Freesurfer April 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
170 discussions

Infant freesurfer
by COLLEEN PLETCHER 26 Apr '20

26 Apr '20

External Email - Use Caution Hello. I am working with the infant Freesurfer pipeline. I have noticed that some of our subjects may need to be manually edited, and then run through the pipeline again. However, when I try to do an infant_recon_all command combined with something like autorecon2-wm, I am getting an error that says the command cannot be found. Are there any commands specific to infant Freesurfer that can be used in combination with manual edits? Thanks!

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Re: [Freesurfer] How is Total cortical gray matter volume calculated
by Xiaojiang Yang 25 Apr '20

25 Apr '20

External Email - Use Caution Ian, You can use the mris_anatomical_stats command with the -b option. E.g., mris_anatomical_stats -b subjectid lh will give you a tabular output containing the total gray matter volume in the 3rd column: 128449 86239 *243375 *2.588 0.876 0.123 0.026 1496 133.3 /xxx./subjects/QEN001/surf/lh.white See https://surfer.nmr.mgh.harvard.edu/fswiki/mris_anatomical_stats for more information. Xiaojiang

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Generating Surfaces Meshes
by Peter, Jonah 24 Apr '20

24 Apr '20

Hello, I'm trying to generate surface meshes for different brain regions that can be imported into a software like MeshLab or Blender (i.e. .STL, .PLY, .OBJ, etc.). I ran recon-all on my T1 images, and the parcellation/segmentation looks fine. However, I noticed that when I imported this data into 3DSlicer, the volumes of these regions did not match the volumes in the aseg.stats file. In some cases, the differences were quite substantial. I tried removing all smoothing filters in 3DSlicer but the outcome was the same. Do you know what could be going wrong here? Alternatively, is there an easier way to generate surface meshes from the aparc or aseg atlases? I'm using the ICBM 2009c Nonlinear Asymmetric template ( http://nist.mni.mcgill.ca/?p=904) as a generic brain volume (though alternative suggestions are welcome). Thanks! Jonah -- Jonah Peter Graduate Student in The Biophysics Program Harvard University P: 646-306-0848 E: jonahpeter(a)g.harvard.edu

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matlab runtime error - Hippocampal subfield segmentation
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 24 Apr '20

24 Apr '20

External Email - Use Caution Dear Freesurfer experts, I am having trouble installing matlab runtime to be used for hippocampal subfield segmentation. I run the code following the instructions on the website, but nothing is installed. This is what happens: /home/alex/Documents/freesurfer/bin# cd $FREESURFER_HOME/bin && curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_inst… -o fs_install_mcr && chmod +x fs_install_mcr % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1801 100 1801 0 0 17485 0 --:--:-- --:--:-- --:--:-- 17485 Any ideas why this isn't loading? Thanks, Alex Job

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creating label from volume mask in MNI space
by Tammi Kral 24 Apr '20

24 Apr '20

External Email - Use Caution Hello, I have tried multiple strategies to create labels in subject space from a couple subcortical (brainstem and cerebellum) volume-based ROIs (masks) defined from a thresholded statistical map. The ROI file is a simple binary mask in MNI space. However, the results are misaligned and appear as a grid of dots. First I tried using mri_vol2vol to go from MNI space to FS space (I tried using both the fsaverage brain and the mni205 brain). I previously ran the MNI152 brain through recon_all, per advice I found in the archives. For example, using the below command: mri_vol2vol --mov ${ROI_DIR}${roi}.nii.gz --s MNI152_T1_2mm \ --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z \ --o ${ROI_DIR}${roi}_FSvol.nii.gz --nearest Since the MNI space ROIs also overlaid in FS space, I also tried skipping this first step and going straight to the next step, which was to use mri_vol2label to create the label file. For example, like this: mri_vol2label --i ${ROI_DIR}${roi}_FSvol.nii.gz --id 1 --l ${ROI_DIR}${roi}_FSvol.label Then I used mri_label2label to move the label to each subject's space, like so: mri_label2label --srcsubject fsaverage \ --srclabel ${ROI_DIR}${roi}.label --trgsubject ${subfolder} \ --trglabel ${SUBJECTS_DIR}/rois/${sub}_${roi}_FSvol.label --regmethod volume I also tried moving the label output of this final step (in subject space) back to a volume, though this doesn't seem necessary, as I could extract the data from the label file: mri_label2vol --label ${SUBJECTS_DIR}/rois/${sub}_${roi}_mni.label \ --o ${SUBJECTS_DIR}/rois/${sub}_${roi}_FSvol.mgh --identity --temp ${SUBJECTS_DIR}/${subfolder}/mri/T1.mgz I have attached a screenshot of the label file for the cerebellar ROI (in yellow) in subject space, overlaid on the subject's T1 from: /subject_directory/mri/T1.mgz (I apologize that it's not the best view, as I'm working from home and it's very slow using the GUI to change the view). I also apologize in advance if I've left out critical info to answer this question - please let me know. I appreciate any advice you might have! This seems like it should be a pretty common, straightforward process, yet I have not been able to find anything that works. Thank you, Tammi RA Kral, PhD Center for Healthy Minds University of Wisconsin-Madison she/her

1 0

Re: [Freesurfer] Password VM FStutorial
by fsbuild 24 Apr '20

24 Apr '20

External Email - Use Caution I will send it to your email shortly. - R. On Apr 24, 2020, at 07:43, Etienne Abassi <etienne.abassi(a)isc.cnrs.fr> wrote:       External Email - Use Caution        Dear all,I tried to install the virtual image of Freesurfer you provided on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67_winIt worked well, but I can't find the password for the "Developer" account, and so I can't log into the VM. Could you please provide the password ?I thank you in advance for you time.Best,Etienne-- Etienne Abassi, PhD StudentInstitut  des Sciences Cognitives Marc Jeannerod - CNRS UMR 522967, Boulevard Pinel - 69675 BRON (Lyon), France_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Password VM FStutorial
by Etienne Abassi 24 Apr '20

24 Apr '20

External Email - Use Caution Dear all, I tried to install the virtual image of Freesurfer you provided on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67_win It worked well, but I can't find the password for the "Developer" account, and so I can't log into the VM. Could you please provide the password ? I thank you in advance for you time. Best, Etienne -- Etienne Abassi, PhD Student Institut des Sciences Cognitives Marc Jeannerod - CNRS UMR 5229 67, Boulevard Pinel - 69675 BRON (Lyon), France

1 0

Trac-All NaN
by Hua, Jessica 23 Apr '20

23 Apr '20

External Email - Use Caution Hi FreeSurfer, I ran the trac-all -stat command on some of my participants, and I noticed that some of the values that were outputted contained NaN. Why are the values coming out as NaN? fmajor_PP.avg33_mni_bbr.AD_Avg.txt S11018a_LGI S11019a_LGI S11021a_LGI NaN NaN 0.00109668 0.00116704 NaN 0.00110631 0.00118262 NaN 0.00113231 0.00119589 NaN 0.00116401 0.00121558 NaN 0.00117549 0.00123733 NaN 0.00119309 0.00126087 NaN 0.00123177 0.00127355 0.00116328 0.00127236 0.00126695 0.00115413 0.00129993 0.00125837 0.00117334 0.00131861 0.00125611 0.00117423 0.00134501 0.00130347 0.00117161 0.00135121 0.00133526 0.00117097 0.00136288 0.00135801 0.00116546 0.00136839 0.00138131 0.0011961 0.00141117 0.00137605 0.00126803 0.00143167 0.00139927 0.00132198 0.00144947 0.00140814 0.00135481 0.00145095 0.00141403 0.00136342 0.00144231 0.00143846 0.00136409 0.0014307 0.00144842 0.00134806 0.00141466 0.00144669 0.00138324 0.00139904 0.00144974 0.00143263 0.00139749 0.00146505 0.00145596 0.00143352 0.00149473 0.0014523 0.00144366 0.00150771 0.0014622 0.00144891 0.00151567 0.00148269 0.00147786 0.0015513 0.00151399 0.00153047 0.00158431 0.00155476 0.00160898 0.00163524 0.00162621 0.00166298 0.00166918 0.0016651 0.0016538 0.00165915 0.00165803 0.00169534 0.00171513 0.00164646 0.00176355 0.00178509 0.00167836 0.00179073 0.00186456 0.00175883 0.00181997 0.00187805 0.00183493 0.00178465 0.00189962 0.00187421 0.00175515 0.00192235 0.00189781 0.00171387 0.0019091 0.00184765 0.00160073 0.00191175 0.00181558 0.00157862 0.00191679 0.00182829 0.00165907 0.00185513 0.00185947 0.0017003 0.00181572 0.00189271 0.00172307 0.00181154 0.0018763 0.00159418 0.0018311 0.0018657 0.00159179 0.00172958 0.00189407 0.00164795 0.00165341 0.00191997 0.00167435 0.00156794 0.00190814 0.00168963 0.00146072 0.001859 0.00172164 0.00138372 0.00178192 0.00175954 0.00136893 0.00170486 0.0018261 0.0013654 0.00164533 0.0018264 0.00135974 0.00155251 0.00176598 0.00137226 0.00149038 0.00166574 0.00133654 0.00146834 0.00152383 0.00134757 0.00148128 0.00138086 0.00136271 0.00147022 0.00132929 0.00136545 0.00144934 0.00127674 0.00137979 0.00145088 0.00125313 0.00137398 0.00151918 0.00125802 0.00137699 0.00151537 0.00126461 0.00136867 0.00146195 0.00126159 0.00136882 0.00140568 0.0012639 0.00134777 0.00138923 0.00126469 0.00127934 0.00138564 0.00127229 0.00122813 0.00138057 0.00128295 0.00118596 0.00138419 0.00129555 0.00117204 0.0013933 0.00131012 0.00114282 0.0013934 0.00129255 0.00114104 0.00141831 0.0012982 0.00116965 0.00141932 0.00128999 0.00118427 0.00139441 0.00128321 0.00117267 0.0013619 0.00127428 0.00117105 0.00133817 0.00124349 0.00114046 0.00131501 0.00121045 NaN 0.0012865 0.00117847 NaN 0.00126657 0.00114993 NaN 0.00123952 0.00113779 NaN NaN 0.00112863 Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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ROIs to surface overlays / Arithmetic on surface overlays
by Funk, Quentin 23 Apr '20

23 Apr '20

External Email - Use Caution Freesurfer experts, I have a volumetric ROI (integer valued) in MNI space. I'd really like to display them on the fsaverage brain as a surface overlay so that it's clear what regions I'm looking at. Using something like this, I get pretty good results: mri_vol2surf --mov ROI_integers.nii --regheader fsaverage --hemi lh --out left_overlay.mgh --projfrac-max 0.15 .17 .01 but the edges are kind of a mess, see: https://imgur.com/a/53RVGCM Is there any way to smooth these edges while maintaining the "lookup table' nature of the surface overlay? Any kind of interpolation ruins that, so it's a bit hard (you can't see in that image, but there are multiple regions shown). Alternatively, is there any way I can do arithmetic with surfaces? If there were a tool like fslmaths for surface overlays, solving this problem would be relatively straightforward. Thanks for any help you can provide! -quentin funk Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas and among the top 20 hospitals nationwide. Houston Methodist is the only nationally ranked Honor Roll hospital in the state and is designated as a Magnet hospital for excellence in nursing. houstonmethodist.org | twitter.com/MethodistHosp | facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 1

Cortical thickness measure for external analysis.
by Miguel Ángel Rivas Fernández 23 Apr '20

23 Apr '20

External Email - Use Caution Dear Freesurfer experts, We are interested in running external analysis with thickness measurements of two brain regions. Can we use safely the metrics exported or by contrary a previous transformation is required before export the stats of each subject? Thanks for your time. Best regards, -- *Miguel Ángel Rivas Fernández*

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Freesurfer April 2020