Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30056 discussions

tkregister2
by Margo McKenna Benoit 28 Nov '05

28 Nov '05

Hi, I am trying to manually check the talairach registration from recon-all using tkregister2, but it appears to be looking for files in <subjectname>talairach/mri/orig. This directory structure does not exist in my dataset. The tutorial recommended the following command line: *tkregister*2 --mgz --s <subjectname> --fstal --surf orig --fstal Check and edit the talairach registration that was created during the FreeSurfer reconstruction. Sets the movable volume to be $SUBJECTS_DIR/talairach/mri/orig and sets the registration file to be $SUBJECTS_DIR/subjectid/transforms/talairach.xfm. User must have write permission to this file. Do not specify --reg with this flag. It is ok to specify --regheader with this flag. The format of the anatomical can be changed with --mgh or --mghz My data is in /space/lucy/2/users/margo/subjects/avm002 and I am using the std environment. Can I run this command without the --fstal? What should I specify as the target and movable volumes in that case? Thank you, Margo

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skull stripping
by Sasha Wolosin 28 Nov '05

28 Nov '05

Dear all, To improve skull stripping, I adjusted the watershed threshold using wsthresh, but this did not work well with our data. Do you have any other suggestions for improving skull stripping when there is too much membrane included? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Script: setfile sulc
by Henrik Ormåsen 28 Nov '05

28 Nov '05

Newbie questions: I'm doing some stuff inn a script (with the -tcl option in freesurfer). This is very nice, but I have problems with the following: 1) I don't get the curvature file to work. I've tried with: setfile sulc (and then the full path to the file). No error, but the files effects isn't being added. 2) Is it possible to save as tif from the script? (I use now: set rgb and save_rgb) Regards! Henrik Ormåsen IT analyselab, Psykologi

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question about aseg.stat data
by tulu 28 Nov '05

28 Nov '05

Dear freesurfer experts, I use freesurfer and bert data to run recon-all script. It can finish without error. However, when I check the aseg.stats data and find some regions such as inslula or operculum volume are zero. Is it right ? or I should change something other than default setting ? thanks replay Sincerely KL chen

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Postdoc Position, Berlin, Germany
by isabell.wartenburger＠charite.de 24 Nov '05

24 Nov '05

A postdoctoral position ("Wissenschaftlicher Mitarbeiter") is available at the Berlin NeuroImaging Center, Berlin, Germany. Focus of research is in language acquisition. More specifically, we are interested in functional and structural brain changes due to learning a new language in adulthood. The position is integrated in a young, interdisciplinary team in the field of cognitive neuroscience. We employ a combination of psychophysical methods, functional, and structural neuroimaging (EEG, fMRI, MRI, NIRS). The successful applicant will need to have a PhD in a field related to cognitive neuroscience (e.g. neuroscience, psychology, medicine, linguistics, engineering, physics, or informatics). Applicants should have a background in cognitive neuroscience and/or neuroimaging (MEG, EEG, fMRI, MRI, or other brain imaging techniques), experience in language research, and experience in experimental design, computer programming and statistical methods (software packages FreeSurfer, FSL, AFNI, or SPM; and/or manual tracing methods of brain structures). The position is for two years, available immediately and has the option of extension. Salary will be according to BAT IIa. For further information, please email Isabell Wartenburger at isabell.wartenburger(a)charite.de - - - Dr. Isabell Wartenburger Berlin NeuroImaging Center, Dept. of Neurology Charité Campus Mitte Humboldt-University Schumannstr. 20/21, 10117 Berlin, Germany Phone: ++49-30-450 560 194 Fax: ++49-30-450 560 952 berlin-neuroimaging-center.de/groups/executiveFunctionAndLanguage - - -

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inorm report file
by Margo McKenna Benoit 23 Nov '05

23 Nov '05

Hi, I was checking the normalization report file (snfmc6.report) as suggested by the tutorial -- the OV Zmax and OU Mean numbers checked out ok, but the last bit of the file has a listing of all of the time points for each run, and it seems that the final time point (23) for all of my functional runs is smaller that the others (0-22). Is this a concern? I copied part of the file at the end of this message. My data is in /subjects/2/lucy/users/margo/subjects/avm002 and this particular file is avm002/bold/013. All of the functional runs (013-016) have a similar pattern. Any suggestions would be very much appreciated. Thanks, Margo # FS-FAST Intensity Normalization Report > ## Over-Threshold Stats > # OV SNR 804.635775 > # OV ZAvg 1.370247 > # OV ZMax 2.929180 > # OV ZMax Index 13 > # OV Drift 0.010509 > # > # Over/Under Stats f > # OU Mean 31.301884 > # OU Cor 0.273331 > # OU eCorStd 0.150227 > # OU tCor 1.819459 > # OU tSigCor 0.076332 > # OU log10tSigCor 1.117294 > # > ##Slc NOver Mean SFStd SFSNR Min Max SFOut ZMax Trend > 0 802 710.16 4.0282 176.30 700.99 719.10 0 1.86 0.1133 > 1 792 800.50 2.3820 336.06 794.63 806.45 0 2.09 0.1016 > 2 749 798.92 1.4041 569.00 794.01 802.68 0 2.56 0.0259 > 3 901 850.98 2.4112 352.93 844.78 856.03 0 2.11 0.0541 > 4 1102 751.45 1.8588 404.27 745.07 756.79 0 2.69 -0.0110 > 5 1419 842.61 1.4566 578.46 838.50 846.58 0 2.10 0.0302 > 6 1515 812.11 1.8256 444.84 807.73 823.31 2 3.85 0.0452 > 7 1643 896.05 1.7593 509.33 891.18 899.55 0 2.31 -0.0032 > 8 1656 902.37 1.1276 800.27 898.76 905.52 0 2.46 0.0023 > 9 1827 991.34 1.3256 747.85 988.74 993.90 0 1.69 -0.0113 > 10 1929 947.41 1.2123 781.47 942.96 950.44 1 2.83 0.0337 > 11 1930 1058.96 1.4401 735.31 1053.59 1061.73 1 2.89 0.0165 > 12 1856 1041.14 1.0919 953.49 1037.65 1044.65 0 2.39 -0.0073 > 13 1827 1108.90 0.9528 1163.87 1105.51 1111.37 1 2.75 0.0154 > 14 1743 1040.16 1.0334 1006.51 1037.04 1042.70 0 2.47 0.0033 > 15 1690 1109.25 1.1567 959.01 1105.44 1112.41 0 2.55 0.0027 > 16 1531 1080.77 1.3189 819.42 1074.60 1084.36 1 3.46 -0.0214 > 17 1401 1128.64 1.8007 626.79 1123.37 1132.94 0 2.37 -0.0533 > 18 1229 1087.47 1.4961 726.87 1082.90 1090.38 0 2.45 -0.0075 > 19 1036 1125.01 1.9457 578.22 1117.93 1129.73 1 2.76 0.0056 > 20 811 1056.52 1.8471 572.00 1051.30 1061.48 0 2.19 0.0009 > 21 597 913.11 4.5987 198.56 898.56 923.17 0 2.47 -0.0416 > 22 256 664.28 9.0225 73.62 646.30 683.92 0 1.88 0.0574 > 23 12 271.97 10.5053 25.89 241.67 295.42 0 2.25 0.0053 > > --

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RE: [Freesurfer] good news and bad news
by Bruce Fischl 22 Nov '05

22 Nov '05

sorry, I didn't mean to say it is half broken. I meant that we haven't had time to go through the set of regression and system tests that we want to in order to make sure that everything works as well as we can make it. We've been going through that process and finding little things that we can improve, and have decided to make the improvements and retest rather than release things. Mostly the current dev version works extremely well. sorry for the confusion. Bruce On Sat, 22 Oct 2005, Fornito, Alexander wrote: > Hi Bruce, Just wanted to clarify: When you say the dev releases are "half > broken" does that mean there may be some minor niggles but results > generated should be (on the whole) trustworthy, or does it mean that we > should definitely avoid doing a complete study (eg., from surface > generation through to morphometric or fMR analysis) using a dev version? > Thanks, Alex > > Alex Fornito > M.Psych/PhD (clin. neuro.) candidate > Melbourne Neuropsychiatry Centre and Department of Psychology > The University of Melbourne > alexander.fornito(a)wh.org.au > > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl > Sent: Sat 22/10/2005 2:57 AM > To: freesurfer(a)surfer.nmr.mgh.harvard.edu > Subject: [Freesurfer] good news and bad news > > Hi All, > > I'll start with the good: > > thanks to Anders Dale (UCSD), Howard Pinsky (CorTechs) and Christian > Euseman (MGH), we have finally signed an open source agreement for > FreeSurfer. We will be posting a "read-only" tarball on the website in the > next couple of weeks, and anyone is free to download it and look at it. We > will *not* be supporting a make/configure type env for people to download > and build, as we simply aren't ready to do so. We plan to implement such a > procedure, but it will be a while. Instead of waiting until that was ready, > I thought people would like to have access to the source to at least see > what things are doing, and be able to see file formats and such. > > Now the bad news. I know we've been promising a new release, but it is > being delayed for another month or two. Partially this is due to the > opensourcing, which has taken our time and resources, but it is also > because we *really* don't want to release something that is half broken. > There are also a number of features that we want to get into the release, > and not have updates to it right away. We have continued to post current > versions on the website as prereleases, but *please* be aware that we can't > guarantee that these versions will be compatible with the one we ultimately > release. I think they will be, but can't say for sure. Our hope is that > datasets processed with the prerelease versions can be rerun automatically > with recon-all --rerun or something like that, but again, no guarantees. > > cheers, > Bruce > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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MAC OS X Tiger version
by peggy christidis 22 Nov '05

22 Nov '05

Does the MAC OS X Tiger developmental release of FreeSurfer have the MNI tools? I ask this because I installed this version and created a surface (via the GUI for demonstrative purposes), but I get that "cannot find talairach.xfm file" comment in the logs and no talairach coordinates for my surface. Thanks, Peggy

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request
by hengameh haghighat 22 Nov '05

22 Nov '05

Dear Professor Bruce Fischle Thank you for your reply . I would like to use Freesurfer for segmenting the hippocampus . I am a MSC student and the dead time of my thesis is very close. Please explain me in detail how can I use the software for segmenting . Thanks in advance for your helping. Best Regard -- Tehran University of Medical Sciences (www.tums.ac.ir)

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Postdoc Position in Berlin, Germany
by Hauke Heekeren 22 Nov '05

22 Nov '05

The independent junior research group "Neurocognition of Decision-Making" at the Max-Planck-Institute for Human Development in Berlin, Germany invites applications for a postdoctoral position ("Wissenschaftlicher Mitarbeiter"). We are a young, interdisciplinary team investigating mechanisms of decision-making in the human brain. We employ a combination of psychophysical methods, computational modeling, functional and structural neuroimaging (MRI, MEG, EEG, simultaneous EEG-fMRI), and we are using both the MPI's as well as the Berlin NeuroImaging Center's infrastructure. A successful applicant will need to have a PhD in a field related to cognitive neuroscience (e.g. informatics, neuroscience, engineering, physics, medicine, psychology). Applicants should have a background in computational (cognitive) neuroscience and/or neuroimaging (experience with MEG, EEG, fMRI or other brain imaging techniques) and experience in experimental design, computer programming and statistical methods. The position is for three years, available immediately and has the option of extension. Salary will be according to "EG 13 TVöD", formerly BAT Ib/IIa. For further information, please email Hauke Heekeren at heekeren(a)mpib-berlin.mpg.de. http://www.heekerenlab.org/ http://www.mpib-berlin.mpg.de/en/forschung/snwg/

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Freesurfer