Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Question about compare left and right hemi of longitudinal data
by lanbo Wang 24 Jan '18

24 Jan '18

Hi, all experts. I want to compare changes rate between left and right hemisphere of longitudinal data, How should I do that, how to combine xhemi with two stage or LME? Best, Lanbo

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Freesurfer longitudinal templates failed - time points from different scanners
by Ambrosino di Bruttopilo-3, S. 24 Jan '18

24 Jan '18

Dear experts, I run FreeSurfer 6.0 longitudinal pipeline on a set of scans acquired with identical protocol (ADNI) but 2 different Philips 3T scanners (all time 1 with Achieva, all time 2 with Ingenia). Unfortunately ~ 50% of the within-subjects templates completely failed. Is there anything I could try to fix this, or should just accept that is not possible to run FS longitudinal with this data? Thanks a lot! Sara ------------------------------------------------------------------------------ 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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external WM and GM masks as input to recon-all?
by MIKHAEL Shadia 23 Jan '18

23 Jan '18

Dear FreeSurfer experts, Could you please advise on whether it would be possible to run recon-all in FreeSurfer 6.0 using externally-derived probabilistic white matter and grey matter masks, both of which include the cerebellum but not the ventricles, and if so, how? Would the flag -autorecon2-pial suffice? Thank you in advance. Shadia -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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recon-all exited with error
by Trisanna Sprung-Much 23 Jan '18

23 Jan '18

Hi there I ran Freesurfer 6.0 on a subject last night and it took about 12 hours (seemed to get to the very end) and then exited with errors. I can open my surfaces so I think it ended roughly with the atlas labelling. I attach the recon-all log file here. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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[CVS_register] Warp field reading through Matlab
by Stefano Zappalà 23 Jan '18

23 Jan '18

To whom it may concern, I am Stefano Zappalà, a second year PhD student at Cardiff University. I would like to use the CVS registration tool of the FreeSurfer software for elastic registration. I was very impressed by its accuracy even in aligning fiber tracts. My project is based on reading the warp field files as output of elastic registration for estimating displacement fields. I wrote to Lilla Zollei few months ago who kindly shared with me a Matlab script for reading .m3z files, output of cvs_register. I played with it for several months, without being able to properly read the deformation field. What I obtain does not represent the real warp (that i can extract and compare with, using another software). By checking the output image, I can tell that the registration was successful, so I am expecting the warp field to be consistent with the real one. When I use the Matlab function given me by Ms Zollei, I notice a gradient in each of the component (x,y,z) of the vector field, that varies according to the coordinate of each voxel (as you can see in Figure1 attached). I therefore subtracted, for each voxel, its coordinate to the corresponding component of the vector, using the cycle: T=zeros(256,256,256,3); for k=1:256 for j=1:256 for i=1:256 T(i,j,k,:)=squeeze(vol_orig(i,j,k,:))-[i;j;k]; end end end where vol_orig is the output of the function you gave me [vol_orig, vol_dest, vol_ind0, spacing, exp_k] = mris_read_m3z('FILELOC'). The result is compared to vol_orig in Figure1. By doing so I obtained something acceptable but still distant from the truth (which comparison is reported in Figure2, where the truth is the right vector field). In the attachment you can find the function, as well as Figure1 representing a slice of vol_orig on the left and the modified version where the coordinates are subtracted to each component of the vectors. Finally, in Figure2 you can find the warp field estimated with cvs_register and the corresponding truth. The two warp fields seem different, unfortunately. I was wondering if you have any suggestion on how to properly read it, or if you could confirm that what I have done is correct. Thank you for your consideration. Best regards, Stefano.

2 1

Loading talairach-space images into FSL
by Helen Beaumont 23 Jan '18

23 Jan '18

Hi I have a series of T1 images that I have transformed in Freesurfer to .nii.gz images in talairach space with mri_convert -at transforms/talairach.xfm. I am using the skull-stripped image brain.mgz produced by recon-all. When I view them in freeview they look well-registered, and similarly when I view them in MRIcron. However, if I use FSLeyes they seem to have a different origin for each subject, and fslmerge complains that they have Inconsistent orientations. Is there any inconsistency that you know of between freeview and FSLeyes? Helen Beaumont PhD

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Value of ROIs different between FreeSurfer versions?
by KALEY E ELLIS 23 Jan '18

23 Jan '18

Hello FreeSurfer Developers, I am extracting ROIs of cross-sectional data using FreeSurfer v6.0. We looked at this data preliminarily about 2 years ago using FreeSurfer v5.3. It looks like there are slight differences in the values of the same subject (see below). Do you know the reason for this difference and whether there is something I should do differently? Subject 2000_1, lh_G_and_S_frontomargin_thickness: v5.3 = 2.416 v6.0 = 2.482 command used: aparcstats2table --hemi lh --subjects $subjectlist --skip --delimiter comma --meas thickness --parc aparc.a2009s --tablefile /PATH/lh_aparc-destrieux-thickness-table.csv Thank you for your time! Kaley Ellis Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

2 1

[error] no installation candidates for curl
by Darko Komnenić 23 Jan '18

23 Jan '18

Dear FreeSurfer experts, I am trying to perform hippocampal subfield segmentation with FreeSurfer 6. I followed the instructions found on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields which said that I first need to download Matlab Runtime. Which brought me to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime I reach the stage where I type in curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&d…" -o "runtime.tar.gz" after which I receive the following: Die Anwendung »curl« ist momentan nicht installiert. Sie können sie durch folgende Eingabe installieren: sudo apt-get install curl (my computer is in German, it basically says that curl is not installed and that I can install it via apt-get command). When I then type in that command and give my password, I receive: Paketlisten werden gelesen... Fertig Abhängigkeitsbaum wird aufgebaut Status-Informationen einlesen... Fertig Paket curl ist nicht verfügbar, wird aber von einem anderen Paket referenziert. Das kann heißen, dass das Paket fehlt, dass es veraltet ist oder nur aus einer anderen Quelle verfügbar ist. E: Paket curl hat keinen Installationskandidaten Which roughly translates to: reading package lists... done building a dependency tree reading status information... done Package curl is not available, but is referred to by another package. This could mean that the package is missing, outdated or available only from a different source. E: Package curl has no installation candidates. I would be grateful for any solution suggestions! Best, Darko

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Re: [Freesurfer] recon-all error
by Bruce Fischl 23 Jan '18

23 Jan '18

we don't have much experience with it. Can you cc the FS list so that others can answer? I'll do so on this email. Maybe try some other tool for conversion? If recon-all fails it is not surprising that mri_convert also fails since they use the same DICOM code cheers Bruce On Tue, 23 Jan 2018, Julia Ströhlein wrote: > > Hi Bruce, > > thank you very much for your reply. > > > > I’m sure that I use the right series. I tried to convert my DICOM files to > nifti, but this produces > the same error and the command also doesn`t create the NIFTI file. > > > > Julias-MacBook-Air:~ Jule$ cd > /Applications/freesurfer/subjects/MRtest2/001/001/9 > > Julias-MacBook-Air:9 Jule$ mri_convert 00010001 00010001.nii > > mri_convert.bin 00010001 00010001.nii > > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > > reading from 00010001... > > Starting DICOMRead2() > > dcmfile = /Applications/freesurfer/subjects/MRtest2/001/001/9/00010001 > > dcmdir = /Applications/freesurfer/subjects/MRtest2/001/001/9 > > ERROR: don't know how to get DWI parameters from --Hitachi Medical > Corporation -- > > ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 > > DICOM File: /Applications/freesurfer/subjects/MRtest2/001/001/9/00010001 > > break DICOMRead.c:5228 > > Ref Series No = 9 > > Found 302 files, checking for dicoms > > ERROR: don't know how to get DWI parameters from --Hitachi Medical > Corporation – > > > > Do you know problems like this with this type of MR scanner? > > > > Kind regards, > > Julia > > > > Unbenannt > > > > >

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Re: [Freesurfer] [Re] medial wall label in Freesurfer 6
by M del Mar Velasco 23 Jan '18

23 Jan '18

Yes, it solves medial_wall label problem but not mri_aparc2aseg error.log. I attached you in a previous message: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56610.html Many thanks, M del Mar

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Freesurfer January 2018