Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Thalamic nuclei longitudinal analysis
by Antti Cajanus 13 Mar '19

13 Mar '19

External Email - Use Caution Dear FS experts, I'm using the thalamic nuclei segmentation on T1-images. Is it possible to perform longitudinal analysis with this data, or could I just segment the different time points separately to see volume reduction of specific nuclei? Best, Antti Cajanus PhD student

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'mghRead -1 error: could not open file' when running mri_info from Matlab
by Suzanne Witt 12 Mar '19

12 Mar '19

External Email - Use Caution Dear all, I have a matlab script that includes the following call to freesurfer: [status, result] = system(‘mri_info fsaverage/mri/brain.mgz —vox2ras-tkr'); The matlab script errors out at this step with the following output: status = 1 result = ‘mghRead(fsaverage/mri/brain.mgz, -1): could not open file’ If I run the mri_info command on the exact same file outside of matlab, I get the correct 4x4 matrix as output. I am running freesurfer 5.3.0 and matlab 2018b on a HPC system. I think I have all of the necessary paths for freesurfer set correctly in my matlab startup.m file: freesurfer/bin freesurfer/fsfast/bin freesurfer/mni/bin I am not sure why mri_info is giving correct input when run from the bash terminal prompt but throws this mghRead error when attempting to run the same command through matlab. The matlab script itself works on the mac desktop computer of the author (not sure what version of freesurfer or matlab the author is running), so the problem does not appear to be with the matlab system call to mri_info per se. Any suggestions of what else to troubleshoot (or if I am missing any path specifications in my startup.m file) would be much appreciated. For completeness, below is the output from ‘source $FREESURFER_HOME/SetUpFreeSurfer.sh’: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0<http://soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0> FSFAST_HOME /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0/fsfast<http://soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0/…> FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0/subjects<http://soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0/…> MNI_DIR /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0/mni<http://soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0/…> Thanks, suzanne [cid:67412C66-BB70-409C-BE50-7BADCECDE5F9@uwo-x-11.wireless.uwo.pri]

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Postdoctoral fellowship in Neuroimaging, genetics, and addiction at UVM
by Shana Adise 12 Mar '19

12 Mar '19

External Email - Use Caution Hello all, Please see the below postdoctoral advertisement sent on behalf of Hugh Garavan and Scott Mackey. We are seeking a postdoctoral fellow who will join a consortium of leading addiction researchers to work on an exceptionally large neuroimaging-genetics project. ENIGMA-Addiction (http://www.enigmaaddiction.com<http://www.enigmaaddiction.com/>) performs secondary analyses on datasets contributed by labs from over the world. The uniquely large sample sizes with multi-modal neuroimaging data enable numerous in-depth investigations of the neurobiology of drug dependence. The successful applicant will join a vibrant lab with considerable experience working with large datasets. We host a T32 trainee grant that focuses on applying machine learning analytic techniques to large neuroimaging-genetic datasets, and we are a member of the ABCD and IMAGEN consortia. The successful applicant will be able to conduct novel and robust analyses encompassing genetics, neuroimaging and behavioral measures focused on understanding the neurobiology of drug use and dependence. The University of Vermont is a premier small research university and is based in Burlington Vermont, a town that is perennially ranked as one of the USA’s most livable small cities known for its healthy lifestyle, music and food scenes. Interested applicants should contactHugh.Garavan(a)uvm.edu<mailto:Hugh.Garavan@uvm.edu> and msmackey(a)uvm.edu<mailto:msmackey@uvm.edu> for informal enquiries.

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Trouble updating free surfer
by Shana Adise 12 Mar '19

12 Mar '19

External Email - Use Caution Hello, I originally ran into some hiccups with AFNI’s @SUMA_make_spec_FS, which stems from a freesurfer error: 1. Error one: Abort 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 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 Abort c_ras: Subscript out of range. c_ras: Subscript out of range. 2. It appears that you are already aware of this issue: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes 3. However, I have a new issue when trying to run sudo -E fs_update rsync -zbrlv --progress --suffix=.1552339020_bakrsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesurfer receiving file list ... rsync: change_dir "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in pub) failed: No such file or directory (2) 0 files to consider sent 4 bytes received 9 bytes 26.00 bytes/sec total size is 0 speedup is 0.00 rsync error: some files could not be transferred (code 23) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52.200.1/rsync/main.c(1404) [receiver=2.6.9] 4. Navigating to this site gives file not found: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freesurfer/patches/f… Any suggestions? Thanks, Shana

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Parcelation in gadolinium image
by María Martínez Rodrigo 12 Mar '19

12 Mar '19

External Email - Use Caution Good morning, When I am using T1 with gadolinium, some errors appear in the later 3D mapping obtained. In particular, the boundaries of some of the structures which have gadolinium in the original image are not well defined in the parcelation. Do you know any solution for this problem? Thanks in advance.

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Thalamic Nuclei {Disarmed}
by 郑凤莲 12 Mar '19

12 Mar '19

External Email - Use Caution Hi Experts, I am using Freesurfer dev version for the segmentation of thalamic nulei. Previously, I have used this version for amygdala and hippocampus segmentation. However, the segmentThalamicNuclei.sh file can't be found in this version. Is there another new version for the thalamic? Could you share me the new version? Thanks very much in advance. Look forward to your reply. 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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Error with FSGD format
by Jennifer Legault 11 Mar '19

11 Mar '19

External Email - Use Caution Hi Freesurfer experts, I am trying to run the mris_preproc command, however I keep getting the following error: ERROR: format for <path> not recognized. Even when I create files in linux (using vi), TextEdit, or Notepad, and make sure that there are no extra spaces at the end of lines, I still get this error. I am attaching one such file here. Any feedback would be greatly appreciated. Best, Jen -- Jennifer Legault PhD, Neuroscience Postdoctoral Scholar Language Acquisition and Brain Lab University of Delaware

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Changing Thresholds in dmri_pathstats: --pthr option not changing results
by Adam Schadler 11 Mar '19

11 Mar '19

External Email - Use Caution Dear freesurfer community, I have been trying to experiment a bit with the dmri_pathstats command that TRACULA uses to compute tract statistics. I read previously that one could change the default threshold value that stats are computed with by using the "--pthr .##" option. (I was curious about using this since I often run into the peculiar problem of some tracks, e.g. forceps major/minor, having mostly normal looking path.pd maps, with a few voxels having unusually high values, thus potentially biasing results. These tracks are often set at abnormally high thresholds when visualizing the tracks. e.g. a forceps major normally has a threshold [30,45], while some may be thresholded as high 100 or 150, making the tract look problematic). I experimented by running the dmri_pathstats command with a few different values for "--pthr .##": * --pthr .01 * --pthr .05 * --pthr .10 * --pthr .20 * --pthr .80 * --pthr 1.00 However, the outputted "pathstats.overall.txt" and "pathstats.byvoxel.txt" files are all identical. Suspecting a potential bug, I did a few more tests, with values such as: * --pthr 2.0 * --pthr 100 * --pthr 50000000000000 * --pthr hi * --pthr goodbye * --pthr Interestingly, all of the outputted "pathstats.overall.txt" and "pathstats.byvoxel.txt" files were all identical to the previous six tests. The program does not return an error message either. Is this a potential bug? Or was the "--pthr" functionality removed from dmri_pathstats? Incidentally, I am using freesurfer version 5.3.0. Maybe this was updated in a further release? Thank you for any clarification! Sincerely, Adam Schadler

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Welch's t-test for HOV violation
by Hannah CK 11 Mar '19

11 Mar '19

External Email - Use Caution We are conducting t-test comparisons across groups in which there is a large discrepancy in group sizes. HOV is violated. I've searched for ways to run Welch's t-test in FreeSurfer (or a similar analysis that does not assume homogeneity of variance) but am not finding one. Could anyone please advise on how to do this? Thank you.

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Recon-all, hippocampal segmentation issue
by Faezeh Vedaei 11 Mar '19

11 Mar '19

External Email - Use Caution Hello Freesurfer Developer I have an issue of running Freesurfer command on the Mac terminal in order to do recon-all and hippocampal segmentation. I used the command line as I provide here, but it shows me an error message due to can not find the input file (.nii)! This is so weird as the .nii input data is in the directory I am running this command. Really appreciate your help if you take a look at my command line, input data and error message and let me know how I can resolve this issue. 1-Freeaasurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2-Command: recon-all -all -i CID750.anat.nii -hippocampal-subfields-T1 ERROR: cannot find CID750.anat.nii 3- Platform: MacOS Mojave, Version 10.14.3 (18D109). Thanks Faeze

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