Freesurfer October 2018

freesurfer@nmr.mgh.harvard.edu

113 participants
156 discussions

Morphing Buckner2011 MNI152 to subject's space {Disarmed}
by Peled, Noam 05 Oct '18

05 Oct '18

Dear group, I'm trying to morph the Buckner2011<http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011> cerebellum segmentation map from MNI152 to subject's space: mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --m3z talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest --inv-morph It worked with the 17 networks, but didn't work with the 7 networks version. Any ideas? This is really strange. Thanks, Noam

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Definition of circular label centered on peak vertex
by Milde, Christopher 05 Oct '18

05 Oct '18

External Email - Use Caution Dear FS experts I`m interested in extracting beta values from a FSFAST analysis performed in the subject`s native space. The beta values shall be extracted from a circular label around the peak vertex. How can you define a circular label centered on the peak to extract average stats (e.g. betas) from that label? I`m aware how to create mask from the whole clusters in a given ROI saving them as labels and extracting stats. However I`m not sure how to define a circular mask or label. Thanks in advance Chris

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Re: [Freesurfer] Error running setup_configure
by Hoopes, Andrew 05 Oct '18

05 Oct '18

You’re attempting to build the dev version of freesurfer, in which case you should follow the build instructions on this page - https://surfer.nmr.mgh.harvard.edu/fswiki/BuildGuide. If you’d like to build freesurfer 6, you’ll have to checkout the "stable6" git branch before running setup_configure. Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Jennewein, Douglas M" <Doug.Jennewein(a)usd.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, October 5, 2018 at 2:07 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Error running setup_configure External Email - Use Caution We are attempting to build Freesurfer 6 on CentOS 7 x76_64. After cloning the git repo we see the following when running ./setup_configure configure.in:3866: the top level Makefile.am: error: required file './NEWS' not found Makefile.am: error: required file './AUTHORS' not found Makefile.am: error: required file './ChangeLog' not found automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' Makefile.am:27: error: required directory ./mri_warp_concat does not exist The folder mri_warp_concat/ does not exist in the cloned directory, and does not appear to exist in the github repo online<https://github.com/freesurfer/freesurfer> either. How can we build Freesurfer 6 from source on CentOS 7? Thank you Doug Jennewein

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Error running setup_configure
by Jennewein, Douglas M 05 Oct '18

05 Oct '18

External Email - Use Caution We are attempting to build Freesurfer 6 on CentOS 7 x76_64. After cloning the git repo we see the following when running ./setup_configure configure.in:3866: the top level Makefile.am: error: required file './NEWS' not found Makefile.am: error: required file './AUTHORS' not found Makefile.am: error: required file './ChangeLog' not found automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' Makefile.am:27: error: required directory ./mri_warp_concat does not exist The folder mri_warp_concat/ does not exist in the cloned directory, and does not appear to exist in the github repo online<https://github.com/freesurfer/freesurfer> either. How can we build Freesurfer 6 from source on CentOS 7? Thank you Doug Jennewein

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How to convert enhanced dicom format
by Craggs, Jason G. 05 Oct '18

05 Oct '18

External Email - Use Caution Greeting, Our radiology department recently installed a Siemens Vida system. It apparently exports in "enhanced dicom” format, which doesn't work with any of my software. Does anyone know anything about this format? Cheers, Jason

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QAtools for Freesurfer version6?
by Lee, Seonjoo 05 Oct '18

05 Oct '18

External Email - Use Caution I tired to use QA tools for freesurfer version6, but did not have much success. Is anyone know how to tweak QA tools for freesurfer version 6? Thank you. -Seonjoo Lee

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Mac OS free surfer instalation (Vasile, Eduard)
by Vasile, Eduard 04 Oct '18

04 Oct '18

Hi Rob, I have matlab installed on my laptop. I am based in South Central, 149, is there anywhere I can come to talk to you guys? I am in need of the software. Kind regards Eduard On 10/4/18, 12:00 PM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu> wrote: Mac OS free surfer instalation (Vasile, Eduard)

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mri_surf2surf --mapmethod nnf not working?
by Viessmann, Olivia M. 04 Oct '18

04 Oct '18

Hello, I am using mri_surf2surf and would like to use the vertex map method nnf ("neighest neighbor, forward only") which according to the --help description exists and avoids multiple source vertices to be mapped and averaged onto a single target vertex (crucial to my analysis here). However, when I run this the output suggests that it is running the nnfr (neighest-neighbor forward and reverse) method. Is this a bug or am I misinterpreting the console output? This is the command and output: /usr/local/freesurfer/dev/bin/mri_surf2surf --srcsubject 994273 --sval 994273/Results/Orientations/lh_SSangle_depth00_rfMRI_REST1_LR.mgz --trgsubject fsaverage --mapmethod nnf --o lh_SSangle_depth00_rfMRI_REST1_LR_inFSAv.mgz --hemi lh sysname Linux machine x86_64 user omv4 srcsubject = 994273 srcval = 994273/Results/Orientations/lh_SSangle_depth00_rfMRI_REST1_LR.mgz srctype = trgsubject = fsaverage trgval = lh_SSangle_depth00_rfMRI_REST1_LR_inFSAv.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /cluster/olivia/Data/994273/T1w/994273/surf/lh.sphere.reg Loading source data Reading target surface reg /cluster/olivia/Data/994273/T1w/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 26240 nTrg121 = 163842, nTrgMulti = 0, MnTrgMultiHits = 0 nSrc121 = 78298, nSrcLost = 26240, nSrcMulti = 62974, MnSrcMultiHits = 1.3584 Saving target data Saving to lh_SSangle_depth00_rfMRI_REST1_LR_inFSAv.mgz I'd appreciate any suggestions. Thanks Olivia

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Problem with new tool on thalamus segmentation
by stdp82＠virgilio.it 04 Oct '18

04 Oct '18

External Email - Use Caution I'm reposting my questions that I have done some week ago because without your helpfulness is impossible to go ahead with my analysis. 1- I have installed dev version. I have run the segmentThalamicNuclei.sh but .stats file has been not produced in any subjects. I have also try to re-run recon-all but without success. 2 - I have used FS-FAST previously. However, when I use the thalami segmentation as seed fcseed-config -segid 8103 -fcname L_AV.dat -fsd rest -mean -cfg mean.L_AV.config fcseed-sess -sf sessid -cfg mean.L_AV.config I obtain the error listed below: Voxel Volume is 36.3469 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 0 segmentations Using PrintSegStat Computing spatial average of each frame ERROR: no voxels found in segmentation Please could you give me can help? Thanks Stefano

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Mac OS free surfer instalation (Vasile, Eduard)
by Vasile, Eduard 03 Oct '18

03 Oct '18

Hi, Coming back with an update from the previous email. I installed it but it tells me that it cannot be open because of a problem and then I get the above error. The version is 6.0. Is there a place where I can come with my laptop and see what is the problem? Process: prelaunch [1300] Path: /Applications/freesurfer/*/segmentSubject.app/Contents/MacOS/prelaunch Identifier: segmentSubject Version: 1 Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: prelaunch [1300] User ID: 501 Date/Time: 2018-10-03 15:47:11.569 -0400 OS Version: Mac OS X 10.13.6 (17G2307) Report Version: 12 Bridge OS Version: 3.0 (16P375) Anonymous UUID: C3615BC6-2956-15B2-00D8-9F435B158DB0 Sleep/Wake UUID: 2988BAC2-9FC2-422B-AF82-6F0576A1E894 Time Awake Since Boot: 3200 seconds System Integrity Protection: enabled Crashed Thread: 0 Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY Termination Reason: DYLD, [0x1] Library missing Application Specific Information: dyld: launch, loading dependent libraries Dyld Error Message: Library not loaded: @rpath/libmwcpp11compat.dylib Referenced from: /Applications/freesurfer/*/segmentSubject.app/Contents/MacOS/prelaunch Reason: image not found Binary Images: 0x100000000 - 0x100000ff7 +segmentSubject (1) <BF09BC5D-285F-35DE-BE47-E8F723B03986> /Applications/freesurfer/*/segmentSubject.app/Contents/MacOS/prelaunch 0x105013000 - 0x10505dacf dyld (551.4) <8A72DE9C-A136-3506-AA02-4BA2B82DCAF3> /usr/lib/dyld Kind regards Eduard On 10/3/18, 12:00 PM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu> wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Error during decompression of DICOM JPEG compressed series (Greve, Douglas N.,Ph.D.) 2. Re: Error during decompression of DICOM JPEG compressed series (Dicamillo, Robert) 3. Re: Error during decompression of DICOM JPEG compressed series (Greve, Douglas N.,Ph.D.) 4. Mac OS free surfer instalation (Vasile, Eduard) 5. Re: Mac OS free surfer instalation (Hoopes, Andrew) 6. Re: amygdala segmentation atlas influence (Iglesias Gonzalez, Eugenio) 7. Deadline approaching: PhD in visual perceptual learning at the Neural Circuits and Cognition lab @ ENI & German Primate Center G?ttingen (Caspar M. Schwiedrzik) 8. Re: Overlay electric field distribution on pial surface (Meusen - Klooster, D.C.W.) 9. Re: Overlay electric field distribution on pial surface (Bruce Fischl) 10. output values of vertices on surface into a textfile (Sims, Sara A) ---------------------------------------------------------------------- Message: 1 Date: Tue, 2 Oct 2018 17:00:09 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <9b313c16-98ba-9434-e1a9-85febbbd28d3(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Sorry, I meant to change your default shell. That command is being run using the system() command from inside of a c-program, which undoubtedly starts your default shell. Just see if it works. On 10/02/2018 10:36 AM, k3ops(a)free.fr wrote: > External Email - Use Caution > > I am using bash shell but I tried with many others as mentioned in my first post (zsh, tcsh, csh, sh) and nothing worked so far... > > > ----- Mail original ----- > De: "Douglas N. Greve,Ph.D." <DGREVE(a)mgh.harvard.edu> > ?: freesurfer(a)nmr.mgh.harvard.edu > Envoy?: Mardi 2 Octobre 2018 15:18:14 > Objet: Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series > > What shell are you using? Try using cshell or tcshell to see if it works. > > On 10/2/18 4:56 AM, k3ops(a)free.fr wrote: >> External Email - Use Caution >> >> Hi FS team, >> >> I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and everything runs well for most of the subjects that I process so first thanks for this great tool. >> I am facing an issue with a JPEG compressed DICOM series that I am not able to precess, I always get the following error during "mri_convert" procedure (before calling recon-all), I also wrote the last command that produces this error: >> >> fsdcmdecompress --i freesurfer_18/6858304 --o /tmp/root.tmp.decompressed.dcm.v1uqEv --jpeg >& /tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out >> sh: 1: Syntax error: Bad fd number >> >> After some investigations, it looks it is related to the way standard outputs are redirected to "/tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out" file (which is missing by the way). >> It looks like ">&" redirection is not a correct syntax in bash (the shell I am using), so I tried with others but unfortunately none of them worked so far (zsh, tcsh, csh, sh). >> >> Do you have any recommendation for the way to use "mri_convert" tool? or any other tool that could convert DICOM to nifty efficiently? >> >> Thanks for your feedbacks. >> >> Regards, >> Florent >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 2 Date: Tue, 2 Oct 2018 17:43:26 +0000 From: "Dicamillo, Robert" <RDICAMILLO(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <8A4D4B9A-2E49-445A-A616-C74122B3A599(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="us-ascii" It may be complaining about >& for redirection. Try using 2>&1 instead. On Oct 2, 2018, at 4:56 AM, k3ops(a)free.fr<mailto:k3ops@free.fr> wrote: sh: 1: Syntax error: Bad fd number

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Freesurfer October 2018