Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

hew hippocampal and amygdala subfields
by Frodl, Thomas 12 Mar '18

12 Mar '18

Dear All, could you pease give me some advice? When I tried to run the new hippocampal subfield analysis on our high Performance System I got the following error (copied below). It seems the it can't find this MEX file. Many thanks and best wishes Thomas #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Sat Mar 10 16:54:52 GMT 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/MCRv84//runtime/glnxa64:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/MCRv84//bin/glnxa64:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/MCRv84//sys/os/glnxa64:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/lib/vtk/lib/vtk-5.6:/home/support/apps/cports/rhel-6.x86_64/gnu/glib/2.46.2/lib:/home/support/apps/libs/qwt/6.1.3/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/vtk/5.10.1/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/Python/2.7.12/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/tcl/8.5.19/lib:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/MCRv84//sys/opengl/lib/glnxa64:/home/support/tcin/apps/freesurfer/6-dev-20180122/freesurfer/lib/vtk/lib/vtk-5.6:/home/support/apps/cports/rhel-6.x86_64/gnu/glib/2.46.2/lib:/home/support/apps/libs/qwt/6.1.3/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/vtk/5.10.1/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/Python/2.7.12/lib:/home/support/apps/cports/rhel-6.x86_64/gnu/tcl/8.5.19/lib Invalid MEX-file '/tmp/MCR_500598999/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64': /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/MCR_500598999/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64) 　 Error in kvlClear (line 11) 　　　 Error in segmentSubjectT1_autoEstimateAlveusML (line 115) 　　　 MATLAB:invalidMEXFile

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TRACULA -stat coord output file
by Carissa Nicole Weis 12 Mar '18

12 Mar '18

Hello, Are the contents of the *.coords.mean.txt file generated from the trac-all -stat command, the average MNI coordinates along the tract across subjects? Or average coordinates in native space? Thanks! Carissa

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FreeSurfer Error Edit Sequence
by David S Lee 12 Mar '18

12 Mar '18

Hello Experts, Do you suggest FreeSurfer users to *strictly* follow the *error edit sequence* (Brain Mask --> WM --> GM --> Control Points) listed here (link below)? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData If not, can users follow this sequence instead: Brain Mask --> Control Points --> GM --> WM? The justification here is to minimize the time spent to perform hand edits. Thank you for your time, -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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e-mail error {Disarmed}
by 郑凤莲 09 Mar '18

09 Mar '18

Hi FS list, When I sent an e-mail to you, I always recieved a disarmed e-mail, as follows: What' wrong? Is there any way to resolve it? Sincerely, Zheng | | 13181786167 邮箱：13181786167(a)163.com | 签名由网易邮箱大师定制

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Recon-all {Disarmed}
by 郑凤莲 09 Mar '18

09 Mar '18

Hi experts, I am using FS 6.0 for LGI. My data is fetal images. I ran "recon-all" pipeline for cotical thickness and LGI. Is it suitable? Or are the results reliable, such as the LGI value of precental? I am looking forward to your reply. Thank you very much. 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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Potential ways to overlay perfusion ROIs onto cortical thickness maps
by Arsenije Subotic 09 Mar '18

09 Mar '18

Dear experts, I am trying to figure out the best way to overlay areas of low CVR reactivity and correlate that with cortical thickness measurements in those given regions. I was able to overlay our CVR map onto an inflated cortical surface in 3D and modify the configuration to see areas of low perfusion in blue. Using QDEC, I also know that you can manually trace an ROI and generate cortical thickness measurements within that ROI for a given subject. My question is, is it possible to manually trace an ROI in freeview? I tried doing it but it doesn't allow me to use the 'new ROI' when I use the drop down menu. And additionally, is there some way to accurately generate perfusion values within that ROI and then precisely transfer this ROI outline into QDEC so that the cortical thickness ROI is as close to the ROI in the CVR map as possible? Please let me know what you think. Thanks! Arsenije

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Can't open tkmedit
by Levitas, Daniel 09 Mar '18

09 Mar '18

Hi, I tried opening tkmedit but received the following error: libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast X Error of failed request: GLXBadContext Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 6 (X_GLXIsDirect) Serial number of failed request: 26 Current serial number in output stream: 25? >From what I've read online, it seems to be a graphics card issue, but I'm unsure how to resolve the problem because I'm using my university's linux cluster. Thanks for the help.

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mri_ca_normalize error: Abort (core dumped)
by Marschall, T.M. 09 Mar '18

09 Mar '18

Dear all, I’m currently running the -reconall command on 40 subjects. One of them exited the mri_ca_normalize step with an error saying: Abort (core dumped) I tried rerunning it, however the error keeps occurring. So I have search the list, but could not find a solution to my problem. Does anyone have an idea on how I can fix this problem? I attached the recon-all.log file, maybe it can help finding the error. Furthermore some information about the system I am running the analysis on: 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 16.04.4 LTS 3) uname -a: Linux theresa-Lenovo-IdeaPad 4.13.0-36-generic #40~16.04.1-Ubuntu SMP Fri Feb 16 23:25:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Kind regards, Theresa Marschall ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Reg Mapping automatic segmentations to functional space
by Anita S 09 Mar '18

09 Mar '18

Hello all, I have mapped a subject's fMRI Feat data onto the anatomical scan and then mapped the segmentations to the functional space using the following commands: reg-feat2anat --feat feat_folder.feat --subject sub_name aseg2feat --aparc+aseg --feat feat_folder.feat The file created does not contain Middle Frontal Gyrus which is found in 2009 or 2005 aparc versions. How do I change the aparc file used in the above step(s) -- Thanks! - Anita

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getting h/o atlas into individual surface (and then volume) space
by Dorit Kliemann 09 Mar '18

09 Mar '18

Hi, I’m trying to get an atlas (Harvard/Oxford sub&cortical) into individual space via surface registration. Motivation is to replicate a finding in volume space (functional data) in a normal population with that atlas in a lesion data set where transformation to template volume space is not feasible. I think I found a way described in principle for one region below but it seems clumsy with a lot of steps , so I’d like to check if there is a better/more accurate ways with less transforms? Any feedback appreciated! Thanks, Dorit 1) create a registration file from FSL-MNItemplate to Freesurfer space and fsaverage bbregister --s fsaverage --mov MNI152_T1_1mm_brain.nii.gz --init-fsl --init-header --reg mni2fsaverage.dat --T1 --o mni2fsaverage.nii 2) warp atlas from FSL-MNI space onto surface of fsaverage mri_vol2surf --mov HarvardOxford-cort-maxprob-thr25-1mm.nii.gz --reg mni2fsaverage.dat --projdist-max 0 1 .01 --interp nearest --hemi lh --out lh.atlas.mgh 3) writing label for id = 1 mri_cor2label --i lh.atlas.mgh --surf fsaverage lh --id 1 --l ./lh.1.atlas 4) move label from fsaverage onto individual subject space mri_label2label --srclabel lh.1.atlas --srcsubject fsaverage --trglabel lh.1.atlas --trgsubject subject --regmethod surface --hemi lh 5) create voluem form label mri_label2vol --label subject/label/lh.1.atlas --subject subject --hemi lh --identity --temp subject/mri/brain.mgz --o lh.1.atlas.volume.nii --proj frac 0 1 .01 6) fix wholes/border ribbon mri_binarize --dilate 1 --erode 1 --i lh.1.atlas.volume.nii --o lh.1.atlas.volumebin.nii --min 1 mris_calc -o lh.1.atlas.volumebinfixed.nii lh.1.atlas.volumebin.nii mul subject/mri/lh.ribbon.mgz 7) bring from subject T1-FS space (1mm) into subject's functional space bbregister --s subject --mov func.nii --init-fsl --init-header --reg anat2func_register.dat --bold 8) warp atlas image from individual subject anat space to subject bold space mri_label2vol --seg lh.1.atlas.volumebinfixed.nii --temp func.nii --reg anat2func_register.dat --fillthresh .5 --o lh.atlas.func.nii

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