': Operation not supported Return code: 1 180711-01:39:51,447 workflow ERROR: could not run node: fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs 180711-01:39:51,452 workflow ERROR: could not run node: fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs 180711-01:39:54,738 cli WARNING: Errors occurred while generating reports for participants: 18042401 (2). The call to freesurfer is made by fmriprep, which is doing so within a docker container, so unfortunately I don't know the exact version of freesurfer. I'm using fmriprep version 1.0.13. I make the call to fmriprep from a CentOS Linux box: uname -a: Linux xxx.xxx.xxx.columbia.edu <http://xxx.xxx.xxx.columbia.edu/> 3.10.0-862.2.3.el7.x86_64 #1 SMP Wed May 9 18:05:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux I've attached: 1) the complete terminal output from fmriprep (which is reporting the output of freesurfer) 2) recon-all-status-rh.log 3) recon-all.log Thanks very much for your help! Best, Daniel

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Freesurfer July 2018