Freesurfer

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30076 discussions

Segmentation of thalamic nuclei - no reticular nucleus
by Hyun Seok Kim 30 Oct '18

30 Oct '18

External Email - Use Caution Dear all, I ran thalamic nuclei segmentation tool using the "freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa" version. The segmented thalamic nuclei were visualized well by FreeView and were able to find most nuclei. But there is no reticular nucleus (R). I also checked the existence of the reticular nucleus with the following matlab code, but it did not exist. y = MRIread('ThalamicNuclei.v10.T1.FSvoxelSpace.mgz'); find(y.vol == 8125) Is there any way to find the reticular nucleus? Best regards, Hyun Seok Kim

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Third party dependencies directory not found when building from source
by Christian Lee Mcdaniel 30 Oct '18

30 Oct '18

External Email - Use Caution Hello Developers, I am attempting to build Freesurfer from source on my Ubuntu 18.04.1 LTS machine. I have followed the instructions on the freesurfer_linux_developers<http://freesurfer.net/fswiki/freesurfer_linux_developers_page> wiki, and have successfully gotten through steps 1 and 2. However, when trying to install the third party dependencies at step 3 via wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x…, I get the following response: ~$ wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x… --2018-10-30 21:25:16-- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x… => ‘centos6-x86_64-packages.tar.gz’ Resolving surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/> (surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/>)... 132.183.240.105 FreeSurfer<http://surfer.nmr.mgh.harvard.edu/> surfer.nmr.mgh.harvard.edu FreeSurfer Software Suite An open source software suite for processing and analyzing (human) brain MRI images. Skullstripping; Image Registration FreeSurfer<http://surfer.nmr.mgh.harvard.edu/> surfer.nmr.mgh.harvard.edu FreeSurfer Software Suite An open source software suite for processing and analyzing (human) brain MRI images. Skullstripping; Image Registration Connecting to surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/> (surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/>)|132.183.240.105|:21... connected. FreeSurfer<http://surfer.nmr.mgh.harvard.edu/> surfer.nmr.mgh.harvard.edu FreeSurfer Software Suite An open source software suite for processing and analyzing (human) brain MRI images. Skullstripping; Image Registration FreeSurfer<http://surfer.nmr.mgh.harvard.edu/> surfer.nmr.mgh.harvard.edu FreeSurfer Software Suite An open source software suite for processing and analyzing (human) brain MRI images. Skullstripping; Image Registration Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/dist/fs_supportlibs/prebuilt/centos6_x86_64 ... No such directory ‘pub/dist/fs_supportlibs/prebuilt/centos6_x86_64’. I looked in the pub/dist directory and there is no folder named ‘fsl_supportlibs’. I found a file ‘freesurfer-linux-centos6_x86_64-dev.tar.gz’ in the folder pub/dist/freesurfer/dev/‘ but I’m not sure if this contains the third party dependencies and did not want to download without knowing. I do not have build-stamp.txt file in my $FREESURFER_HOME to provide you with the freesurfer version, but I am using the current version on the github repo (although that shouldn’t matter for this issue). Do you have any advice? I couldn’t find any similar issues in the archives, and the wiki says it was last updated this past September, so I believe it is still a current wiki. Thank you! Christian McDaniel ___________________________________________ Christian McDaniel President, Deep Learning @ UGA Data Scientist, UGA CVIOG ITOS Data Analytics Team Master’s Student, Institute for Artificial Intelligence Boyd GSRC University of Georgia Athens, GA

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Pediatric longitudinal pipeline
by Stoyell, Sally Morgan 30 Oct '18

30 Oct '18

Hi all, We are looking at analyzing cortical thickness across time in a group of children. Ages are 6-16 and children each have one followup visit, between 1-3 years from first visit. We first ran the cross-sectional pipeline and analyzed change that way before coming across the longitudinal pipeline. The longitudinal pipeline finished without errors and both cross sectional and longitudinal surfaces seem good at first pass. When comparing the results (change in cortical thickness from first to second timepoint), there are large differences from the cross-sectional to the longitudinal processing in some, but not all of the subjects. The differences in the change of the cortical thickness range from 0.005 all the way up to a difference of 0.04, a difference between processing streams that's as big as the greatest difference in cortical thickness seen within a subject. Some participants switch from a positive to negative difference (i.e. now showing cortical thinning rather than thickening as the cross sectional indicated). Additionally, most of these participants show a greater change with the longitudinal pipeline, which makes us concerned that head size changes are influencing the results. What would be causing such differences between processing streams? Our conclusions from our data will differ slightly depending on which pipeline we use. Other questions and answers from the Freesurfer mail archive seem to indicate that if the pipeline worked it should be fine. Since it seems to work in our case should we just assume the longitudinal did better, or is there a reason we should be concerned that head growth from pediatric participants might have biased the longitudinal pipeline and caused these differences even though it seems to have run correctly? We weren't expecting the magnitude of differences we saw with the longitudinal pipeline, so we want to make sure before moving forward. Thanks, Sally Sally Stoyell Clinical Research Coordinator Department of Neurology Massachusetts General Hospital sstoyell(a)mgh.harvard.edu<mailto:sstoyell@mgh.harvard.edu> M: 607-280-9614

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Getting the volume of a ?h.pial-outer-smoothed file
by Riccardo Falsini 30 Oct '18

30 Oct '18

External Email - Use Caution Dear Freesurfer experts, Hello, I am a student currently working in Frank Guenther's lab at Boston University. I am quite new to freesurfer, so forgive me if the following question may be elementary. I am interested in using freesurfer to compare the level of atrophy (preferably for different brain areas) in an individual subject to several controls. I'm wondering if there is any way to determine the volume of the '?h.pial-outer-smoothed', and corresponding '?h.pial' file generated from running the 'recon-all -s <subj> -localGI' command. The idea is that I could generate a metric representing a general level of atrophy in subjects by comparing these two volumes (or by comparing the '?h.pial-outer-smoothed' to intracranial volume), however, I have been unable to find a way to retrieve these values. Does anyone have any suggestions? I would greatly appreciate any help in this regard. Thank you for your help! Best, Riccardo Falsini

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Re: [Freesurfer] Segmentation fault
by fsbuild 30 Oct '18

30 Oct '18

External Email - Use Caution Hello Jon, Since trac-all is a tcsh script, you could try prefacing it with "tcsh -x" to get extra output about what it is doing, i.e., $ tcsh -x trac-all  ....rest of args... - and then look thru the trac-all output to see where it actually runs a binary command.  Or if you can find in the output of the trac-all script where it runs the binary command that fails, then you could cut and paste that binary command line and try running it directly from the terminal.  If you can reproduce the error from running the binary command line on the terminal, then you could run it in gdb - which might give some more info than just hex output if the binary has symbolic info.  Sometimes scripts run other scripts before they exec and binaries, so the first level output may not show anything useful, but it could be worth a try.. A segfault can be caused by a memory error, but meanwhile I will try to get in touch with the developer since the trace we have so far does not contain any useful symbolic info. On Oct 30, 2018, at 11:02, Whitney, Jon <jon.whitney(a)ert.com> wrote:        External Email - Use Caution        Also, I have located the core dump file if that helps.Thanks!On Tue, Oct 30, 2018 at 11:01 AM Whitney, Jon <jon.whitney(a)ert.com> wrote:Hey!  Thanks for your help. Looking at the end of the system log:<image.png>It's a bunch of mysterious hex. using gdb on trac-all doesn't work because gdb claims it will only work on executable files, not scripts.  However, my Linux guru was able to get the backtrace for the crash.<image.png>which is also in inscrutable hex.  He says that the only way to really identify the error is by combining data (such as the core dump) with the original code to decode this hex data.Thoughts?

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Re: [Freesurfer] Segmentation fault
by fsbuild 30 Oct '18

30 Oct '18

External Email - Use Caution Hello Jon, Looks like you are already running with -debug and -allowcoredump option, and the shell limits do not look like they are too small to allow the coredump to be written.  I don't know offhand if that coredump option causes a file to be written somewhere, but I will try and find out if there is a location for it. When the program exits you could try looking at the end of the system log to see if their is any info logged there, e.g., $ tail -50 /var/log/syslog - and look for events that match the timestamp of when the program ran/stopped running. If you can reproduce running a trac* command from the terminal that causes the crash, then you could try running that same command with gdb, e.g., $ gdb /usr/local/freesurfer/bin/trac-all  -debug -allowcoredump -path -c /data/Abeona/648TT/run_648TT_path.txt .... gdb will output some text then at the gdb prompt type run... (gdb)  run .... then wait for the program to stop and try to get the backtrace with the back trace command  .... (gdb)  bt  full .... which may yield some more info about the crash ..... On Oct 29, 2018, at 16:59, Whitney, Jon <jon.whitney(a)ert.com> wrote:        External Email - Use Caution        I got someone to help me, and based on what they told me the trac-all.log is where the debug information gets stored (I tried using -x +x in my bash command script and it only gave me upper level debugging information), so I have attached the trac-all.log file.  I also was able to get help from someone who was able to save the core dump for when the system crashed, but it is extremely large (1.7GB). I can upload the core dump file if that would be helpful.  I watched the system resources while the program ran, and I noticed that the memory usage only got up to 4% while the CPU usage was 100%, so I don't think I'm running out of memory.  We looked at the core dump file, and my linux expert friend suggested that it may be a memory overflow error because it references memory at 0x0000000etc.<image.png>unfortunately, without the source code to help us interpret the core dump, I don't think I can provide much more in the way of specific information.  Please let me know if there's somewhere I can upload the core dump if you want to look at it.Thanks!

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Postdoctoral position, University of Oslo (UiO)
by Dídac Vidal 30 Oct '18

30 Oct '18

External Email - Use Caution I am delighted to advertise the following postdoctoral position on behalf of Prof Anders M Fjell: At the Center for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have an available postdoc position for an excellent candidate, on the "The Missing Link of Episodic Memory Decline in Aging". The aim is to systematically test how within-person variability in several different variables affect encoding, consolidation, and retrieval of memories using experimental data, functional and structural neuroimaging. The position is for a period of 3 years. The application deadline is: 10.12.2018 Please see more info here: https://www.jobbnorge.no/en/available-jobs/job/159506/postdoctoral-fellowsh… P.S. Interested candidates are welcome to contact Anders M Fjell a.m.fjell(a)psykologi.uio.no if they have questions. All the best, Dídac -- Dídac Vidal Piñeiro

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segmentHA_T2.sh issue, ERROR: cannot find transform file
by Chen Guoyang (IMH) 30 Oct '18

30 Oct '18

External Email - Use Caution Dear Freesurfer experts, I am currently attempting to include an additional T2 MRI scan in the segmentation of our T1 scan. The freesurfer version that I'm using is the freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version). However, I ran into this issue, ERROR: cannot find transform file. I've pasted the output below. Will like your advices for the this matter. Thanks! Sincerely, Guoyang OS Darwin Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 ------------------------------ #-------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib: Registering norm.mgz to additional volume /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass single frame MRI target /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii. /Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz --maskmov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz --dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 ERROR: cannot find transform file /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta gunzip: can't stat: /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz (/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz.gz): No such file or directory 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 segmentSubjectT1T2_autoEstimateAlveusML (line 207) MATLAB:badSwitchExpression Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64 T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018

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Cortical Parcellation: ROIs not covering gray matter in depth direction
by Yixin Ma 29 Oct '18

29 Oct '18

External Email - Use Caution Hi, I’m writing to ask about cortical parcellation (Desikan-Killiany and Destrieux), which do not work well on my recent anatomical scan (a new anatomical scan sequence that gives better grey and white matter contrast). I’m writing to ask if you know what is causing this artifact (ROIs are not covering all gray matter in depth direction) and from which step should I start to debug. Thank you for your help. Best regards, Yixin Ma [image: Screen Shot 2018-10-29 at 12.19.43 PM.png]

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resampling data onto cortical surface
by GREGORY R KIRK 29 Oct '18

29 Oct '18

External Email - Use Caution I have R1 values that I want to resample onto the cortical surface. The R1 values were computed from a multi echo T1 sequence that was also used to create the T1 weighted image that was used in recon-all to produce the cortical surface reconstructions and thus is inherently in registration to the 001.mgz that was used to start recon. There will be a difference in orientation in the volume in that orig.mgz is in coronal and in the .mgz format. I was thinking that if I run the first step of recon-all it should give me an volume named orig.mgz that is in registration to the freesurfer space for the subject ... or else some call to mri_convert reslice_as or whatever is used in the recon-all script to convert 001.mgz to orig.mgz then my problem is to get a file with the resampling of the R1 onto the cortical surface withR1 values at each vertex. when i work with fmri data I run bbregister and get the transformation from the epi volume to the freesurfer space and then use mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface --reg bb.register.dat \ --projfrac 0.5 --interp nearest \ --hemi lh --o lh.sig.mgh to resample the epi data onto the cortical surface. however in this case the R1 data is already in perfect registration to the T1 other than the reorientation and reslicing done to prepare the orig.mgz volume. so can someone tell me what is the proper way to cook this goose Greg

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