Freesurfer

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19 participants
30088 discussions

brainstem - partial volume effects
by Dusan Hirjak 16 May '19

16 May '19

External Email - Use Caution Dear Freesurfer experts, I have one question regarding the partial volume effects on brainstem volume when using Freesurfer 6.0 brainstem tool: Could partial volume effects in a comparatively small sample (n=92) have an influence on the results (group difference in SCP volumes)? How should I deal with this effect? Any suggestions are welcome. best regards Dusan

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Re: [Freesurfer] mri_convert segmentation fault (core dumped) in v5.3 on centos6
by fsbuild 16 May '19

16 May '19

External Email - Use Caution Hello Caspar, So far, I have not found a CentOS rpm with that 2.14 version of libcrypt, but you can download the source from the GNU project and try building it on your machine with the following steps. - R. 1) Become root in your terminal window and cd somewhere to download and build $ su – $ cd /home/user/Downloads 2) get the source $ wget http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz OR $ curl -O http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz 3) unpack it and cd there $ tar zxvf glibc-2.14.tar.gz $ cd glibc-2.14 4) do the build and set it to install into some convenient location, e.g., /opt/glibc-2.14 $ mkdir build $ cd build $ ../configure --prefix=/opt/glibc-2.14 $ make 5) If all goes well, then install $ make install 6) Check that the library is under opt/glibc-2.14/lib and then you can set LD_LIBRARY_PATH to reference it $ export LD_LIBRARY_PATH=/opt/glibc-2.14/lib On May 16, 2019, at 05:17, Caspar M. Schwiedrzik <cschwiedrz(a)mail.rockefeller.edu> wrote:        External Email - Use Caution        Hi! We are getting segmentation fault (core dumped) error when trying to run mri_convert on NIFTI files. This is running Freesurfer v5.3 on Centos6, specifically v1.179.2.7 of mri_convert. I suspect that this has to do with libcrypt incompatibilities described for other operating systems , e.g., here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-Sept… in the known issues list of v5.3. here https://surfer.nmr.mgh.harvard.edu/fswiki/PreviousReleaseNotes.&n… have libcrypt version 2.17 installed and do not have access to libcrypt-2.14.1.so. Is there a way to get libcrypt-2.14.1.so from you or is there another known workaround (other then updating to Freesurfer 6)? Thank you very much! Caspar_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer$

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mri_convert issues
by jennifer sorinas 16 May '19

16 May '19

External Email - Use Caution Hello, I was trying to convert nifti1 files (.hdr and .img) to nii files using the command: > mri_convert -i input.hdr -it nifti1 -ot nii -o output.nii.gz But this error pop-up: mri_convert.bin: unknown flag '-i input.hdr' The same command was working on my unit a few months ago. Does anybody know wha's going on? Thank you very much. Best, Jennifer

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Partial volume effects - brainstem
by Dusan Hirjak 16 May '19

16 May '19

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Projecting subcortical ROI to the cortical surface
by Nillo, Ryan Michael R 15 May '19

15 May '19

External Email - Use Caution Hello FreeSurfer users/developers, I have a subcortical ROI that I want to project to the nearest cortical vertex (see screenshot). So far, I have used the command mri_vol2surf --mov subject/mri/lh.het.nii --reg subject/mri/transforms/talairach.lta --hemi lh —o subject/surf/lh.het.mgh to project these voxels to the nearest vertex on the cortex. I am not sure if this is the correct way to do this because using mris_anatomical_stats on the result does not produce any thickness file. Any help would be greatly appreciated. [cid:1E78E0E0-0881-4508-A885-F0579F1FB3E4] Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

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Re: [Freesurfer] Obtaining stats for a custom label
by Greve, Douglas N.,Ph.D. 15 May '19

15 May '19

what do you mean when you say you "load it on FreeSurfer"? Do you mean FreeView? Please send command lines, and also please post to the list. On 5/15/19 5:38 PM, Nillo, Ryan Michael R wrote: > > External Email - Use Caution > > When I run tkregisterfv --mov subject/surf/rh.custom.nii --reg > subject/mri/transforms/talairach.lta --subject subject, the nii file > does not seem to be in register with the orig.mgz. However, when I > load it on FreeSurfer, they are in register. I am including a > screenshot of what I see when I am running regular Freeview. > > > > Ryan Michael Nillo > Staff Research Associate I > University of California San Francisco > Department of Radiology and Biomedical Imaging > >> On May 15, 2019, at 1:46 PM, Greve, Douglas N.,Ph.D. >> <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: >> >> You should check the registration with tkregisterfv, eg, >> >> >> tkregisterfv --mov subject/mri/rh.custom.nii --regheader --reg >> deleteme.lta --s subject >> >> >> On 5/15/19 4:28 PM, Nillo, Ryan Michael R wrote: >>> >>> External Email - Use Caution >>> >>> I reran the command with —regheader subjectname instead of —reg. When >>> I try to visualize the mgh file, I am still getting an overlay of zeros. >>> >>> Ryan Michael Nillo >>> Staff Research Associate I >>> University of California San Francisco >>> Department of Radiology and Biomedical Imaging >>> >>>> On May 15, 2019, at 11:41 AM, Greve, Douglas N.,Ph.D. >>>> <DGREVE(a)mgh.harvard.edu >>>> <mailto:DGREVE@mgh.harvard.edu><mailto:DGREVE@mgh.harvard.edu>> wrote: >>>> >>>> Is that registration accurate? That says that the rh.custom.nii is in >>>> "talaiarch" space. Actually, this it is its own space. I thought that >>>> your label was in the space of the orig.mgz. If so, then just use >>>> --regheader subjectname instead of --reg >>>> >>>> On 5/15/19 2:12 PM, Nillo, Ryan Michael R wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> Hi Doug, >>>>> >>>>> I ran this command: >>>>> >>>>> >>>>> mri_vol2surf --mov subject/mri/rh.custom.nii --reg >>>>> subject/mri/transforms/talairach.lta --hemi rh --o >>>>> subject/surf/rh.custom.mgh >>>>> >>>>> However, when I try to visualize the resulting mgh file on the >>>>> surface, I get a surface overlay of 0s, even though rh.custom.nii is a >>>>> binary mask. Is this what is supposed to happen? I thought this would >>>>> map the subcortical ROI to the nearest vertex? >>>>> >>>>> Ryan Michael Nillo >>>>> Staff Research Associate I >>>>> University of California San Francisco >>>>> Department of Radiology and Biomedical Imaging >>>>> >>>>>> On May 14, 2019, at 10:50 AM, Greve, Douglas N.,Ph.D. >>>>>> <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>>>>> <mailto:DGREVE@mgh.harvard.edu><mailto:DGREVE@mgh.harvard.edu>> >>>>>> wrote: >>>>>> >>>>>> Sorry, slipped through the cracks. That command will not generate a >>>>>> valid surface-based label. You should probably sample your >>>>>> volume-based >>>>>> mask (rh.custom.nii) to the surface with mri_vol2surf, then use >>>>>> mri_vol2label with the --surf option. >>>>>> >>>>>> On 5/14/19 12:53 PM, Nillo, Ryan Michael R wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Hi Doug, >>>>>>> >>>>>>> I wanted to touch base with you on this. Is this the correct way to >>>>>>> project subcortical voxels to the nearest cortical vertex? We >>>>>>> want to >>>>>>> project subcortical ROI to the nearest cortical vertex. >>>>>>> Additionally, >>>>>>> is it possible to record which ROI in the Desikan atlas these >>>>>>> projected ROI fall under? >>>>>>> >>>>>>> Ryan Michael Nillo >>>>>>> Staff Research Associate I >>>>>>> University of California San Francisco >>>>>>> Department of Radiology and Biomedical Imaging >>>>>>> >>>>>>>> On Apr 24, 2019, at 10:50 AM, Nillo, Ryan Michael R >>>>>>>> <RyanMichael.Nillo(a)ucsf.edu <mailto:RyanMichael.Nillo@ucsf.edu> >>>>>>>> <mailto:RyanMichael.Nillo@ucsf.edu><mailto:RyanMichael.Nillo@ucsf.edu> >>>>>>>> <mailto:RyanMichael.Nillo@ucsf.edu>> wrote: >>>>>>>> >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> >>>>>>>> Hi Doug, >>>>>>>> >>>>>>>> I used the command below to convert a volume to a label file. The >>>>>>>> volume is a binary mask highlighting a subcortical ROI that I am >>>>>>>> projecting to the closest vertex. I can visualize the label on the >>>>>>>> fsaverage lh.white surface. >>>>>>>> mri_vol2label --i >>>>>>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/rh.custom.nii >>>>>>>> >>>>>>>> --id 1 --l >>>>>>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label >>>>>>>> >>>>>>>> Ryan Michael Nillo >>>>>>>> Staff Research Associate I >>>>>>>> University of California San Francisco >>>>>>>> Department of Radiology and Biomedical Imaging >>>>>>>> >>>>>>>>> On Apr 24, 2019, at 9:48 AM, Greve, Douglas N.,Ph.D. >>>>>>>>> <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> >>>>>>>>> <mailto:DGREVE@mgh.harvard.edu><mailto:DGREVE@mgh.harvard.edu> >>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> wrote: >>>>>>>>> >>>>>>>>> How did you create the label? Is it a surface-based label? Ie, >>>>>>>>> does >>>>>>>>> it have valid vertex indices as the first item in each label point >>>>>>>>> in the label file? >>>>>>>>> >>>>>>>>> On 4/24/2019 2:44 AM, Nillo, Ryan Michael R wrote: >>>>>>>>>> >>>>>>>>>> External Email - Use Caution >>>>>>>>>> >>>>>>>>>> Hello Freesurfer developers, >>>>>>>>>> >>>>>>>>>> I am using the code below to generate the stats table for the >>>>>>>>>> ROI. >>>>>>>>>> mris_anatomical_stats -l >>>>>>>>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label >>>>>>>>>> >>>>>>>>>> -b subject rh white >>>>>>>>>> >>>>>>>>>> However, when I run this command, I get this output: >>>>>>>>>> >>>>>>>>>> limiting computations to label >>>>>>>>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/label/rh.custom.label. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> reading volume >>>>>>>>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/mri/wm.mgz... >>>>>>>>>> reading input surface >>>>>>>>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white... >>>>>>>>>> reading input pial surface >>>>>>>>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.pial... >>>>>>>>>> reading input white surface >>>>>>>>>> /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc/subject/surf/rh.white... >>>>>>>>>> >>>>>>>>>> table columns are: >>>>>>>>>> number of vertices >>>>>>>>>> total surface area (mm^2) >>>>>>>>>> total gray matter volume (mm^3) >>>>>>>>>> average cortical thickness +- standard deviation (mm) >>>>>>>>>> integrated rectified mean curvature >>>>>>>>>> integrated rectified Gaussian curvature >>>>>>>>>> folding index >>>>>>>>>> intrinsic curvature index >>>>>>>>>> structure name >>>>>>>>>> >>>>>>>>>> I am getting no values for any of the metrics listed above. >>>>>>>>>> Is this >>>>>>>>>> a bug? >>>>>>>>>> >>>>>>>>>> Thanks in advance, >>>>>>>>>> >>>>>>>>>> Ryan Michael Nillo >>>>>>>>>> Staff Research Associate I >>>>>>>>>> University of California San Francisco >>>>>>>>>> Department of Radiology and Biomedical Imaging >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> 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 >>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… >>>>>> . 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. >>>>>> >>>>> >>>> >>>> >>>> >>>> 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 >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli…. >>>> 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. >>> >> >> >> >> 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 >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli…. >> 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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Spatial smoothing kernel in fsfast
by Zhi Li 15 May '19

15 May '19

External Email - Use Caution Dear Freesurfer experts. Now I am using preproc-sess to preprocess functional MRI data. I would like to smooth the data first and then resample them into the standard space. Hence I run 'preproc-sess -s sub001 -fsd func -stc odd -fwhm 0 -per-run' first, and then 'spatialsmooth-sess -s sub001 -fsd func -i fmcpr.odd -o fmcpr.odd.sm5 -fwhm 5', finally 'preproc-sess -s sub001 -fsd func -stc odd -surface fsaverage lhrh -mni305 -fwhm 0 -per-run' (I have already renamed the stem of smoothed file from fmcpr.odd.sm5 to fmcpr.odd). However, the preprocessed data 'fmcpr.odd.sm0.mni305.2mm.nii.gz' contains both cortical and subcortical data. If I use '-fwhm 1' this file only contains the subcortical area. May I know why and how to fix it? About each stage embedded in 'preproc-sess', if I would like replace one stage with other software/algorithms, can I just change the name of the generated file by other software/algorithms to the name of file in this stage of 'prepoc-sess', and them rerun 'preproc-sess' while keep the flag '-update' on? For example, if I would like to use FSL/SPM to register the functional image to structural data, can I just rename the mat-file which describes the affine registration generated by FSL/SPM to 'register.dof6.mat'? Looking forward to your kind suggestions. Thanks and best wishes, Lizhi

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Issue with vol2surf
by Martin Juneja 15 May '19

15 May '19

External Email - Use Caution Hi FS experts, I am interested in displaying my ROI: ROI.nii (which is in standard space: avg152T1.nii.gz) on to fsaverage space. For that, I performed following steps: (1). Registered my template to fsaverage and saved the transformation matrix TT.dat as following: fslregister --s fsaverage --mov ROIs/avg152T1.nii.gz --reg TT.dat (2). Mapped my ROI to fsaverage using the transformation matrix TT.dat as following: mri_vol2surf --mov ROIs/ROI.nii --reg TT.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out ROIs/ROI_Trans.mgh This works for 12 out of my 14 ROIs, but two of the ROIs are not displaying properly, and after the transformation when I displayed those on fsaverage space, these ROIs cover the whole hemisphere (please see attached: e.g. overlaying an ROI_Trans on fsvaerage space). I confirmed that both of these (non-working) ROIs (in .nii form) look fine on avg152T1.nii.gz, and on fsaverage when applying the transformation as following: tkmedit fsaverage T1.mgz -overlay ROIs/ROI.nii -overlay-reg TT.dat -fthresh 0.5 -surface lh.white -aux-surface lh.white I would really appreciate any help. Thanks.

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Control Points to Include Hyperintensity in WM Surface
by Rachel Hoel 15 May '19

15 May '19

External Email - Use Caution Dear Freesurfer Developers, We're still struggling with editing a subject where a hyperintensity in the right temporal lobe leads to poor white and grey matter segmentation. The coordinates are [83, 163, 139]. Our study is using the longitudinal processing pipeline with version 6.0. Even after adding several control points and running recon-all, the white matter is still not fully being included in the surface. I've also tried filling in the wm voxels instead of adding control points, but no luck there either. We are performing white and grey matter edits starting at the cross sectional. I was wondering what would be the best way to go about editing this subject? If it helps, I just ftp'ed the subject and attached some screenshots of the error. Please let me know if there's any other information I can provide you with. Thanks in advance, Rachel

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Voxel to Surface Coordinates
by Song, Da-Yea 15 May '19

15 May '19

External Email - Use Caution Hello, We have an anatomical atlas that we have incorporated in the FreeSurfer pipeline. Is it possible to convert this voxel based atlas into MNI152 surface coordinates? Any suggestions or comments would be greatly appreciated. Thank you, Da-Yea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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