Freesurfer

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30083 discussions

Re: [Freesurfer] libs dependents for ''preproc-sess'' command {Disarmed}
by fsbuild 11 Aug '19

11 Aug '19

External Email - Use Caution Hello Zoe, You should use the package install tools on Debian to install libpng (or any other missing libraries) for your distribution. On CentOS 7 you would do something like, $ sudo yum install libpng12.x86_64 libpng12-devel.x86_64 But like Ubuntu linux, I’m not sure that libpng12 is directly available in recent releases of Debian linux.  I found this link for getting and installing libpng12 for Debian,https://packages.ubuntu.com/xenial/amd64/libpng12-0/download Although we do not officially support building freesurfer on Debian Linux, it would be good to know what version of Debian linux you are running. - R. On Aug 11, 2019, at 05:38, Hang Zeng <zenghang14(a)gmail.com> wrote:        External Email - Use Caution        Dear Sir or Madam,I am running preproc-sess command on Linux Debian. The thing is it shows error msg like '3dvolreg.afni error while loading shares library :libXp.so.6. No such file or directory. After I installed the libXp.so.6, other lib like libpng is required. I am wondering what might be the causes, and how to fix it. If it is indeed the problem of libs, can I have a list of the dependent libraries for that command? Best regards,Zoe_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] I got a problem with open Freeview via X
by fsbuild 11 Aug '19

11 Aug '19

External Email - Use Caution Did you use the Ubuntu package manager tools to install X and also a driver for the graphics card?   It may not work to download a driver from the NVIDIA web site depending upon what is on your machine - or if it is not supported. For X install you could do, $ sudo apt-get install xorg xorg-dev libx11-dev This post might help for installing the NVIDIA drivers, https://linuxconfig.org/how-to-install-the-nvidia-drivers-on-ubuntu-18-04-b… - R On Aug 11, 2019, at 11:53, 송민석학부생 <21700371(a)handong.edu> wrote:        External Email - Use Caution        When I try to execute commands "glxgears" or "glxinfo", I got similar error message.Both of error message says same messages.X Error of failed request:  BadValue (integer parameter out of range for operation)  Major opcode of failed request:  149 (GLX)  Minor opcode of failed request:  24 (X_GLXCreateNewContext)  Value in failed request:  0x0  Serial number of failed request:  19  Current serial number in output stream:  20I thought my graphic card is ok because the Firefox run on X11 after I install graphic card driver, but... umm.. it is sure that error on graphic card settings. I try to found the error about GLX. Thanks for your help.2019년 8월 11일 (일) 오후 5:59, Tim Schäfer <ts+ml(a)rcmd.xn--org>-4f21ay07k 작성:        External Email - Use Caution        I'm quite sure that this is a general problem with your graphics setup that is unrelated to FreeSurfer. Can you run other software that uses your graphics card (e.g., does running glxgears produce load on your nvidia GPU), and could you post the output of `glxinfo`?Tim> On August 11, 2019 at 8:44 AM 송민석학부생 <21700371(a)handong.edu> wrote:> > >         External Email - Use Caution        > > I installed ubuntu 18.04.3 in my new server and also installed Freesurfer..> In this server, I have two graphic cards which are RTX 2080 ti.> > First, I tried to open Freeview without graphic driver, it is failed.> So I install the graphic driver.>   NVIDIA 418.56 / CUDA 10.1> > After I run the Freeview, I got this error message.> > X Error: BadValue (integer parameter out of range for operation) 2> >   Extension:    149 (Uknown extension)> >   Minor opcode: 3 (Unknown request)> >   Resource id:  0x0> > Abort (core dumped)> > > I can't find any log files, and can't get help on google search.> How can I solve this?> If you need any information about my server, please let me know.> > Thank you.> Harine.> _______________________________________________> Freesurfer mailing list> Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, Germany_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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TRACULA - OrientLAS issue for a subject
by Daniel Callow 11 Aug '19

11 Aug '19

External Email - Use Caution Hello, An additional one of my subjects (2/66) is having the exact same issue. I can send his dcminfo.dat information and .log info if that might help with troubleshooting the issue? I have still had no luck determining why OrientLAS in TRACULA doesn't seem to be working for these two subjects. Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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I got a problem with open Freeview via X
by 송민석학부생 11 Aug '19

11 Aug '19

External Email - Use Caution I installed ubuntu 18.04.3 in my new server and also installed Freesurfer. In this server, I have two graphic cards which are RTX 2080 ti. First, I tried to open Freeview without graphic driver, it is failed. So I install the graphic driver. NVIDIA 418.56 / CUDA 10.1 After I run the Freeview, I got this error message. X Error: BadValue (integer parameter out of range for operation) 2 Extension: 149 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 Abort (core dumped) I can't find any log files, and can't get help on google search. How can I solve this? If you need any information about my server, please let me know. Thank you. Harine.

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libs dependents for ''preproc-sess'' command
by Hang Zeng 11 Aug '19

11 Aug '19

External Email - Use Caution Dear Sir or Madam, I am running preproc-sess command on Linux Debian. The thing is it shows error msg like '3dvolreg.afni error while loading shares library :libXp.so.6. No such file or directory. After I installed the libXp.so.6, other lib like libpng is required. I am wondering what might be the causes, and how to fix it. If it is indeed the problem of libs, can I have a list of the dependent libraries for that command? Best regards, Zoe

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Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
by Jessica Bourgin 09 Aug '19

09 Aug '19

External Email - Use Caution It seems to work. Thanks a lot ! Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France

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CORRECTING DEFECT
by Balken, Brendan 09 Aug '19

09 Aug '19

External Email - Use Caution Hello! So I am attempting to use freesurfer's recon-all script but for one of our subjects I keep getting stuck at this point: "CORRECTING DEFECT 29 (vertices=19321, convex hull=4029, v0=32423) XL defect detected..." It has already corrected 28 defects, but they were much smaller. It has been running for about 48 hours on a very powerful machine and I'm wondering how long I should wait. Will it eventually move on? If no, what is my contingency plan for processing this? I'm using the output anatomy folder in brainstorm for source analysis. Any guidance or information would be greatly appreciated. Thanks a million! Brendan Here's what the lh and rh.inflated.nofix look like (is that the defect?): [cid:image001.png@01D54E9B.E7838030]

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TRACULA - runlist longer than subject list
by Daniel Callow 09 Aug '19

09 Aug '19

External Email - Use Caution Hello, When trying to run TRACULA on my data I keep getting the following error. domainname: Command not found. INFO: SUBJECTS_DIR is /Volumes/DANIEL/freesurfer_Tracy INFO: Diffusion root is /Volumes/DANIEL/dti_Tracy/trac Actual FREESURFER_HOME /Applications/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20190326-01e71dc Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /Applications/freesurfer_dev /Volumes/DANIEL/trac-all -c /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/dmrirc.local -log /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.log -cmd /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.cmd domainname: Command not found. ERROR: run list is longer than subject list I have never had this issue before and have tried multiple options for the run list from () to (1 2 3) to include a number for every subject. However, I always get this error. I wonder if there is some issue with the formatting this go around that could be causing the issue but I can't find it. Below is what I have for the initial part of my dmrirc folder. *# FreeSurfer SUBJECTS_DIR* *# T1 images and FreeSurfer segmentations are expected to be found here* *# * setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_Tracy/ *# Output directory where trac-all results will be saved* *# Default: Same as SUBJECTS_DIR* *#* set dtroot = /Volumes/DANIEL/dti_Tracy/trac *# Subject IDs (one per time point per subject)* *#* set subjlist = (HMN002 HMN003 HMN005 HMN006 HMN007 HMN011 HMN014 HMN018 HMN020 HMN021 HMN022 HMN025 HMN029 HMN035 HMN037 HMN039 HMN045 HMN050 HMN055 HMN057 HMN060 HMN064 HMN065 HMN069 HMN072 HMN073 HMN079 HMN085 HMN087 HMN088 HMN095 HMN097 HMN098 HMN099 HMN101 HMN102 HMN103 HMN105 HMN108 HMN110 HMN112 HMN113 HMN115 HMN118 HMN120 HMN121 HMN123 HMN135 HMN141 HMN144 HMN152 HMN156 HMN160 HMN163 HMN175 HMN180 HMN186 HMN187 HMN189 HMN190 HMN191 HMN193 HMN195 HMN196 HMN200 HMN201) *# Longitudinal base template subject IDs (one for each time point above)* *#* set baselist = () *# In case you want to analyze only Huey and Louie* *# Default: Run analysis on all time points and subjects* *#1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66* set runlist = () *# Input diffusion DICOMs (file names relative to dcmroot)* *# If original DICOMs don't exist, these can be in other image format* *# but then the gradient table and b-value table must be specified (see below)* *#* set dcmroot = /Volumes/DANIEL/Tracy/HMN_W1 set dcmlist = ( HMN002/image000001.dcm HMN003/image000001.dcm HMN005/image000001.dcm HMN006/image000001.dcm HMN007/image000001.dcm HMN011/image000001.dcm HMN014/image000001.dcm HMN018/image000001.dcm HMN020/image000001.dcm HMN021/image000001.dcm HMN022/image000001.dcm HMN025/image000001.dcm HMN029/image000001.dcm HMN035/image000001.dcm HMN037/image000001.dcm HMN039/image000001.dcm HMN045/image000001.dcm HMN050/image000001.dcm HMN055/image000001.dcm HMN057/image000001.dcm HMN060/image000001.dcm HMN064/image000001.dcm HMN065/image000001.dcm HMN069/image000001.dcm HMN072/image000001.dcm HMN073/image000001.dcm HMN079/image000001.dcm HMN085/image000001.dcm HMN087/image000001.dcm HMN088/image000001.dcm HMN095/image000001.dcm HMN097/image000001.dcm HMN098/image000001.dcm HMN099/image000001.dcm HMN101/image000001.dcm HMN102/image000001.dcm HMN103/image000001.dcm HMN105/image000001.dcm HMN108/image000001.dcm HMN110/image000001.dcm HMN112/image000001.dcm HMN113/image000001.dcm HMN115/image000001.dcm HMN118/image000001.dcm HMN120/image000001.dcm HMN121/image000001.dcm HMN123/image000001.dcm HMN135/image000001.dcm HMN141/image000001.dcm HMN144/image000001.dcm HMN152/image000001.dcm HMN156/image000001.dcm HMN160/image000001.dcm HMN163/image000001.dcm HMN175/image000001.dcm HMN180/image000001.dcm HMN186/image000001.dcm HMN187/image000001.dcm HMN189/image000001.dcm HMN190/image000001.dcm HMN191/image000001.dcm HMN193/image000001.dcm HMN195/image000001.dcm HMN196/image000001.dcm HMN200/image000001.dcm HMN201/image000001.dc) Any help debugging the issue would be greatly appreciated! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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TRACULA - OrientLAS issue for a subject
by Daniel Callow 09 Aug '19

09 Aug '19

External Email - Use Caution Hello, I am running TRACULA on my data set and am having issues with one of my subjects. For this subject, I get the following error. INFO: input image orientation is LIS INFO: input image determinant is 18.4229 rdc_new: Undefined variable. rdc_new: Undefined variable. rdc_new: Undefined variable. ny_new: Undefined variable. I have attached the dcminfo.dat file of this subject. It seems like mri_info is having trouble either extracting or writing cdc, rdc, and sdc values from this subject's dcminfo.dat file? Any idea why this might be? I have looked through this subjects dcminfo.dat file and compared it to others but have been unable to identify the issue. I have also included the trac-all log for this subject. Some advice on what the issue might be would be greatly appreciated! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Hippocampal subfields
by 郑凤莲 09 Aug '19

09 Aug '19

External Email - Use Caution Hi exports, I am using FS6.0 to segment hippocampus. I run "recon-all -s bert -hippocampal-subfields-T1" and it said "recon all bert finished without error". However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And in tmp directory, there are two directories, "hippoSF_T1_v10_left" and "hippoSF_T1_v10_right". But in these two directories, the l(r)h.hippoSfLabels-T1.v10.mgz file is still not exsit. What's the matter? I need your help. Thanks very muxh in advance. Sincerely, Zheng

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