Freesurfer

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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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hippocampal subfields error
by Marcel Heers 03 Oct '18

03 Oct '18

External Email - Use Caution Dear Eugenio, I am currently testing the newest version of your hippocampal subfield analysis script. If I process the data on my macbook the files hipposubfields.lh.T2.v21.file_ID contain the volumes of the different nuclei, but on the linux server these files remain empty. On the server I installed freesurfer as local user. Do you have any suggestions how to check what might go wrong? Thanks for your help! Marcel

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Re: [Freesurfer] Overlay electric field distribution on pial surface
by Meusen - Klooster, D.C.W. 03 Oct '18

03 Oct '18

External Email - Use Caution Dear Prof. Fischl, Sorry for the lack of clarity. I used bbregister to generate a registration.dat file. I used simnibs to calculate the Efield distribution and this has the option to convert the Efield mesh files to .nii files. So I registered the high resolution T1 (from simnibs, that aligns with the Efield) to the original T1 data. Consecutively, I used tksurfer to visualize. bbregister --s Dep48_T1_origANAT --mov /home/debby/Desktop/FigModPap_Depr48/fs_HeadmeshDep48_origT1/mri/T1.mgz --reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat --t1 tksurfer FigModPap_Depr48 lh pial -sdir /home/debby/Desktop -overlay /home/debby/Desktop/FigModPap_Depr48/Dep48_DLPFC_normE_CORRECTED.nii -overlay-reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat -fthresh -2 -fmid 150 Best, Debby ________________________________________ Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Verzonden: zaterdag 15 september 2018 17:21 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface Hi Debby you need to give us a lot more information. What commands did you use to sample the field onto the surface? What was the output of those commands? Note that tksurfer is deprecated, so I wouldn't worry about how it looks cheers Bruce On Sat, 15 Sep 2018, Meusen - Klooster, D.C.W. wrote: > > External Email - Use Caution > > Dear all, > I am studying transcranial magnetic stimulation (TMS) and would like to nicely visualize my TMS > induced electric fields over a pial surface, preferably using Freesurfer to stay in line with my > other images. I have a .nii file of the electric field distribution, registered to T1, representing > field strengths in every voxel. Visualization in freeview looks okay, but visualization using > tksurfer does not really give the right results (most of the brain is yellow... no field > distribution visible). I guess something goes wrong in the setting of the colorbar. Preferably I > would like to see the field strengths (min:max) in a blue-red colorscheme. Can anybody tell me how > to accomplish this? > Thank you very much in advance. > Best, > Debby > >

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Deadline approaching: PhD in visual perceptual learning at the Neural Circuits and Cognition lab @ ENI & German Primate Center Göttingen
by Caspar M. Schwiedrzik 03 Oct '18

03 Oct '18

External Email - Use Caution The European Neuroscience Institute in Göttingen (ENI-G) Germany, a partnership between the University Medical Center Göttingen and the Max-Planck-Society, is seeking a *Ph.D. student * About us: The Neural Circuits and Cognition lab of Caspar Schwiedrzik at the European Neuroscience Institute (ENI-G) and the German Primate Center <http://www.dpz.eu/de/startseite.html> (DPZ) in Göttingen, Germany is looking for an outstanding PhD student interested in studying the neural basis of perceptual learning in vision. The project investigates neural mechanisms of learning and perception at the level of circuits and single cells, utilizing functional magnetic resonance imaging (fMRI) in combination with electrophysiology and behavioral testing in humans and non-human primates. It is funded by an ERC Starting Grant (Acronym VarPL; “Specificity or generalization? Neural mechanisms for perceptual learning with variability”). The PhD student’s project will focus on developing new perceptual learning paradigms and investigating the neural basis of perceptual learning in humans using fMRI. In addition, the PhD student will cooperate with other lab members on parallel electrophysiological and fMRI experiments as well as comparative research exploring the same questions in non-human primates. The lab seeks to understand the cortical basis and computational principles of perception and experience-dependent plasticity in the macaque and human brain (see http://www.eni-g.de/groups/neural-circuits-and-cognition) To this end, we use a multimodal approach including fMRI-guided electrophysiological recordings in non-human primates and fMRI and ECoG in humans. The PhD student will play a key role in our research efforts in this area. The lab is located at the ENI (http://www.eni-g.de) and the DPZ ( http://www.dpz.eu) which are interdisciplinary research centers with international faculty and students pursuing cutting-edge research in neuroscience. The PhD student will have access to a new imaging center <http://www.dpz.eu/en/infocenter/> with a dedicated 3T research scanner, electrophysiology, and behavioral setups. ENI-G is engaged in experimental molecular and cellular research on the central and peripheral nervous systems as well as cognitive and systems neurosciences research. ENI is part of the University Medical Center Göttingen and associated with the Max Planck Society. The University Medical Center Göttingen is a tertiary care center. Its 7,400 employees work in over 65 departments and facilities to provide top-quality patient care, excellent research and modern teaching facilities. Göttingen provides a vibrant and stimulating neuroscience community with a strong background in computational as well as experimental neurosciences. The PhD student will have the opportunity to join one of the fourteen programs of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (http://www.ggnb.uni-goettingen.de) Your profile: The position will be available starting in November 2018 with an initial appointment for 3 years and a salary according to 50% TVL-13. Candidates should have a degree (master, diploma or equivalent) in a relevant field (e.g., neuroscience, psychology, biology), and ideally prior experience in fMRI, strong quantitative, programming, and experimental skills, and share a passion for understanding the neural basis of visual perception and its plasticity. Interested candidates should send their curriculum vitae, a description of their scientific interest and the names and contact information of up to two references who are able to comment on your academic background and who agreed to be contacted to c.schwiedrzik(a)eni-g.de, preferably before *October 10th, 2018*, but later expressions of interest will be considered until the position is filled. A good command of English is a requirement, but fluency in German is not essential. Please apply by 10.10.2018 to: Universitätsmedizin Göttingen European Neuroscience Institute Göttingen Neural Circuits and Cognition Lab Dr. Caspar Schwiedrzik Grisebachstr. 5 37077 Göttingen Germany Tel.: +49-(0)551-39-61371 E-Mail: c.schwiedrzik(a)eni-g.de

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Re: [Freesurfer] amygdala segmentation atlas influence
by Iglesias Gonzalez, Eugenio 02 Oct '18

02 Oct '18

External Email - Use Caution Thanks, Raj. I’d argue that, if the volumes of the nuclei were completely driven by the global volume of the amygdala, e.g., in an extreme case, V_nuc = alpha x V_whole, then the effect size of the nucleus at hand would be the same as for the whole amygdala. Whether such effect size is higher or lower than the “real” effect size in presence of perfect segmentation… depends on the nucleus ;-) Doug: any thoughts? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: "Dr Rajendra Morey, M.D." <rajendra.morey(a)duke.edu> Date: Monday, 1 October 2018 at 21:53 To: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk>, Freesurfer support list <Freesurfer(a)nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] amygdala segmentation atlas influence Hi Eugenio Thanks for your response it is helpful. In the dataset that I just analyzed with about 375 scans I suspect that the segmentation for some nuclei is heavily driven by the atlas. This is resulting in relatively low variance in both the patient group and the control group. The implication is that the between-group statistical test is overly sensitive and therefore produces higher than the expected chance of a significant result. Is this a reasonable concern. The counterargument is that the means of the two groups are closer to each other than the true means because of a heavy reliance on the atlas. The implication here is that the between group statistical test is going to be more conservative than the true difference. Or does it mean the significance of the test is not affected but that the effect size is artificially low. Let me know your thoughts! Thanks raj From: Iglesias Gonzalez, Eugenio [mailto:e.iglesias@ucl.ac.uk] Sent: Sunday, September 30, 2018 10:44 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Cc: Dr Rajendra Morey, M.D. <rajendra.morey(a)duke.edu> Subject: Re: [Freesurfer] amygdala segmentation atlas influence Dear Raj, A few years ago, we published a paper on how Monte Carlo sampling could be used to quantify this. Unfortunately, the method was incredibly slow and difficult to tune, and the performance gain was tiny, so we never put it in FreeSurfer. But this is a direction I’m still interested in, and which I’m planning to revisit in the future. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Emily K Clarke <ekc23(a)duke.edu<mailto:ekc23@duke.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, 26 September 2018 at 15:15 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>> Cc: "Dr Rajendra Morey, M.D." <rajendra.morey(a)duke.edu<mailto:rajendra.morey@duke.edu>> Subject: [Freesurfer] amygdala segmentation atlas influence External Email - Use Caution Hello all, I have run the amygdala segmentation in my datasets to obtain volumes of nuclei. I am aware from the fswiki that the volumes should be interpreted with caution because of the reliance on the atlas. When running FS, is there a way to get some metric about how much the segmentation relied on the atlas relative information from the T1 being segmented. If this metric is not available to the user, is some version of it calculated by the software and therefore available internally. Thanks in advance for your help! raj

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Re: [Freesurfer] Mac OS free surfer instalation
by Hoopes, Andrew 02 Oct '18

02 Oct '18

Hi Eduard, we’ll need some more information. What kind of errors are you running into? Are you trying to download v6.0 or the dev version? best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Vasile, Eduard" <EVASILE(a)mgh.harvard.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, October 2, 2018 at 4:31 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Mac OS free surfer instalation Dear Free Surfer Developers, I have installed freesurfer on my laptop and followed all steps you suggested online for a mac computer but freesurfer is still not working. Could you please assist me in installing it? Kind regards Eduard

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Mac OS free surfer instalation
by Vasile, Eduard 02 Oct '18

02 Oct '18

Dear Free Surfer Developers, I have installed freesurfer on my laptop and followed all steps you suggested online for a mac computer but freesurfer is still not working. Could you please assist me in installing it? Kind regards Eduard

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Error during decompression of DICOM JPEG compressed series
by k3ops＠free.fr 02 Oct '18

02 Oct '18

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

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analyzing and reporting parcellation results
by Tamir Eisenstein 02 Oct '18

02 Oct '18

External Email - Use Caution Hi FS experts, When I'm analyzing regional volumes/thickness using one of the atlases ROI's parcellation, and for example want to compare all the ROI's between two groups, should I correct for multiple comparisons (for the entire number of the atlas ROI's)? or is it acceptable to report the results as it is? Best, Tamir

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