Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

e-TIV
by 박경일 26 Nov '18

26 Nov '18

External Email - Use Caution Dear experts, When I see the images through freeview to edit, upper brainstem and optic chiasm were always included in wm or brainmask.mgz, as an attached picture below. Left side seems to be recognized as white matter, and right side as cortex. My concern is that this could affect the final value of e-TIV after recon-all process, so I need to edit these areas manually. I'd appreciated your help. Thanks so much. Kyung

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error while loading shared libraries, FSLVm7_64
by Karin Markenroth Bloch 25 Nov '18

25 Nov '18

External Email - Use Caution Dear all, I'm afraid this is a very basic Linux question, but I am not that familiar with it. I downloaded and installed FSLVm7_64 on a Windows7 host. Installation went well, and if I type fsl in the terminal window, a GUI (a menu list) pops up. My first attempt was to click "BET", select an input image and Run standard brain extraction using bet. Then I get the messages (see below): " error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory" The libopenblas.so is in my /home/flsuser/Data directory. I tried installing it sudo yum install libopenblas.so, but get the reply "No package libopenblas.so available." (see below) I have set the $FSLDIR variable : [fsluser@localhost Data]$ echo $FSLDIR /usr/local/fsl What can I do? Very grateful for help! Yours Karin ------------ [fsluser@localhost ~]$ fsl /usr/local/fsl/bin/bet /home/fsluser/Data/s20181112-0601-00006-000001-01 /home/fsluser/Data/s20181112-0601-00006-000001-01_brain -f 0.5 -g 0 /usr/local/fsl/bin/bet2: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory Finished /home/fsluser [fsluser@localhost ~]$ cd Data/ [fsluser@localhost Data]$ ls libopenblas.so s20181112-0601-00006-000001-01.nii [fsluser@localhost Data]$ sudo yum install libopenblas.so [sudo] password for fsluser: Loaded plugins: fastestmirror, langpacks Loading mirror speeds from cached hostfile * base: mirror.hh.se * extras: mirror.hh.se * updates: mirror.hh.se No package libopenblas.so available. Error: Nothing to do [fsluser@localhost Data]$ flirt /v flirt: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory

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extracting FA from FA_skeletonised with freesurfer parcellation
by Winkelbeiner, Stephanie A 23 Nov '18

23 Nov '18

External Email - Use Caution Hi, I try to extract FA values from the FSL FA skeleton using the freesurfer aparc.a2009s+aseg+2mm parcellations. I did the following: 1. Recon-all to obtain --> aparc.a2009s+aseg+2mm 2. TBSS in FSL to obtain --> all_FA_skeletonised 3. Tbss_deproject to split up all_FA_skeletonised into individual skeletons (native space) (*_FA_FA_all_FA_skeletonised.nii.gz) 4. Non-linear transformation of aparc.a2009s+aseg+2mm to subjects' native space (parc2dwi.nii.gz) 5. Creating binary mask for each subjects FA skeleton to exclude 0 voxels (*_FA_skeleton_mask.nii.gz) 6. Extracting FA values using mri_segstats with the following command: cd subj1/ mri_segstats \ --seg mri/parc2dwi.nii.gz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i skeletons/SPN01_CMH_0001_01_FA_FA_all_FA_skeletonised.nii.gz \ --mask skeletons/SPN01_CMH_0001_01_FA_skeleton_mask.nii.gz \ --excludeid 0 \ --sum skeletons_FA.stats The FA values I obtain are around 0.1 which is highly unlikely, especially for regions such as the corpus callosum. Is there some obvious error in my approach? Or can someone recommend a different approach? I would be very grateful for some help! Thanks, Steph Stephanie Winkelbeiner, MSc Research Coordinator Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: swinkelbei(a)northwell.edu<mailto:swinkelbei@northwell.edu> Northwell Health Visit us at Northwell.edu<http://northwell.edu/> The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Re: [Freesurfer] thalamic nuclei additional scan error
by Iglesias Gonzalez, Eugenio 23 Nov '18

23 Nov '18

External Email - Use Caution Dear Zhac, Apologies for the mistake in the wiki. As explained in the error message, the subjects directory is the second argument. Also, if you are using a T2 scan, I would replace t1 by t2 in the last argument. The call should be: (For a T1 additional scan) segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/ /Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t1 (For a T2 additional scan) segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/ /Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t2 Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London, and Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of zhac looch <Z30D(a)hotmail.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 23 November 2018 at 16:32 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] thalamic nuclei additional scan error External Email - Use Caution Hi Freesurfer Team, I want to add additional scan my thalamic segmentation. but my code is not working. where is the error in my code? thanks for help my code: segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t1 my error: Usage: segmentThalamicNuclei.sh SUBJECT_ID [SUBJECT_DIR] [ADDITIONAL_VOL ANALYSIS_ID BBREGISTER_MODE] Or, for help segmentThalamicNuclei.sh --help

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thalamic nuclei additional scan error
by zhac looch 23 Nov '18

23 Nov '18

External Email - Use Caution Hi Freesurfer Team, I want to add additional scan my thalamic segmentation. but my code is not working. where is the error in my code? thanks for help my code: segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t1 my error: Usage: segmentThalamicNuclei.sh SUBJECT_ID [SUBJECT_DIR] [ADDITIONAL_VOL ANALYSIS_ID BBREGISTER_MODE] Or, for help segmentThalamicNuclei.sh --help

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White brainmask.mgz
by Rosalia Dacosta Aguayo 23 Nov '18

23 Nov '18

External Email - Use Caution Dear Free Surfer experts, I am experiencing a problem with 4 participants. Whrn I open the brainmask with freeview, it appears white (binarized). I was editing this brainmask and at sone point I switched something and it changed to white. I deleted alk the files and I run recon-all - autorecon1. The problems persists and recob-all -autorecon1 finished with errors. I do not know how to solve this problem. I would much appreciate your help. Best regards, Rosalia

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Fsgd-File
by Larissa Bechtle 23 Nov '18

23 Nov '18

External Email - Use Caution Hi freesurfer-experts, I am currently trying to run mris_prepoc. However FreeSurfer keeps telling me that there are no subjects specified. Thus, I think that the fsgd-file I created is the problem. I already checked it several times but still don’t know what’s wrong. I would be very thankful for some tips. -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni [kpsy-mac84024:~/Desktop/larissa/Gewalt] Forschung% setenv SUBJECTS_DIR /Users/Forschung/Desktop/Larissa/Gewalt/ [kpsy-mac84024:~/Desktop/larissa/Gewalt] Forschung% mris_preproc --fsgd FSGD.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gewalt.10.mgh ERROR: no subjects specified [kpsy-mac84024:~/Desktop/larissa/Gewalt] Forschung% GroupDescriptorFile 1 Title Aggression Class Group1 Class Group2 Variables Age Input zv75 Group1 27 Input xp09 Group1 26 Input wn79 Group2 24 Input wi40 Group1 19 Input vg03 Group1 33 Input va82 Group2 24 Input ui42 Group2 23 Input ud16 Group1 26 Input tp38 Group2 22 Input to98 Group2 22 Input th01 Group1 23 Input tg08 Group2 23 Input so80 Group2 21 Input re37 Group1 27 Input pt12 Group2 27 Input pl96 Group2 22 Input pi04 Group2 27 Input oo75 Group1 22 Input ob56 Group2 23 Input nh85 Group2 27 Input mw53 Group2 23 Input lu75 Group1 22 Input lt62 Group2 22 Input le00 Group1 23 Input lc79 Group2 24 Input kp89 Group1 22 Input ko71 Group2 25 Input ke93 Group1 29 Input ju55 Group1 20 Input jc49 Group1 21 Input in19 Group2 29 Input if27 Group1 29 Input hc55 Group2 23 Input gs02 Group1 43 Input fp50 Group2 21 Input ez57 Group2 25 Input et53 Group2 24 Input ei77 Group2 27 Input dn20 Group2 28 Input cp97 Group1 25 Input cn18 Group2 52 Input cm66 Group1 21 Input cg21 Group2 22 Input bw90 Group1 29 Input bg38 Group2 25 Input ab35 Group1 22 Best, Larissa

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Problem with freesurfer installation on mint 19 (ubuntu based OS)
by Mahshid Fouladivanda 23 Nov '18

23 Nov '18

External Email - Use Caution Hi Dear experts, I downloaded and installed freesurfer on CentOS without any problem and also worked with it. Recently I've switched on mint 19 (an Debian based operating system) and I tried to setup freesurfer but, it does not worked. I would appreciate your help to make it work on ubuntu (or mint). Regards, Mahshid

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Re: [Freesurfer] Problem with freesurfer installation on mint 19 (ubuntu based OS)
by fsbuild 23 Nov '18

23 Nov '18

External Email - Use Caution Hello Rashid, I would start with getting a cmake command to succeed to try and do the build.  Try looking over the cmake build page here,  https://surfer.nmr.mgh.harvard.edu/fswiki/CMake - where there is also makefile (makefile.wiki) you can download that should default to some useful settings for the cmake command on CentOS 6, 7, Ubuntu 16, 18, and MacOS   If you are on debian it will probably default to the CentOS 7 settings, but you could start from there. - R. Mahshid Fouladivanda November 23, 2018 at 06:49         External Email - Use Caution         Hi Dear experts,   I downloaded and installed freesurfer on CentOS without any problem and also worked with it. Recently I've switched on mint 19 (an Debian based operating system) and I tried to setup freesurfer but, it does not worked. I would appreciate your help to make it work on ubuntu (or mint).   Regards, Mahshid   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freeview showing results in a strange manner
by 姜时泽 22 Nov '18

22 Nov '18

External Email - Use Caution | | Dear freesurfer experts, I am using freesurfer to analyze my PET data according to the tutorial online. It works pretty well and I write the values of the results of each region to the template with Matlab (file attached here entitled "lh.subj1.mgz"). However, when I try to open it with freeview, the image looks quite strange ('Picture_1') but it works with tksurfer (Picture_2). Does any one know what is wrong with this? Did I plot the result in a wrong way? Thanks very much Shize -- Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13(a)fudan.edu.cn | | | |

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Freesurfer November 2018