Freesurfer

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30132 discussions

Running qcache on old FS data
by Jamie Hanson 18 Jun '18

18 Jun '18

External Email - Use Caution Hello all, I was trying to run qcache on some previously processed Freesurfer data from a colleague, but ran into some issues with missing files and wondered how best to proceed. Details: -The data was processed with (Freesurfer) v4.5.0 and I would ideally like to not reprocess it with a newer version (to keep in concordance with past published work, and also it's a large number of subjects, n=800+). -The qcache flag was not used with the data previously (to my knowledge), so I was attempting to run this command: recon-all -s $subj -qcache -When I try that command, I get an error regarding a missing lh.white.K file. I've uploaded the log file here: https://www.dropbox.com/s/94mnsy7wrps5ce2/recon-all.log?dl=0 I wondered if it was possible to complete qcache with the data as is? I searched on the list previously and saw one or two other folks had run into this issues; I, however, didn't see a final solution to things. Any thoughts or suggestions are greatly appreciated! Thanks much! Best, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org

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Recon-all exited with errors
by Ryan Flores 18 Jun '18

18 Jun '18

External Email - Use Caution Dear FS developers, I tried running recon-all using the -parallel flag over the weekend, but to my surprise they all exited with errors. I’m hoping the problem is something subtle, but I’m having trouble understanding the error log (please see attached). Can someone point out the issue? Thank you for your help. Best, Ryan -- Ryan Flores Clinical Research Coordinator

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Can freesurfer do SC (superior colliculus) segmentation?
by He Chen 17 Jun '18

17 Jun '18

External Email - Use Caution Hi all, I need ROIs of SC(Superior Colliculus). Can freesurfer distinguish it from other brainstem structures in segmentation? I also need to see responses of distinct layers of SC. Can freesurfer do layers segmentation according to the distance between each voxel and SC surface layer? That is, I need ROIs of different depth in the SC. The depth should be calculated by the distance from the voxel to SC surface. How to modify the 'recon-all -all' code if I just need the segmentation function mentioned above? Please forgive the ignorance of a freesurfer beginner. Thank you in advance! Chen He

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Contrast interpretation - between-groups mean
by Pedro Rosa 16 Jun '18

16 Jun '18

External Email - Use Caution Dear FreeSurfers, I got results from a cortical area analysis that intrigued me: Upon the inspection of clusters that survived Monte-Carlo simulation, I found a cluster with larger area among a first group in contrast to a second group. However, when I calculated the cortical areas means from that cluster (as available in the glmdir), the second group had values slightly larger than the first group (i.e., showing a difference in the opposite direction). How would you explain such findings? Must I have committed a mistake in the analysis or its interpretation? Best, Pedro Rosa - University of São Paulo - Brazil.

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mri_gtmpvc
by Alshikho, Mohamad J. 15 Jun '18

15 Jun '18

Dear Dr Greeve, Kindly, I'd like t to inquire about the command "mri_gtmpvc" in PET surfer. Can I use this command to apply partial volume correction on non-PET data (e.g. DTI or ASL)? Thanks! Mohamad

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TotalGrayVol and SubCortGrayVol for multiple subjects
by Fernanda Hansen P. de Moraes 15 Jun '18

15 Jun '18

External Email - Use Caution Good morning all, I want to get the TotalGrayVol and SubCortGrayVol for multiple subjects. Is there any flag that I can use with asegstats2table? Or how should I use mri_segstas to creata a new aseg.stats file for my subjects? If that's the case, how should I define the output file from mri_segstats so asegstats2table can read it? Thank you very much in advance, Fernanda Hansen P. de Moraes -- Fernanda Hansen P. de Moraes Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz

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Cortical Thickness Using N30R83 Atlas
by Ryan Flores 15 Jun '18

15 Jun '18

External Email - Use Caution Hello all, I am hoping to obtain structural information (e.g., cortical thickness, surface area, and volume) based on the n30r83 (aka Hammersmith) atlas, which is in MNI space. The atlas differentiates between the hemispheres by using odd/even numbers in the labels. After looking through the archives I found a potential solution, which entails using the mri_vol2surf & mri_surf2surf commands. I’ve recon-ed the MNI brain to obtain the proper space; however, I’m unsure of how exactly to implement the commands and which flags are relevant. Any advice would be greatly appreciated. Thank you for your time. I look forward to hearing from you. Best, Ryan -- Ryan Flores Clinical Research Coordinator

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Is amygdala nuclei segmentation possible in freesurfer version 5.3?
by Sally Grace 15 Jun '18

15 Jun '18

External Email - Use Caution Hi there, I wish to segment amygdala nuclei in Freesurfer Version 5.3, is it possible? I can find documentation only for Freesurfer version 6.0 here (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) Can the scripts be adapted to Freesurfer v5.3? Thanks in advance, Sally. HippocampalSubfieldsAndNucleiOfAmygdala - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…> surfer.nmr.mgh.harvard.edu Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal) This functionality has been available in the development version of FreeSurfer since August 31st 2017

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Re: [Freesurfer] Offset in surface rendering
by Douglas N. Greve 14 Jun '18

14 Jun '18

So FS was not used to create the surface? If not, then you need to talk to the nipype people about how their gii interacts with your visualization tool. doug ps. Please post the FS list and not to us personally. thanks! On 06/14/2018 03:51 PM, Laura Jeyaseelan wrote: > > > Hi Douglas, > > Thanks for looking into this issue. I was using of nipype which > internally makes use of the freesurfer marching cubes implementation > mri_mc. This directly converts the nifti image to a gifti surface. The > python code is shown below > > import nipype.interfaces.freesurfer as fs > mc = fs.MRIMarchingCubes() > mc.inputs.in_file = './lung.nii.gz' > mc.inputs.label_value = 1 > mc.inputs.out_file = 'fs_lung.surf.gii' > mc.run() > > > Thanks, > Laura > > On Wed, Jun 13, 2018 at 8:49 AM, Douglas N. Greve > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: > > How did you convert to gii? > > > On 06/11/2018 08:09 PM, Laura Jeyaseelan wrote: > > > External Email - Use Caution > > Hi FreeSurfer Developers, > > I'm attempting to convert a 3D label mask (saved as a .nii.gz > image) into a surface rendering (saved as .surf.gii). > > /import nipype.interfaces.freesurfer as fs/ > /mc = fs.MRIMarchingCubes()/ > /mc.inputs.in_file = './lung.nii.gz'/ > /mc.inputs.label_value = 1/ > /mc.inputs.out_file = 'fs_lung.surf.gii'/ > /mc.run() / > > The code above does not throw any errors, but there appears to > be an offset when viewing the surface reconstruction using the > Papaya viewer on the browser. If I try creating the surface > using Papaya's companion software Mango there is no offset seen. > > Does anyone have any ideas to trouble-shoot this issue? > > I've attached screenshots to show the difference: > > FreeSurfer generated .surf.gii file viewed on Papaya: > > > Mango generated .surf.gii file viewed on Papaya: > > > Thanks, > Laura > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline > <http://www.partners.org/complianceline> . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > >

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bash: mri/T1.mgz: Permission denied
by Brad Matushewski 14 Jun '18

14 Jun '18

External Email - Use Caution Not sure what happened here, but running Freesurfer on Ubuntu and not getting this error when trying to view volumes: freeview -v \ mri/T1.mgz \ mri/brainmask.mgz \ mri/wm.mgz:visible=0 \ mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f surf/lh.white:edgecolor=blue \ surf/rh.white:edgecolor=blue \ surf/rh.pial:edgecolor=red \ surf/lh.pial:edgecolor=red \ surf/rh.inflated:visible=0 \ surf/lh.inflated:visible=0 But it get the error: bash: mri/T1.mgz: Permission denied No idea why or how to fix this. I have also tried other subjects but same thing.

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