Freesurfer

freesurfer@nmr.mgh.harvard.edu

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neuroimaging job announcement
by David Ziegler 30 Nov '05

30 Nov '05

The Behavioral Neuroscience Lab at MIT is seeking a technical assistant who will take a lead role in the design, implementation, and analysis of our structural and functional MRI studies. A candidate with Freesurfer/FSL experience will have a distinct advantage. Here is a link to the full job description and online application page: http://sh.webhire.com/servlet/av/jd?ai=631&ji=1642175&sn=I -- David A. Ziegler Department of Brain and Cognitive Sciences Massachusetts Institute of Technology Building 46-5121, 32 Vassar St Cambridge, MA 02139 Tel: 617-258-0765 Fax: 617-253-1504 daz(a)mit.edu <mailto:daz@mit.edu>

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RE: [Freesurfer] version history question
by Goldman, Aaron (NIH/NIMH) 29 Nov '05

29 Nov '05

Okay. Related to that question, if I reran people with the latest tools, would it be possible/make sense to read in my control point files from the old version? Thanks, -Aaron- -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, November 29, 2005 4:17 PM To: Goldman, Aaron (NIH/NIMH) Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] version history question Hi Aaron, one of the things we are trying to put in place is something like recon-all -rerun that will retain all manual interventions but reapply the newest tool to all your data. And yes, those tools have changed in the last year so you don't want to compare across versions if you can help it. cheers, Bruce On Tue, 29 Nov 2005, Goldman, Aaron (NIH/NIMH) wrote: > Hi, I'm interested in analyzing subcortical segmentations, and have a question about potential systematic differences between freesurfer versions. Specifically, I have a large number of subjects who've been through a year-old version of recon-all -stage1 (the skull strip, normalization, etc), and was wondering if I need to keep using the old version for consistency's sake. Have those initial steps been substantially upgraded or changed over the past year? Also, is there somewhere I can find a guide to version history? > > > > The versions concerned are: > > OLD: 08/31/04, recon-all version 1.5, tosa > > NEW: 09/28/05, recon-all version 1.114, nicks > > > > Thanks, > > > > -Aaron- > > > > Aaron L. Goldman > > Post-Bacc IRTA > > Genes, Cognition and Psychosis Program, NIMH > > Building 10, Room 3C108 > > Phone: (301) 435-0944 > > Email: aarong(a)mail.nih.gov > > > >

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version history question
by Goldman, Aaron (NIH/NIMH) 29 Nov '05

29 Nov '05

Hi, I'm interested in analyzing subcortical segmentations, and have a question about potential systematic differences between freesurfer versions. Specifically, I have a large number of subjects who've been through a year-old version of recon-all -stage1 (the skull strip, normalization, etc), and was wondering if I need to keep using the old version for consistency's sake. Have those initial steps been substantially upgraded or changed over the past year? Also, is there somewhere I can find a guide to version history? The versions concerned are: OLD: 08/31/04, recon-all version 1.5, tosa NEW: 09/28/05, recon-all version 1.114, nicks Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: aarong(a)mail.nih.gov

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mri_ca_normalize error
by Michele Perry 28 Nov '05

28 Nov '05

Hi, mri_ca_normalize failed for a subject. Here is the CA normalize portion of recon-all.log: =========================================== CA Normalize Thu Nov 17 17:02:05 PST 2005 $SUBJECTS_DIR/<subjid>/mri mri_ca_normalize -mask brain.mgz nu.mgz /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta norm.mgz using MR volume brain.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca'... setting gca type = Normal gca type Direction cosines read: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000 x_a = 0.0000, y_a = 0.0000, z_a = 1.0000 x_s = 0.0000, y_s = -1.0000, z_s = 0.0000 c_r = 0.0000, c_a = 0.0000, c_s = 0.0000 reading transform from 'transforms/talairach.lta'... mghRead: encountered error executing: 'zcat $SUBJECTS_DIR/<subjid>/mri/nu.mgz',frame -1 mri_ca_normalize: could not read input MR volume from nu.mgz reading input volume from nu.mgz... ERROR: mri_ca_normalize with non-zero status ======================================================= $SUBJECTS_DIR/<subjid>/mri contains nu.mgz and the talairach looks normal. How do I fix this? Michele

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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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