Freesurfer

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30084 discussions

Issue opening .dmg file for installing freesurfer patch/code addition for brainstem. Error is "image not recognized"
by Jonathan Plasencia 24 Oct '15

24 Oct '15

Hello, I'm trying to segment the brainstem into subparts. I found online for freesurfer 5.3 you can use the following link to install the need codes: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ which was from the following freesurfer question/solution: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42064.html However, when I open the ftp as a guest and try to open the .dmg file I get the error "image not recognized". Looking into why this happens it sounds like the download went bad. I've tried re-downloading the file a few times and am now wondering if the uploaded file was bad? Is there another solution so I can segment the brainstem? Thank you for your help, Jon

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autorecon2 vs autorecon2-cp
by Kasper Jessen 24 Oct '15

24 Oct '15

Dear freesurfer group I have edited my subjects with both control points and brainmask edits. For the re-processing both my CPs and brainmask edits, at the same time i used the following command: - recon-all -base Subject_base -tp Tp1 -tp Tp2 -autorecon2 -autorecon3 -3T Is this a correct way of doing it? I have become in doubt since i have noticed that some use -autorecon2-cp or -autorecon2-pial. However, i have only used -autorecon2-cp if i ONLY have made control points. But since i have done both CPs and brianmask edits i used -autorecon2 -autorecon3. Best regards, Kasper Phd Student -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j(a)cnsr.dk eller kasper.jessen(a)regionh.dk

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Re: [Freesurfer] Sulcal depth units
by Simon Vandekar 24 Oct '15

24 Oct '15

Hi Bruce, I think that unnormalized sulcal depth would be useful. However, I am also curious what the units are in the standard output, because they appear to not be z-score standardized in each hemisphere. Thanks again, Simon >H I Simon >Do you need the unnormalized sulc? It would be pretty easy to put something in to generate it >Bruce > >> On Oct 22, 2015, at 3:23 PM, Simon Vandekar <simonv(a)mail.med.upenn.edu> wrote: >> >> Hi Bruce, >> >> I chose a random subject from the ADNI dataset and computed the mean and variance for the left and right hemispheres separately. It looks like the mean is close to 0, however the variance is not 1. Do you think it is possible that the surfaces are demeaned, but the units are still something meaningful (i.e. not unitless)? >> >> >> sulc = read.table('rh.sulc.asc', header=FALSE, col.names=c('v', 'x', 'y', 'z', 'sulc')) >>> mean(sulc$sulc) >> [1] -1.236923e-08 >> >>> var(sulc$sulc) >> [1] 0.3276958 >> >>> quantile(sulc$sulc) >> 0% 25% 50% 75% 100% >> -1.72503 -0.42128 -0.03963 0.40072 1.80980 >> >> >> Thanks again, >> Simon >> >> >> >> >> >> Hi Simon >> >> they are originally mm, but I believe we z-score normalize them so that >> the sulc file is 0 mean and unit variance. >> >> cheers >> Bruce >> On Wed, 21 Oct 2015, Simon >> Vandekar wrote: >> >>> Dear Freesurfer experts, >>> >>> >>> I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, Sereno, and Dale (1999) where the estimation of sulcal depth is described on page 199, however from the description I am still unsure of the exact units of sulcal depth. >>> Are the units for sulcal depth in mm or are they in arbitrary units? >>> >>> Thanks in advance, >>> Simon

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Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
by Yun Wang 23 Oct '15

23 Oct '15

Can the recon-all for high resolution fMRI data be used in V6 beta freesurfer now? If so, how to use it? > On Jun 25, 2015, at 13:36, Allison Moreau <almoreau(a)nmr.mgh.harvard.edu> wrote: > > Hi Falk and Thomas, > > We are actually working on testing the -hires flag now for the v6 release. We intend to release it with v6. > > -Allison > > On 06/25/2015 07:09 AM, Falk Lüsebrink wrote: >> Hi Thomas, >> >> this looks like a really nice script and a lot better than my own. In the upcoming release of FreeSurfer v.6 my work-around probably is not needed anymore. However, I haven’t been able to have a look at the dev release yet and whether the standard recon-all features a flag to process high resolution data. >> >> Best, >> Falk >> >> P.S. Following your instructions one will definitely become a coffee junkie. :D >> >> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] Im Auftrag von Emmerling Thomas (PSYCHOLOGY) >> Gesendet: Mittwoch, 24. Juni 2015 14:35 >> An: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> >> Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data >> >> Hello! >> >> I wrote a bash script some time ago to process data acquired at a sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon <https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon>). I thought it might be helpful for others, too, as there are some questions about it in the mailing list archives, so here it is: https://github.com/thomastweets/freesurfer-7t-pipeline <https://github.com/thomastweets/freesurfer-7t-pipeline>. I am happy about any comments! >> >> Best, >> Thomas >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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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Re: [Freesurfer] Help with V6
by Douglas Merkitch 23 Oct '15

23 Oct '15

Hello Noah, Could you be more specific as to how you were able to resolve this problem? What additional tweaks were necessary? I too received the same error message: ERROR: Flag -subfields-T1 unrecognized. -all -s 1048_v6beta_hippsubfieldsT1 -subfields-T1 Darwin glenn-stebbins-computer.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 recon-all -s xxxx exited with ERRORS at Fri Oct 23 13:10:17 CDT 2015 I'm running freesurfer-Darwin-OSX-stable-v6-beta-20150921 on a mid 2012 MacPro (OS X 10.8.5). I also installed the Matlab runtime as instructed. Any help would be greatly appreciated! Thanks, Doug Doug Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu> Thanks Noah. It doea say on the website that you need the 2012b runtime, but its definitely buried among too much other, less critical stuff Cheers E Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com<http://www.jeiglesias.com> www.bcbl.eu<http://www.bcbl.eu> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer<http://www.bcbl.eu/legal-disclaimer> ----- Original Message ----- From: Noah Markowitz <noahb.markow...(a)gmail.com<http://gmail.com>> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Sent: Sat, 04 Jul 2015 13:57:53 +0200 (CEST) Subject: Re: [Freesurfer] Help with V6 Hey Eugenio, I was able to resolve it with the help of another expert. One of the problems definitely was that 2014b doesn’t run on the hippocampal-subfields module. Maybe try adding that as a note to the website as numerous people have access to the 2014b version and 2015a was just released. Thanks again for all the help. Cheers, Noah > On Jul 3, 2015, at 5:12 PM, Eugenio Iglesias <e.igles...(a)bcbl.eu<http://bcbl.eu>> wrote: > > Hi Noah, > this error is pretty weird. Can you please send us the exact command you > executed? > Regarding the runtime: your 2014b runtime won't work. You need to follow the > instructions here: > https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime > Cheers, > Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com<http://www.jeiglesias.com> > www.bcbl.eu<http://www.bcbl.eu> > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer<http://www.bcbl.eu/legal-disclaimer> > > > ----- Original Message ----- > From: "Noah Markowitz" <noahb.markow...(a)gmail.com<http://gmail.com>> > To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> > Sent: Friday, July 3, 2015 4:20:02 AM > Subject: [Freesurfer] Help with V6 > > Hi, > > I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the > error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv and > source just as described for previous versions. > > Also, I have Matlab 2014b downloaded on the computer (obviously comes with > runtime) but am unsure if the runtime folder needs to be placed in the FS > folder or is fine where it is. > > Any FS experts help with these two problems and concerns? Much appreciated if > you do. > > Cheers, > > Noah Markowitz > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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nifti1Read(): unsupported slice timing pattern 5 -- mri_convert fix?
by Alex Kell 23 Oct '15

23 Oct '15

Hi, I'm analyzing data from a collaborator who used SPM to generate some niftis, and freesurfer is unable to read these. I get the following error: nifti1Read(): unsupported slice timing pattern 5 Someone previously <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29542.html> had the same problem that I currently have, and Doug sent them a modified version of mri_convert. Could you send me the modified version of mri_convert? Thanks, Alex

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Longitudinal analysis with QDEC
by Wrobel, Pawel 23 Oct '15

23 Oct '15

Hello Dear FreeSurfer Developers, Thank You once again for helping me a couple of months ago. Today I came across a new obstacle, as I have been trying to analyse longitudinal material. I have performed all preparation steps and I started performing statistical analysis in Qdec when receiving following message: Error in Analyze: Couldn't open .../FreeSurfer_output/subjects/CT_10/BLD013_/surf/lh.thickness.fwhm15.fsaverage.mgz or .mgh file. I have checked in the surface directory and I could not find this file. There were several variations of it, but not a file with this particular name. I have been working with Freesurfer5.3. Thank You for Your help! Pawel

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Re: [Freesurfer] Sulcal depth units
by Simon Vandekar 22 Oct '15

22 Oct '15

Hi Bruce, I chose a random subject from the ADNI dataset and computed the mean and variance for the left and right hemispheres separately. It looks like the mean is close to 0, however the variance is not 1. Do you think it is possible that the surfaces are demeaned, but the units are still something meaningful (i.e. not unitless)? sulc = read.table('rh.sulc.asc', header=FALSE, col.names=c('v', 'x', 'y', 'z', 'sulc')) > mean(sulc$sulc) [1] -1.236923e-08 > var(sulc$sulc) [1] 0.3276958 > quantile(sulc$sulc) 0% 25% 50% 75% 100% -1.72503 -0.42128 -0.03963 0.40072 1.80980 Thanks again, Simon Hi Simon they are originally mm, but I believe we z-score normalize them so that the sulc file is 0 mean and unit variance. cheers Bruce On Wed, 21 Oct 2015, Simon Vandekar wrote: > Dear Freesurfer experts, > > I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, Sereno, and Dale (1999) where the estimation of sulcal depth is described on page 199, however from the description I am still unsure of the exact units of sulcal depth. > Are the units for sulcal depth in mm or are they in arbitrary units? > > Thanks in advance, > Simon > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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FSFAST -per-run question
by dgw 22 Oct '15

22 Oct '15

Hi, I know that -per-run is the recommended motion correction option, and that it uses the middle frame as the reference for motion correction for each run. I was wondering, if there is a reference, or explanation as to why that was chosen and not some other timepoint. Thanks, d

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How to compute the measures on the average brain?
by Mathieu Dubois 22 Oct '15

22 Oct '15

Hi, I'm a beginner with freesurfer so I apologize if it's a trivial question. I recently run recon-all with the -all on many subjects. As far as I can say, all the steps worked. However, the measures on the average brain (output of mris_preproc and friends) were not computed. A colleague told me that he usually re-run recon-all with the -qcache flag to compute those. This seems to work but I don't understand if it is the recommended way to run mris_preproc and why it is not included with -all. Is it possible to get those measures in one call to recon-all? I don't think that the issue comes from the data (e.g. that the failing of a step stops some branch of the pipeline) because it seems to run correctly with -qcache. I haven't found any help on -qcache and the help of recon-all doesn't mention mris_preproc or mri_surf2surf. Thanks in advance, Mathieu

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