Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Anova Statistical Modelling
by mmoayedi＠uhnres.utoronto.ca 04 Aug '09

04 Aug '09

Hello FreeSurfer Experts, I am trying to run a contrast comparing 3 different classes, and using one covariate as follows (truncated for simplicity's sake!): GroupDescriptorFile 1 Title CTA TMD Patients Low vs Patient High vs Controls Class Control plus blue Class Patient_Low circle green Class Patient_High cross red Variables Age Input c3 Control 25 Input c4 Control 27 .. .. .. Input p1 Patient_Low 22 Input p2 Patient_Low 20 .. .. .. Input p12 Patient_High 50 Input p13 Patient_High 59 Input p14 Patient_High 18 I was wondering how I can 1) Compare cortical thickness between the 3 groups, using the variable as a covariate of no interest and, subsequently, compare between the age slopes of the 3 classes. Any (and all) help is greatly appreciated. Regards, Massieh Moayedi PhD Student Institute of Medical Science University of Toronto Department of Brain, Imaging and Behaviour- Systems Neurosciene Toronto Western Research Institute University Health Network

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Re: [Freesurfer] Registering aseg to base for volume overlap calc ulations
by Elizabeth Selgrade 04 Aug '09

04 Aug '09

Martin and FreeSurfer Users, A few more questions. What is the best way to apply this transform to my aseg.mgz? I've tried using mri_label2vol, but that fails because the transform is a .lta instead of a .dat. Then I used tkregister2 to register my timepoint's aseg.mgz to the base's norm.mgz with the --lta flag, thinking that this would save my .lta as a .dat. But, when I do this (tkregister2 then mri_label2vol) for multiple timepoints and compare the results, the scans are still not overlapping. So, is there a way to change .lta files into .dat files? Or is there a different tool that I should be using to apply the transform? Thank you for your help! Liz Selgrade -----Original Message----- From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] Sent: Monday, August 03, 2009 5:28 PM To: Elizabeth Selgrade Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registering aseg to base for volume overlap calc ulations Liz, to be precise, this is true for the standard FS stream. The longitudinal stream is different, as in FS 4.4 the base actually lives in two similar, but slightly different spaces, because the template is created for T1 and recreated for the norm.mgz. The aseg is in the space of the norm and the maps, I pointed you to, map to that space. We improved the base for the next FS release 4.5, where it lives only in one space, to make things easier. Best, Martin On Mon, 2009-08-03 at 17:05 -0400, Martin Reuter wrote: > Its in the native space of the TP (orig, nu, T1, norm, brainmask, > aseg, brain .. all in the same space). > > -Martin > > On Mon, 2009-08-03 at 16:40 -0400, Elizabeth Selgrade wrote: > > Hi Martin, > > > > Thanks for the quick response. I have a follow-up question: In what > > space do the segmentations take place? (What space is aseg.mgz in?) > > I'm assuming that it must be in the timepoint's native space in > > order to use the inverse transform you pointed me to, but I had > > always thought that they were in a normalized space. > > > > Thank you again! > > Liz > > > > -----Original Message----- > > From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] > > Sent: Monday, August 03, 2009 4:35 PM > > To: Elizabeth Selgrade > > Cc: 'freesurfer(a)nmr.mgh.harvard.edu' > > Subject: Re: [Freesurfer] Registering aseg to base for volume > > overlap calculations > > > > Hi Liz, > > > > the registrations are stored in > > baseid/mri/transforms > > look for files baseid_to_tpNid.lta > > and the inverse tpNid_to_baseid.lta (which is the map you are looking for). > > These should align all your TPs to the base space. > > > > > > Best, Martin > > > > On Mon, 2009-08-03 at 16:19 -0400, Elizabeth Selgrade wrote: > > > Hello FreeSurfer Users, > > > > > > I am using the longitudinal stream to look at four > > > timepoints/subject, and I'd like to transform all of my timepoints > > > to the base scan's unbiased space so that I can calculate ROI > > > volume overlap. I have been using tkregister2 to calculate the > > > transform from my scan.base.long/mri/aseg.mgz to > > > base/mri/rawavg.mgz and then using > > mri_label2vol to apply the transform. > > > When I do this for all of my scans, I expect to see that the > > > brains are overlapping in the same space. But, I'm not getting > > > that. Any suggestions for how to get all of these scans back in the base space? > > > > > > Thank you! > > > Liz Selgrade > > > _______________________________________________ > > > 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 > >

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None
by None 04 Aug '09

04 Aug '09

by outgoing.mit.edu (8.13.6/8.12.4) with ESMTP id n74JZLQ3011917 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for <freesurfer(a)nmr.mgh.harvard.edu>; Tue, 4 Aug 2009 15:35:22 -0400 (EDT) Received: from w92exhub7.exchange.mit.edu (18.7.73.13) by w92exedge3.exchange.mit.edu (18.7.73.15) with Microsoft SMTP Server (TLS) id 8.1.375.2; Tue, 4 Aug 2009 15:35:11 -0400 Received: from w92expo3.exchange.mit.edu ([18.7.49.69]) by w92exhub7.exchange.mit.edu ([18.7.73.13]) with mapi; Tue, 4 Aug 2009 15:35:21 -0400 From: Joseph Barrington Keller <jkeller1(a)MIT.EDU> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Date: Tue, 4 Aug 2009 15:35:19 -0400 Thread-Topic: Mapping from Freesurfer to FSL Thread-Index: AQHKFTq0ACWTP37dOkaADhTLpLZLow== Message-ID: <1249414522.fAa381.16150DEC7EF6FBF97BB488FC479FE6AE8930237990187E0(a)w92expo3.exchange.mit.edu> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 X-Scanned-By: MIMEDefang 2.42 X-Spam-Flag: NO X-Spam-Score: 0.00 X-NMR-MGH-MailScanner-Information: Please contact the ISP for more information X-NMR-MGH-MailScanner-ID: n74JZKtn025639 X-NMR-MGH-MailScanner: Not scanned: please contact your Internet E-Mail Service Provider for details X-NMR-MGH-MailScanner-SpamCheck: not spam, SpamAssassin (not cached, score=0.001, required 5, autolearn=disabled, UNPARSEABLE_RELAY 0.00) X-NMR-MGH-MailScanner-From: jkeller1(a)mit.edu X-Spam-Status: No Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by mail.nmr.mgh.harvard.edu id n74JZKtn025639 Subject: [Freesurfer] Mapping from Freesurfer to FSL X-BeenThere: freesurfer(a)nmr.mgh.harvard.edu X-Mailman-Version: 2.1.9 Precedence: list List-Id: <freesurfer.nmr.mgh.harvard.edu> List-Unsubscribe: <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>, <mailto:freesurfer-request@nmr.mgh.harvard.edu?subject=unsubscribe> List-Archive: <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer> List-Post: <mailto:freesurfer@nmr.mgh.harvard.edu> List-Help: <mailto:freesurfer-request@nmr.mgh.harvard.edu?subject=help> List-Subscribe: <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>, <mailto:freesurfer-request@nmr.mgh.harvard.edu?subject=subscribe> X-List-Received-Date: Tue, 04 Aug 2009 19:35:26 -0000 Hello, I'm in the process of trying to map designated voxels from Talairach space in Freesurfer to the corresponding image in subject space in FSL's gui FDT(Probtrackx). Obviously, there will not be a direct mapping between these two coordinate spaces. How would I go about this? Thanks in advance. -Joe

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read_patch.m
by Daniel Wakeman 04 Aug '09

04 Aug '09

Hello, The code in read_patch.m seems strange in the following versions 4.0.1 & 4.3.0. I could be wrong, but usually you have a section at the top describing it, and it doesn't seem to be declared as a function. I have checked the Release Notes and there doesn't seem to be a description of this changing in the recent version. If need be I can download a new version. Is the attached version incorrect? Dan -- BEGIN:VCARD VERSION:3.0 N:Wakeman;Daniel;Gary;; FN:Daniel Gary Wakeman ORG:University of Cambridge; TITLE:Student 2010 EMAIL;type=INTERNET;type=WORK;type=pref:daniel.wakeman@mrc-cbu.cam.ac.uk EMAIL;type=INTERNET;type=HOME:dgwakeman@gmail.com item1.EMAIL;type=INTERNET:dw348@cam.ac.uk item1.X-ABLabel:_$!<Other>!$_ TEL;type=WORK;type=pref:+44 (0) 1223 355 294 ex. 595 TEL;type=CELL:+44 (0) 7877 043 797 item2.TEL:+1 518-291-4347 item2.X-ABLabel:US TEL;type=WORK;type=FAX:+44 (0) 1223 359 062 item3.ADR;type=HOME;type=pref:;;Wolfson College\nBarton Road;Cambridge;Cambridgshire;CB3 9BB;United Kingdom item3.X-ABADR:us item4.X-AIM;type=pref:dgwakeman@mac.com item4.X-ABLabel:Video X-AIM;type=HOME:WakerCrzy0 X-ABUID:F98E7710-43F5-4D9A-992F-E4FD6FFE5B6B\:ABPerson END:VCARD

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Re: [Freesurfer] Registering aseg to base for volume overlap calc ulations
by Martin Reuter 03 Aug '09

03 Aug '09

Its in the native space of the TP (orig, nu, T1, norm, brainmask, aseg, brain .. all in the same space). -Martin On Mon, 2009-08-03 at 16:40 -0400, Elizabeth Selgrade wrote: > Hi Martin, > > Thanks for the quick response. I have a follow-up question: In what space > do the segmentations take place? (What space is aseg.mgz in?) I'm assuming > that it must be in the timepoint's native space in order to use the inverse > transform you pointed me to, but I had always thought that they were in a > normalized space. > > Thank you again! > Liz > > -----Original Message----- > From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu] > Sent: Monday, August 03, 2009 4:35 PM > To: Elizabeth Selgrade > Cc: 'freesurfer(a)nmr.mgh.harvard.edu' > Subject: Re: [Freesurfer] Registering aseg to base for volume overlap > calculations > > Hi Liz, > > the registrations are stored in > baseid/mri/transforms > look for files baseid_to_tpNid.lta > and the inverse tpNid_to_baseid.lta (which is the map you are looking for). > These should align all your TPs to the base space. > > > Best, Martin > > On Mon, 2009-08-03 at 16:19 -0400, Elizabeth Selgrade wrote: > > Hello FreeSurfer Users, > > > > I am using the longitudinal stream to look at four timepoints/subject, > > and I'd like to transform all of my timepoints to the base scan's > > unbiased space so that I can calculate ROI volume overlap. I have > > been using tkregister2 to calculate the transform from my > > scan.base.long/mri/aseg.mgz to base/mri/rawavg.mgz and then using > mri_label2vol to apply the transform. > > When I do this for all of my scans, I expect to see that the brains > > are overlapping in the same space. But, I'm not getting that. Any > > suggestions for how to get all of these scans back in the base space? > > > > Thank you! > > Liz Selgrade > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >

1 1

Registering aseg to base for volume overlap calculations
by Elizabeth Selgrade 03 Aug '09

03 Aug '09

Hello FreeSurfer Users, I am using the longitudinal stream to look at four timepoints/subject, and I'd like to transform all of my timepoints to the base scan's unbiased space so that I can calculate ROI volume overlap. I have been using tkregister2 to calculate the transform from my scan.base.long/mri/aseg.mgz to base/mri/rawavg.mgz and then using mri_label2vol to apply the transform. When I do this for all of my scans, I expect to see that the brains are overlapping in the same space. But, I'm not getting that. Any suggestions for how to get all of these scans back in the base space? Thank you! Liz Selgrade

2 1

Seg fault during autorecon2
by Nathan Dankner 03 Aug '09

03 Aug '09

Hello all, I¹ve recently been having issues with several scans exiting with errors after autorecon2, and they have exclusively been segmentation faults. I¹m running stable version 4.2 on a machine with plenty of memory. Any ideas what the problem might be? I¹ve included the recon-all.log files for two subjects who have had the problem. Thanks, Nathan

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Segmentation fault
by Ritobrato Datta 03 Aug '09

03 Aug '09

Hello All, I got this error when I ran recon-all -all. I changed machines and the same dataset went all the way through without any errors. I ran another dataset with the machine "taxi" and it ran fine. Any suggestions will be helpful. _________________________________________________________________________________________________________________ SUBJECTS_DIR is /jet/kadivar/freesurfer Segmentation fault Linux taxi.penn.edu 2.8.10-128.1.1.e5 #1 SMP Thu May 7 10:35:59 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Aug 1 06:20:17 EDT 2009 _________________________________________________________________________________________________________________ Thanks Ri Ritobrato Datta, Ph.D. Post Doctoral Fellow Department of Neurology Center for Functional Neuroimaging University of Pennsylvania School of Medicine 3rd Floor Gates Building 3400 Spruce St. Philadelphia Pa 19104

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Postdoctoral Position, University of California, San Diego
by Don Hagler 02 Aug '09

02 Aug '09

Postdoctoral Research Scholar Position in Behavior Genetics and Neuroimaging Departments of Psychiatry and Radiology, University of California, San Diego The Departments of Psychiatry and Radiology at the University of California, San Diego are pleased to invite applications for a postdoctoral research scholar position in neuroimaging and behavior genetics under the direction of Drs. Anders Dale (Neuroscience and Radiology) and William Kremen (Psychiatry). Responsibilities will include analysis of MRI, genetic, and behavioral data collected for the NIH/NIA-funded Vietnam-Era Twin Study of Aging (VETSA). The successful candidate will receive training in psychometric techniques (particularly twin analyses) and the application and development of analysis tools for neuroimaging data (including structural MRI, DTI, fMRI, and ASL). The postdoctoral candidate will be encouraged to develop his or her own research projects that fit within the overall scope of the project. VETSA is a unique longitudinal study of over 600 middle-aged male twin pairs that focuses on understanding cognitive and brain aging. Over 500 twins have undergone structural MRI and DTI in VETSA wave 1. A variety of additional information was also collected, including neurocognitive, personality, and psychosocial assessments, medical history interviews, blood pressure, pulmonary function, and hormonal levels. DNA has been obtained from all subjects and they have been genotyped for APOE. Genome-wide genotyping of all VETSA subjects is planned. Wave 2 of the project will acquire five-year follow-up data, and also include fMRI and ASL scans. Applicants for the position must have completed relevant Ph.D. research activities within the past five years. Applications from many disciplines may be considered, and the position is open to qualified international applicants. Experience or expertise in the following areas is highly desired: 1. computer programming (especially MATLAB, C/C++, or similar) 2. neuroimaging analysis methods (especially FreeSurfer) 3. structural MRI, DTI, fMRI, ASL 4. scientific writing 5. advanced statistical analyses 6. twin modeling (especially using Mx software) 7. genetics This posting is for a 2-year appointment beginning immediately. Salary will be consistent with the NIH/NRSA levels in accordance with the University of California, San Diego policies for Postdoctoral trainees. Compensation includes full staff benefits, including health insurance, and vacation time. Review of applications will begin immediately and will continue until the position is filled. To apply, please send your CV, a brief statement of research interests and goals, and any selected reprints to wkremen(a)ucsd.edu and amdale(a)ucsd.edu with the subject line "VETSA Postdoctoral position". Letters of reference will be required before final approval of hiring. Informal inquiries for more details are welcome. _________________________________________________________________ Get back to school stuff for them and cashback for you. http://www.bing.com/cashback?form=MSHYCB&publ=WLHMTAG&crea=TEXT_MSHYCB_Back…

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RES: Recon-all
by Pedro Paulo de Magalhaes Oliveira Jr 01 Aug '09

01 Aug '09

You can run n recon-all simultaneously where n is the number of cores you have in your machine. In a dual core 2 recon-all In a quad-core 4 recon-all In a MacPro with 8 core you can run 8 recon-all You also should have at least 1GB per recon-all Enviado do meu celular Nokia -----Msg original----- De: Jesse Bledsoe Enviada: 01/08/2009 18:52:57 Assunto: [Freesurfer] Recon-all Hi Everyone, How many reconstructions (recon-all) can one run at a time? It is working nicely (30 + hours) with one going but I have many subjects to reconstruct - can I run 4 or 5 without problems? Thanks, Jesse -- Jesse Bledsoe, M.A. Clinical Psychology Center for Neurodevelopmental Study Michigan State University 110E Psychology Building East Lansing, MI 48824 ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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