Hello Eduard, It looks to me like the application freesurfer/BrainstemSS/mac_osx/segmentSubject.app needs to be run via the script freesurfer/BrainstemSS/mac_osx/run_SegmentSubject.sh which sets the path to pick up the Matlab library libmwcpp11compat.dylib.
While I think we have that library in house because we have a Matlab license, you would need to have a Matlab distribution or download their runtime environment in order to get that library for segmentSubject.app to run. - rob > On Oct 3, 2018, at 3:50 PM, Vasile, Eduard <evas...@mgh.harvard.edu> wrote: > > 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-boun...@nmr.mgh.harvard.edu on behalf of > freesurfer-requ...@nmr.mgh.harvard.edu" > <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > > Send Freesurfer mailing list submissions to > freesurfer@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-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@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." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Error during decompression of DICOM JPEG > compressed series > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <9b313c16-98ba-9434-e1a9-85febbbd2...@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, k3...@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." <dgr...@mgh.harvard.edu> >> ?: freesurfer@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, k3...@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@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@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" <rdicami...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Error during decompression of DICOM JPEG > compressed series > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <8a4d4b9a-2e49-445a-a616-c74122b3a...@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, k3...@free.fr<mailto:k3...@free.fr> wrote: > > sh: 1: Syntax error: Bad fd number > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181002/60fe213c/attachment-0001.html > > > ------------------------------ > > Message: 3 > Date: Tue, 2 Oct 2018 17:45:13 +0000 > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Error during decompression of DICOM JPEG > compressed series > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <1747fcbd-7c32-9668-3077-20b55c2e3...@mgh.harvard.edu> > Content-Type: text/plain; charset="Windows-1252" > > The command is being run from inside of a C-file using the system > command, so there is no way for them to change it > > On 10/02/2018 01:43 PM, Dicamillo, Robert wrote: >> It may be complaining about >& for redirection. ?Try using 2>&1 instead. >> >>> On Oct 2, 2018, at 4:56 AM, k3...@free.fr <mailto:k3...@free.fr> wrote: >>> >>> sh: 1: Syntax error: Bad fd number >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 4 > Date: Tue, 2 Oct 2018 20:30:34 +0000 > From: "Vasile, Eduard" <evas...@mgh.harvard.edu> > Subject: [Freesurfer] Mac OS free surfer instalation > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <9b0bc93c-2256-4e04-bc82-e941136fb...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > 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 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181002/0847099b/attachment-0001.html > > > ------------------------------ > > Message: 5 > Date: Tue, 2 Oct 2018 20:35:52 +0000 > From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Mac OS free surfer instalation > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <66754753-6fae-45ce-9dc9-e8360589d...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > 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-boun...@nmr.mgh.harvard.edu> on behalf of "Vasile, > Eduard" <evas...@mgh.harvard.edu> > Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu> > Date: Tuesday, October 2, 2018 at 4:31 PM > To: FS Help <freesurfer@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 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181002/2a21ea41/attachment-0001.html > > > ------------------------------ > > Message: 6 > Date: Tue, 2 Oct 2018 20:51:27 +0000 > From: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk> > Subject: Re: [Freesurfer] amygdala segmentation atlas influence > To: "Dr Rajendra Morey, M.D." <rajendra.mo...@duke.edu>, Freesurfer > support list <Freesurfer@nmr.mgh.harvard.edu> > Cc: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Message-ID: <a463f9df-e489-4568-90f7-c7bbf7f34...@ucl.ac.uk> > Content-Type: text/plain; charset="utf-8" > > 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.mo...@duke.edu> > Date: Monday, 1 October 2018 at 21:53 > To: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk>, Freesurfer > support list <Freesurfer@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.igles...@ucl.ac.uk] > Sent: Sunday, September 30, 2018 10:44 AM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: Dr Rajendra Morey, M.D. <rajendra.mo...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > on behalf of Emily K Clarke <ek...@duke.edu<mailto:ek...@duke.edu>> > Reply-To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Wednesday, 26 September 2018 at 15:15 > To: > "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> > Cc: "Dr Rajendra Morey, M.D." > <rajendra.mo...@duke.edu<mailto:rajendra.mo...@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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181002/7a7cf33d/attachment-0001.html > > > ------------------------------ > > Message: 7 > Date: Wed, 3 Oct 2018 09:29:09 +0200 > From: "Caspar M. Schwiedrzik" <cschwie...@mail.rockefeller.edu> > Subject: [Freesurfer] Deadline approaching: PhD in visual perceptual > learning at the Neural Circuits and Cognition lab @ ENI & German > Primate Center G?ttingen > To: "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <ca+bx-385pvrzpmrk0ynf584jih+wqzivew8qqv0rktgtbtx...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > The European Neuroscience Institute in G?ttingen (ENI-G) Germany, a > partnership between the University Medical Center G?ttingen 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 G?ttingen, 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 > G?ttingen and associated with the Max Planck Society. The University > Medical Center G?ttingen 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. G?ttingen 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 > G?ttingen 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.schwiedr...@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: > Universit?tsmedizin G?ttingen > > European Neuroscience Institute G?ttingen > > Neural Circuits and Cognition Lab > Dr. Caspar Schwiedrzik > Grisebachstr. 5 > 37077 G?ttingen > Germany > Tel.: +49-(0)551-39-61371 > E-Mail: c.schwiedr...@eni-g.de > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181003/29862e1f/attachment-0001.html > > > ------------------------------ > > Message: 8 > Date: Wed, 3 Oct 2018 13:00:59 +0000 > From: "Meusen - Klooster, D.C.W." <d.c.w.kloos...@tue.nl> > Subject: Re: [Freesurfer] Overlay electric field distribution on pial > surface > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <94d6e99297013f46990eeba320449f6184311...@xserver30a.campus.tue.nl> > Content-Type: text/plain; charset="us-ascii" > > External Email - Use Caution > > Ah, I see now that my configure screen is clipped, so I can click on all > the options but I cannot actually apply them... What are the options for > -colortable? If I have those, I can play with the visualization from the > command line but I cannot find them. > Thank you in advance. > Best, > Debby > ________________________________________ > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Meusen - Klooster, D.C.W. > [d.c.w.kloos...@tue.nl] > Verzonden: dinsdag 2 oktober 2018 17:37 > Aan: Freesurfer support list > Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial > surface > > External Email - Use Caution > > Yes, I made a (pretty stupid) mistake in the coregistration. The overlay > is working perfectly now. Only for the visualization, is it possible to set > my colorbar from 1 (blue) to approx 200 (red)? Can I get rid of the 'double' > color bars for positive (red) and negative (blue) values? > Thank you in advance. > Best, > Debby > ________________________________________ > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas Greve > [dgr...@mgh.harvard.edu] > Verzonden: maandag 17 september 2018 17:04 > Aan: freesurfer@nmr.mgh.harvard.edu > Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial > surface > > Did you look at the results of the registration to make sure that they > are ok? But you probably don't need to run the registration anyway since > the surfaces are in the T1.mgz space anyway. How are you verifying that > the efield is properly aligned to the T1.mgz? Is it also 1mm^3 and > 256^3? Does it have the same vox2ras matrix as the T1.mgz? use mri_info > --vox2ras T1.mgz Dep48_DLPFC_normE_CORRECTED.nii > > > On 9/17/18 8:42 AM, Meusen - Klooster, D.C.W. wrote: >> 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-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl >> [fis...@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 >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > 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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 9 > Date: Wed, 3 Oct 2018 09:38:45 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Overlay electric field distribution on pial > surface > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Cc: Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1810030938280.20...@gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > there may be a keyboard shortcut for "apply". Maybe return? Can't you > resize the window? > On Wed, 3 Oct 2018, Meusen - Klooster, D.C.W. wrote: > >> External Email - Use Caution >> >> Ah, I see now that my configure screen is clipped, so I can click on all the >> options but I cannot actually apply them... What are the options for >> -colortable? If I have those, I can play with the visualization from the >> command line but I cannot find them. >> Thank you in advance. >> Best, >> Debby >> ________________________________________ >> Van: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Meusen - Klooster, D.C.W. >> [d.c.w.kloos...@tue.nl] >> Verzonden: dinsdag 2 oktober 2018 17:37 >> Aan: Freesurfer support list >> Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial >> surface >> >> External Email - Use Caution >> >> Yes, I made a (pretty stupid) mistake in the coregistration. The overlay is >> working perfectly now. Only for the visualization, is it possible to set my >> colorbar from 1 (blue) to approx 200 (red)? Can I get rid of the 'double' >> color bars for positive (red) and negative (blue) values? >> Thank you in advance. >> Best, >> Debby >> ________________________________________ >> Van: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas Greve >> [dgr...@mgh.harvard.edu] >> Verzonden: maandag 17 september 2018 17:04 >> Aan: freesurfer@nmr.mgh.harvard.edu >> Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial >> surface >> >> Did you look at the results of the registration to make sure that they >> are ok? But you probably don't need to run the registration anyway since >> the surfaces are in the T1.mgz space anyway. How are you verifying that >> the efield is properly aligned to the T1.mgz? Is it also 1mm^3 and >> 256^3? Does it have the same vox2ras matrix as the T1.mgz? use mri_info >> --vox2ras T1.mgz Dep48_DLPFC_normE_CORRECTED.nii >> >> >> On 9/17/18 8:42 AM, Meusen - Klooster, D.C.W. wrote: >>> 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-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl >>> [fis...@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 >>>> >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> 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@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > ------------------------------ > > Message: 10 > Date: Wed, 3 Oct 2018 15:48:09 +0000 > From: "Sims, Sara A" <sno...@uab.edu> > Subject: [Freesurfer] output values of vertices on surface into a > textfile > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <3f08dd7f-df68-4f2c-8f8e-867d7a8a6...@uab.edu> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hello! > I would like to output the location and value of each vertex on a surface > to a text file. How could I go about doing this? > > Thanks, > Sara Sims > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20181003/a0f9149f/attachment-0001.html > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 176, Issue 3 > ****************************************** > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
