Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

recon-all -autorecon2-cp -autorecon-wm -autorecon-pial issue
by 冉倩 08 Feb '17

08 Feb '17

Hello Freesurfer Developers, I have had last September Freesurfer course. When I operated my data following that stream I met some problem in reon-all -all step. Because I need put some screenshout to exaplain that problems, I add word document in attachment. Thanks very much! Best Regards, Qian Ran

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ColorLut hippocampus subfields
by Arnaud Boré 08 Feb '17

08 Feb '17

Dear Freesurfer developpers, Is there a Freesurfer ColorLut that includes the new subfields of the hippocampus ? In the current colorlut there is no left/right for these subfields: parasubiculum, GC-DG, HATA, molecular layer and tail. In addition, I think it would be easier if the correct left/right labels would be used for the segmentation. Thank you in advance. Arnaud Boré

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Re: [Freesurfer] dcm2niix
by Antonin Skoch 08 Feb '17

08 Feb '17

Dear Graham, you could also try mrconvert of mrtrix3. This tool is very useful and has very good support. http://mrtrix.readthedocs.io/en/latest/reference/commands/mrconvert.html community.mrtrix.org Regards, Antonin Unfortunately I'm not allowed to share these files without direct IRB approval (even if they are anonymized). I just tried on some Siemens TrioTim data with the same results.Graham ________________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...(a)nmr.mgh.harvard.edu] Sent: Wednesday, February 08, 2017 2:47 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dcm2niix Can you upload the dicoms so I can test it out? filedrop address below On 02/08/2017 02:13 PM, Warner, Graham Cary wrote: > The set I'm look at now was collected on a GE Signa HDxt. > > Graham > ------------------------------------------------------------------------ > *From:* freesurfer-boun...(a)nmr.mgh.harvard.edu > [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Yendiki, > Anastasia [ayend...(a)mgh.harvard.edu] > *Sent:* Wednesday, February 08, 2017 2:09 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] dcm2niix > > What scanner(s) was it acquired on? > > ------------------------------------------------------------------------ > *From:* freesurfer-boun...(a)nmr.mgh.harvard.edu > [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Warner, Graham > Cary [gwar...(a)mgh.harvard.edu] > *Sent:* Wednesday, February 08, 2017 2:07 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] dcm2niix > > I'm using a large dataset from mi2b2 which contains data from multiple > vendors/models collected at different hospitals in the partners > network between 2003 and 2016. The data I tried running mri_convert on > was acquired in 2011. > > Graham > ------------------------------------------------------------------------ > *From:* freesurfer-boun...(a)nmr.mgh.harvard.edu > [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Yendiki, > Anastasia [ayend...(a)mgh.harvard.edu] > *Sent:* Wednesday, February 08, 2017 1:55 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] dcm2niix > > Old versions of mri_convert (before 6.0) used to output a default > Siemens gradient table - this was not read from the header of the > dicom file itself. The 6.0 version reads the table from the header, as > long as it is a relatively modern dicom file that has the table in a > standard position in the header. When/where was your data acquired? > > ------------------------------------------------------------------------ > *From:* freesurfer-boun...(a)nmr.mgh.harvard.edu > [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Warner, Graham > Cary [gwar...(a)mgh.harvard.edu] > *Sent:* Wednesday, February 08, 2017 1:21 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] dcm2niix > > I just tried it on a few and while it was able to generate the nii > files it failed to generate the bval/bvec files I'm looking for. Is it > not typical behavior for mri_convert to generate bval/bvec files for > DTI runs or is this an error? > > Graham > ------------------------------------------------------------------------ > *From:* freesurfer-boun...(a)nmr.mgh.harvard.edu > [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Yendiki, > Anastasia [ayend...(a)mgh.harvard.edu] > *Sent:* Wednesday, February 08, 2017 10:15 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] dcm2niix > > Hi Graham – Have you tried mri_convert? The 6.0 version should be able > to extract diffusion gradient tables and b-value tables from most > standard recent dicoms. > > a.y > > From: <freesurfer-boun...(a)nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Warner, > Graham Cary" <gwar...(a)mgh.harvard.edu <mailto:gwar...@mgh.harvard.edu>> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Wednesday, February 8, 2017 at 10:01 AM > To: "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: [Freesurfer] dcm2niix > > Hi all, > > Can we get dcm2niix added to the system instance of fsl? It can't find > it in 5.0.7 or 5.0.9 (please let me know if it is somewhere else and > I'm just not seeing it). I'm having problems generating .bval and > .bvec files from certain DTI datasets using dcm2nii and the NITRC guys > told me I should be using dcm2niix. > > Thanks, > Graham

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Re: [Freesurfer] dcm2niix
by Yendiki, Anastasia 08 Feb '17

08 Feb '17

Hi Graham – Have you tried mri_convert? The 6.0 version should be able to extract diffusion gradient tables and b-value tables from most standard recent dicoms. a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Warner, Graham Cary" <GWARNER(a)mgh.harvard.edu<mailto:GWARNER@mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, February 8, 2017 at 10:01 AM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] dcm2niix Hi all, Can we get dcm2niix added to the system instance of fsl? It can't find it in 5.0.7 or 5.0.9 (please let me know if it is somewhere else and I'm just not seeing it). I'm having problems generating .bval and .bvec files from certain DTI datasets using dcm2nii and the NITRC guys told me I should be using dcm2niix. Thanks, Graham

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FNIRT all NaN's
by Funk, Quentin 08 Feb '17

08 Feb '17

Freesurfer experts, I have a few fractional anisotropy images linearly registered to an FA atlas. I'd like to run FNIRT on them with reference the FA Atlas, but when I do, the output is entirely NaNs. I ran the program in verbose mode--and everything is NaN's. e.g.: SSD = -nan n = 0 Disp reg = nan Int reg = -nan Total Cost = nan Jacobian range is nan -- nan ***Going to next resolution level*** Setting subsampling Setting reg mode Setting lambda New Lambda: 30 SSD = -nan n = 0 Disp reg = nan Int reg = -nan Total Cost = nan SSD = -nan n = 0 Disp reg = nan Int reg = -nan Total Cost = nan SSD = -nan n = 0 Disp reg = nan Int reg = -nan Total Cost = nan SSD = -nan n = 0 Disp reg = nan Int reg = -nan Total Cost = nan Is this simply because there are NaN's in the input image? Will replacing them with 0 fix the issue, or will it lead to strange behaviour in FNIRT? Any help is appreciated. Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and 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.

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Usage of norm.mgz rather than brain.mgz
by Andrew Davis 08 Feb '17

08 Feb '17

Hello FreeSurfer Developers, I have been using FreeSurfer for segmenting T1-weighted images, and I have a question related to using the two outputs norm.mgz and brain.mgz. It is my understanding that, by default, FreeSurfer uses the norm.mgz volume to do partial volume weighting when outputting segmentation volumes to aseg.stats based on aseg.mgz [^1]. Further, I understand that brain.mgz is output from a second normalization step in the recon-all processing stream, having taken norm.mgz as an input [^2]. The wiki says "*Intensity normalization works better when the skull has been removed. Creates a new brain.mgz volume*". My question is: if brain.mgz is meant to be an improved version of norm.mgz, why not use brain.mgz for partial volume weighting? What advantages does norm.mgz provide? Thanks much, Andrew Davis [^1]: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable [^2]: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

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recon-all issue
by Taylor Hilton 08 Feb '17

08 Feb '17

Hi all, Having trouble with an error running "recon-all -subjid ${i} -autorecon2” across all subjects. Below is where it has the error in recon-all.log. We also tried running the last command (“ln -s …”) manually and got the error “ln: failed to create symbolic link ‘lh.white.H’: Operation not supported.” whereas the rest of the commands ran normally. #-------------------------------------------- #@# Curv .H and .K lh Tue Feb 7 07:29:43 EST 2017 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf mris_curvature -w lh.white.preaparc total integrated curvature = 18.936*4pi (237.960) --> -18 handles ICI = 230.2, FI = 1697.2, variation=29040.790 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux pfc 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 10007 exited with ERRORS at Tue Feb 7 07:29:46 EST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> ———————————————————————————————————————————————— We also tried the solution laid out in this thread with no luck: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/04047… <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/04047…> Any help is very appreciated! - B. Taylor Hilton Lab Data Coordinator, University of Pittsburgh

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cortical thickness f-test correction
by Leon Ernst 08 Feb '17

08 Feb '17

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Recon-all - finished with errors
by Bunday, Karen 08 Feb '17

08 Feb '17

Dear FS members I am having trouble with using the "recon-all" function on one particular subject. "recon-all" does not complete and finishes with errors, it seems it does not complete both hemispheres. I am no expert in FS so I don't really understand why this is happening and I am unable to understand the log (attached). Could someone help interpret the log so that I may be able to process this subject? Many thanks Karen Karen Bunday, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders Institute of Neurology, University College London 33 Queen Square London WC1N 3BG

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selxavg3-sess: F-contrast but multiple dimension in sig
by Seung-Goo KIM 08 Feb '17

08 Feb '17

Dear surfers, I computed F-contrast using selxavg3-sess with an identity matrix as a contrast matrix. My question is about the result file “sig.*”. As far as I understand, the “sig.*” file contains signed-minnus-log-p-values (like, -log10(p)*Sign(t)) for a certain contrast. So I expected the dimension should be #vertices-by-1, but the sig.* file is in the dimension of #vertices-by-1-by-1-by-#regressors. I would appreciate post-hoc tests after F-test, but the dimension doesn’t look like one… or is it? like i-th regressor v.s. (N-i) regressors? If one can tell where I can find p-values for the F-test, and what are the values in the sig.* file. + wait. is "fsig.*” for the F-test? and “sig.*” for a set of one-vs.-the-others contrasts? I would still appreciate if one can confirm it. Best regards, -- Seung-Goo KIM Research Group for Cortical Networks and Cognitive Functions, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstraße 1A, 04103 Leipzig, Germany. Phone: +49 341 9940 2618 | Fax: +49 341 9940 2624 http://www.cbs.mpg.de/~skim <http://www.cbs.mpg.de/~skim>

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Freesurfer February 2017