Freesurfer

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30076 discussions

freeview showing results in a strange manner
by 姜时泽 26 Nov '18

26 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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Paired Analysis Contrasts
by srishti goel 26 Nov '18

26 Nov '18

External Email - Use Caution Hello, I am trying to perform a paired analysis for a data set that has subjects' who belong to either group1 or group2 and have data at time point1 (tp1) and time point2 (tp2). I am following all the steps on the wiki but I want to clarify if the contrasts I plan to use for my analyses are appropriate. For my analyses, I only have two groups and no covariates. I am interested to know if the decrease in cortical thickness of subjects in group 1 across tp1 and tp2 is more than the decrease in cortical thickness of subjects in group 2 across tp1 and tp2. The contrast I think should be used for this is: 1 -1. Is that correct? I am also interested to know if the cortical thickness decreased for subjects regardless of the groups so should I use the contrast: 1 for that? Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig(a)email.unc.edu skype: srishti.goel12

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recon-all after n4 correction
by Kathryn Fitzgerald 26 Nov '18

26 Nov '18

External Email - Use Caution Dear FS experts, I was wondering if it is possible to run recon-all (e.g. autorecon2, autorecon3) on skull-stripped images which have gone through N4 correction. Would it be okay to run? recon-all -i sub1.nii.gz -subjid s1 -autorecon1 -sd . -noskullstrip I saw the work around for already skull-stripped images, but I wasn't sure if this would be appropriate for images which have also been corrected by N4. Or is there another way I should approach this? Thank you for the help in advance! Kind regards, Katie

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Re: [Freesurfer] error while loading shared libraries, FSLVm7_64
by fsbuild 26 Nov '18

26 Nov '18

External Email - Use Caution Hello Karin, If you take a look at this page, https://surfer.nmr.mgh..harvard.edu/fswiki/CMake  you should see there is a link to a file makefile.wiki which you can download.   Besides trying to run the cmake command for you to help with building Freesurfer, there are some notes in the makefile about what packages to install with “sudo yum install <package>” for CentOS/Redhat linux.  So you could try installing those packages, and then also try using that makefile to run cmake and build freesurfer..- R. On Nov 25, 2018, at 17:00, Karin Markenroth Bloch <karin.markenroth_bloch(a)med.lu.se> wrote:        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 $FSLDIR /usr/local/fsl What can I do?   Very grateful for help!  YoursKarin ------------[fsluser@localhost ~]$ 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 directoryFinished /home/fsluser[fsluser@localhost ~]$ cd Data/ [fsluser@localhost Data]$ lslibopenblas.so  s20181112-0601-00006-000001-01.nii [fsluser@localhost Data]$ sudo yum install libopenblas.so[sudo] password for fsluser: Loaded plugins: fastestmirror, langpacksLoading mirror speeds from cached hostfile* base: mirror.hh.se* extras: mirror.hh.se* updates: mirror.hh.seNo package libopenblas.so available.Error: Nothing to do [fsluser@localhost Data]$ flirt /vflirt: error while loading shared libraries: libopenblas.so.0: cannot open shared object file: No such file or directory _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer seems to stop, process still runs
by Renew Andrade 26 Nov '18

26 Nov '18

External Email - Use Caution Dear Community! I am having trouble processing 2 subjects, twice, it stops in CORRECTING DEFECTS 1 and 2 respectively. Watching top output shows CPU is still trying to process the subject. The other day I processed successfully another subject from the same database. Sincerely, Andrade.

2 1

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

3 2

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.

2 1

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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