Freesurfer

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Fwd: Comments Sought on Best Practices in Data Analysis and Sharing (COBIDAS) White Paper
by Douglas Greve 21 Oct '15

21 Oct '15

FYI -------- Forwarded Message -------- Subject: Comments Sought on Best Practices in Data Analysis and Sharing (COBIDAS) White Paper Date: Wed, 21 Oct 2015 09:32:51 -0500 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu Dear OHBM Community, In 2014 OHBM Council created the Committee on Best Practices in Data Analysis and Sharing (COBIDAS), to identify best practices of data analysis and data sharing in the brain mapping community, prepare a white paper organizing these practices, and seek input from the OHBM community before ultimately publishing these recommendations. At long last, the COBIDAS report focused on best practices in MRI is ready for your review and input. Please visit the COBIDAS page <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3668> to view this “Proposed Final” document and provide your feedback. There you will find a link to submit your feedback, or you can send documents to info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> (please include “COBIDAS” in the subject line). Please send comments and suggested revisions by *November 17, 2015*. At that time, COBIDAS will review all feedback and begin creating the “Final” COBIDAS report. Once the final document is available, it will be posted again for the OHBM community to review and provide a Yes/No vote of your support for the report. If approved, the final document will then be submitted for publication. While many MRI guidelines have been produced over the years, this is a comprehensive and collaborative approach that is seeking input and ratification from the entire OHBM community. Your input and involvement is needed to make the final COBIDAS report a success! Read and comment on the Proposed Final draft and encourage your colleagues to do the same. Please use this COBIDAS link (http://www.humanbrainmapping.org/cobidas) when sharing via social media. Sincerely, Karl Zilles OHBM Council Chair Thomas Nichols Chair, COBIDAS *Organization for Human Brain Mapping* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 Fax: 1 952-545-6073 www.humanbrainmapping.org <http://www.humanbrainmapping.org> info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org?subject=Opt%20Out%20of%20Emails>.

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Freesurfer 5.3 Centre of Cortical Parcellations Text File
by Nathan Malitz 21 Oct '15

21 Oct '15

Hi There, Long time listener first time caller, I would like to generate a txt file, each line with 3 values for the XYZ in normalised space, based on the centre of each free surfer cortical parcellation, for each Subject run through freesurfer. Any chance someone could point me in the right direction for this? Kind regards, Nathan

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normalization of structural volumes
by geschwind2013 20 Oct '15

20 Oct '15

Hi, FS Experts, I’m using version 5.3 and have performed hippo-subfields analysis. To perform the statistics, shall I get the normalized volumes of each hippo-subfields? or just to do correction for ICV is enough ? thanks.. Hyon

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Contrast for a group diff correlation with age
by pablo najt 20 Oct '15

20 Oct '15

Hello FS experts,I have a question about setting the following contrast in mri_glmfitMy contrast of interest:Does area.pial --age correlation, accounting for gender, differ between PT and HC? Class Female_PTClass Female_HCClass Male_PTClass Male_HCIf I set my classes are as above, should my contrast be the following: fem_PT, fem_HC, male_PT, male_HC, age1 -1 1 -1 0 ThanksPablo

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volume DTI metrics to sruface
by Victor Montal Blancafort 20 Oct '15

20 Oct '15

FS experts, I have seen several posts regarding volume-to-surface projections, but I am not 100% confident about which parameter should I use with mri_vol2surf that better fit my needs. Currently, my data are several DTI-metric volumes per subject already normalized to MNI152 space (both 1mm and 2mm voxel sizes). My intention is to move cortex values of those volumes into the fsaverage surface space. I know that mri_vol2surf will work, but I have some doubts on how this work. 1) If no extra commands are used (i.e projfrac or projdist), what will each value of the vertex mesh represent? A specific voxel value? 2) If my intention is to project the mean value across white and pial surface, which exact command should I use? 3) There exists any specific command to move from MNI152 volume (FSL) to fsaverage surface (avoiding bbregister)? 4) Statistically, smoothing my data at the surface for further VBM analyisis(i.e moving later the surface values to volumes), will introduce any bias? Thank you in advance for your time and help! Cheers, Victor Montal

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error in FSL group analysis
by Park, Jung Mi 20 Oct '15

20 Oct '15

Hello FS expert While I ran higher level analysis using FSL feat, I received an error message. Does it mean this computer needs to update the FSL program? Computer: brain-vision at martinos center FS environment 5.3 FSL 5.0.7 /usr/pubsw/packages/fsl/current/bin/fsl_sub -T 60 -l logs -N feat4_post -j 4002 /usr/pubsw/packages/fsl/current/bin/feat /autofs/cluster/catanagp/users/jumi/jmi_analyses/2ndoutput/.gfeat/cope1.feat/design.fsf -D /autofs/cluster/catanagp/users/jumi/jmi_analyses/2ndoutput/.gfeat/cope1.feat -poststats 1 while executing "fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -poststats 1" -b 60 -N feat4_post -h $ID -l logs " invoked from within "if { $done_something == 0 } { if { ! $fmri(inmelodic) } { if { $fmri(level) == 1 } { for { set session 1 } { $session <= $fmri(multiple..." (file "/usr/pubsw/packages/fsl/current/bin/feat" line 389) 1445278890582 addons.update-checker WARN Update manifest for {972ce4c6-7e08-4474-a285-3208198ce6fd} did not contain an updates property thank you. Jung Mi

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R: Re: R: import FS-FAST results in FSL
by stdp82＠virgilio.it 20 Oct '15

20 Oct '15

I'd like to open with FSLview the sig.nii.gz which is produced by selxavg3-sess. If I use mri_surf2vol, which is the template to added in --template? It should be in Tailairach space? Where can I find the template that I should added? Thanks, Stefano subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz data_type FLOAT32 dim1 27307 dim2 1 dim3 6 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 1100.000000 cal_max 49.1815 cal_min -12.3855 file_type NIFTI-1+ Thanks, Stefano >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 29-set-2015 22.09 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL > >Do you mean surface-based analysis? You'd have to put them back into the >volume using mri_surf2vol, write them out as nifti and then run fslview >on them > >On 09/29/2015 11:17 AM, stdp82(a)virgilio.it wrote: >> >> Hi list, >> >> I would like to import FS-FAST results (conjunction maps) in FSL, >> opening them by fslview. >> Could you provide me any suggestion? >> >> Thank you very much >> Best regards, >> >> >> Stefano >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >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 . 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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converting surfaces into volumes or integrating them into volumes
by Boris Shabash 19 Oct '15

19 Oct '15

Hello FreeSurfer group How are you? I have currently started working with FS and would like to visualize some of the volume results. I have no issue visualizing the .mgz volumes produced since I can use mri_convert to convert them to .nii format and then visualize them using my software. However, I'd like to know if there is a way to convert the resulting surface labels (e.g. my_output/surf/rh.white or my_output/surf/rh.pial) into .nii files that I can also visualize or combine them with a resulting .mgz file into a single .nii file that contains the information for both volumes and the surfaces. Ideally I'd like to know if there is a way to combine them into a single file via the terminal. Please let me know if FS comes with a tool the allows for this process or if you know of any external tool. Sincerely, Boris

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patching 5.1
by Aaron Tanenbaum 19 Oct '15

19 Oct '15

Hello All Several years ago Freesurfer 5.1 was patched to resolve some issues. I just remember the patch resolved issues plaguing 5.1 and earlier. how does one get the patch version. no where on the FTP server i can see patched versions and instruction on performing a patch. Aaron Tanenbaum

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MPRAGE SNR
by John Anderson 19 Oct '15

19 Oct '15

6 13

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