Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

Qdec analysis with one group and two covariates (1 dichotomic, 1 continuous)
by E. Scariati 21 Sep '13

21 Sep '13

Dear Freesurfer experts, I would like to study the relationship between cortical thickness and one clinical variable with qdec, but correcting for age and gender. Given that I have only one group and 2 covariates (one continuous, one dichotomic) I don't know how I should set the design of my analysis in qdec, especially for the gender variable. I have tried two different ways (both DOSS design): 1) selecting Discrete = gender; Continuous = clinical measure; Nuisance factor = age and looking at the contrast called : "Does the correlation between thickness and clinical measure accounting for gender differ from 0? nuisance factor : age" 2) selecting : continuous = clinical measure; Nuisance Factor = age, gender (coded as 1 and 2) and looking at the contrast called : "Does the correlation between thickness and clinical measure differ from 0, nuisance factor : age, gender" But the two contrasts give very different results, which I find very surprising. I exported cortical thickness at the peak significance of the clusters and tried to run a GLM myself in SPSS and it seems that coding gender as a continuous variable with two values (1 and 2) provides the most realistic results. However, I saw many times on the mailing list that you recommend to use gender as a discrete variable, so I am very confused. Could you explain me the difference between these contrasts and help me to identify which one will accurately identify the correlation between cortical thickness and my clinical variable correcting for the effect of age and gender. Thank you in advance for your answer, Best regards Elisa

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postdoc opening
by Thomas Yeo 20 Sep '13

20 Sep '13

Hi, I am looking to hire talented postdocs to develop novel image analysis and machine learning algorithms for the Human Connectome Project data. This is my research webpage: https://sites.google.com/site/yeoyeo02/. See more information below. Regards, Thomas Requirements: Ph.D. in computer science, electrical engineering, statistics or related fields. Candidates should have previously published research in image processing or statistical analysis, preferably in biomedical applications. Compensation: Competitive and commensurate with experience Institutes: Perform ground-breaking research at the National University of Singapore (NUS), while enjoying the beautiful sceneries and cultures of South-East Asia. NUS is a research-intensive university consistently ranked among the top 30 universities in the world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_ra…) Successful candidates may be required to travel between Singapore and the U.S. for certain projects. Contact: Interested candidates should email Thomas (ythomas(a)csail.mit.edu) with CV and/or questions. To apply, please send cover letter, CV and names/contact information of 3 people who can provide letters of reference.

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Ph.D. student openings
by Thomas Yeo 20 Sep '13

20 Sep '13

Hi, I am looking to recruit talented students to develop novel image analysis and machine learning algorithms for the Human Connectome Project data. This is my research webpage: https://sites.google.com/site/yeoyeo02/. See more information below. Regards, Thomas Application Deadline: Nov 1st, 2013 in order to start in Fall 2014 Requirements: Bachelor's or Master's degree in computer science, electrical engineering, statistics or related fields. Ideal candidates should be highly motivated, and have research experience and/or excellent grades. Compensation: Graduate Student Fellowship Institutes: Perform ground-breaking research at the National University of Singapore (NUS), while enjoying the beautiful sceneries and cultures of South-East Asia. NUS is a research-intensive university consistently ranked among the top 30 universities in the world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_ra…) Successful candidates may be required to travel between Singapore and the U.S. for certain projects. Contact: Interested candidates should email Thomas (ythomas(a)csail.mit.edu) with CV and/or questions.

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ACFFWHM for surface-based analyses in FSFAST?
by Caspar M. Schwiedrzik 20 Sep '13

20 Sep '13

Hi Freesurfer Experts, mkanalysis-sess seems to default to a FWHM of 20 for the smooting of the ACF (in version 5.1). I was wondering whether it makes sense to use the same FWHM for volume and surface based analyses of functional data in FSFAST? I seem to remember that the autocorrelations differ between, e.g., grey and white matter, which might be a reason to use a different FWHM on the surface? Thank you very much, Caspar

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Fwd: Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST SEPTEMBER 27, 2013)
by MCLAREN, Donald 20 Sep '13

20 Sep '13

Dear Colleagues, The Neurobureau <http://www.neurobureau.org> is excited to announce a stipend program for Brainhack 2013 <http://www.brainhack.org> (October 23-26 in Sevres, France (just outside of Paris). The stipend program was created following a generous grant from Siemens Healthcare to assist young investigators in attending Brainhack 2013. Without their support, the stipend program would not exist. The stipend program will provide at least 6 stipends for partial or full registration fees [if 24 attendees apply, you have a 25% chance of getting a stipend]. The exact breakdown of stipends provided will depend on the number of applicants and the cost of attending the conference for those applicants. The application for stipend requires: (1) A poster abstract (2) A 1-2 page Brainhack project proposal (pdf format) (3) NIH Biosketch/CV (pdf format) The Brainhack 2013 Organizing Committee will decide which applications will receive stipends based on their abstract and proposed brainhack projects. Details on Brainhack 2013 can be found here<http://www.brainhack.org/?page_id=27784> . The deadline to apply for one of the stipends is 11:59PM EST on September 27th. All decisions will be made by October 3rd and must be accepted within 24 hours of being awarded. If you have any questions please contact myself (mclaren.donald(a)gmail.com) or one of the organizers. Click here to apply. <http://www.brainhack.org/?page_id=40668> Good luck. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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question about TRACULA
by Lucia Billeci 20 Sep '13

20 Sep '13

Dear Madam/Sir, I am trying to applying TRACULA on my data but when I run the following command: trac-all -prep -c /Users/Desktop/FreesurferData/SUBJECT1/dmrirc_subject1 after some processing I obtain the following error xfmrot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.ecclog /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs printf: .999997: expected numeric value printf: .002040: expected numeric value printf: .001230: expected numeric value printf: 8.010424: not completely converted printf: -4.983286: not completely converted printf: -.000389: expected numeric value printf: -.759652: expected numeric value printf: -5.031242: not completely converted printf: 8.006841: not completely converted printf: 7.864457: not completely converted printf: 3.131627: not completely converted printf: -3.216084: not completely converted printf: -1.957800: not completely converted printf: 7.048668: not completely converted printf: 5.956787: not completely converted printf: -7.998542: not completely converted printf: 1.996216: not completely converted printf: 4.004804: not completely converted printf: 7.008384: not completely converted printf: -2.985687: not completely converted printf: 3.996015: not completely converted printf: -.986002: expected numeric value printf: -9.000231: not completely converted printf: .153834: expected numeric value printf: 7.937660: not completely converted printf: .875656: expected numeric value printf: 4.150514: not completely converted printf: -2.115330: not completely converted printf: 8.962086: not completely converted printf: 2.050965: not completely converted printf: 5.758588: not completely converted printf: 8.092588: not completely converted printf: -4.165180: not completely converted printf: 4.753098: not completely converted printf: 5.079427: not completely converted printf: -6.132490: not completely converted printf: -4.000021: not completely converted printf: 4.007709: not completely converted printf: 6.995579: not completely converted printf: -4.879465: not completely converted printf: -7.066532: not completely converted printf: 1.120257: not completely converted printf: -5.186508: not completely converted printf: -2.066011: not completely converted printf: -7.863320: not completely converted printf: -5.008038: not completely converted printf: 5.995846: not completely converted printf: 3.996178: not completely converted printf: 5.717007: not completely converted printf: 5.121524: not completely converted printf: -7.147437: not completely converted printf: 1.743757: not completely converted printf: 7.060581: not completely converted printf: -9.005971: not completely converted printf: -4.251174: not completely converted printf: 5.953915: not completely converted printf: -4.845450: not completely converted printf: -4.010977: not completely converted printf: -8.049025: not completely converted printf: -2.850488: not completely converted printf: 4.005690: not completely converted printf: -7.995851: not completely converted printf: 1.010371: not completely converted printf: -5.118400: not completely converted printf: -4.070279: not completely converted printf: -6.872761: not completely converted printf: 8.143535: not completely converted printf: 4.835332: not completely converted printf: 1.817269: not completely converted printf: 2.268035: not completely converted printf: -2.989943: not completely converted printf: 7.931980: not completely converted printf: -4.199139: not completely converted printf: -3.025800: not completely converted printf: -8.900100: not completely converted grep: /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dcminfo.dat: No such file or directory fslroi /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.nii.gz /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/lowb.nii.gz 0 Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> fslroi <input> <output> <tmin> <tsize> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension. Could you please give me some help? Thanks a lot Best Regards Lucia Billeci_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.billeci(a)ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

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recon-all-hippo-subfeilds
by Anupa AV 20 Sep '13

20 Sep '13

Dear FS experts, I've a query regarding the recon-all analysis. I ran recon-all using the following command eg. recon-all -i location/nc.nii -s NC -all I got the analysis done. Now I'm interested to calculate the hippocampal structures. I knw the command line for that also recon-all -i location/nc.nii -s NC -all -hippo-subfields Problem for me is that I've 45 subjects. I ran recon-all without hippo-subfields commands. i.e. from motion correction to Ex-vivo Entorhinal Cortex Label rh. (log file) Is there any way to do hippo-sufields alone than running the whole steps again (which is very time consuming). Thanks in advance.

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mri_glmfit without --cortex?
by Caspar M. Schwiedrzik 19 Sep '13

19 Sep '13

Hi FreeSurfer Experts, I am trying to run a group analysis with a custom fsaverage for which I do not have a cortex.label file. It seems that in version 5.1, --cortex is called by default. I did not find a flag to turn this off in the documentation or the help. Is there a way to run mri_glmfit without --cortex or an alternative version where this is turned off? Thanks, Caspar

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Re: [Freesurfer] Editing WM
by Louis Nicholas Vinke 19 Sep '13

19 Sep '13

Hi Francesco, If it is the portion of the wm surface I have circled in red, then I'd suggest looking a couple slices anterior and posterior to the current slice and erase any other falsely labeled wm voxels on the wm.mgz, even if the wm surf (blue line) doesn't currently include them. FYI, I've cc'ed the freesurfer list so others can chime in. -Louis On Thu, 12 Sep 2013, Francesco Siciliano wrote: > Hi Louis, > > Thanks for the reply! I've attached a screen cap. Unfortunately, my cursor gets removed from screen caps, but I had the area highlighted with my cursor and the intensity was a value of 1, indicating that I had edited the area prior to running recon-all again. The area in question is the jagged portion of the WM surface in the lower center of the screen above the right temporal lobe). > > -Francesco > ________________________________________ > From: Louis Nicholas Vinke [vinke(a)nmr.mgh.harvard.edu] > Sent: Tuesday, September 10, 2013 5:55 PM > To: Francesco Siciliano > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Editing WM > > Hi Francesco, > Could you maybe send a snapshot of the brainmask and wm volumes where you > are seeing this? > > If you deleted any voxels on the wm mask then they should be a value of 1. > > You might want to look at the ?h.orig.nofix surfaces to see if that area > in question looks better (or at least different). Ultimately the position > of the wm surface is what is important, not the presence or absence of wm > voxels (in the wm.mgz) which basically just initialize the wm surfaces. > -Louis > > On Mon, 9 Sep 2013, Francesco Siciliano wrote: > >> Hi, >> I've noticed that occasionally when I manually edit recons, the white matter >> surface will be drawn to include a portion of the volume where no white matter >> pixels are present. Therefore, when I go to correct the incorrectly drawn >> surface, there are no pixels to delete under the white matter mask. It is >> almost as if I have deleted the pixels already yet I have not and the white >> matter surface is still drawn to include an area where there are no white >> matter pixels. Why could this be happening? Does it matter as long as there >> are no pixels in the incorrect area? >> >> Thank you, >> >> Francesco >> >> Francesco Siciliano, B.A. Research Assistant >> Department of Child and Adolescent Psychiatry >> The New York State Psychiatric Institute >> Columbia University >> 1051 Riverside Drive, Unit 74 >> New York, NY 10032 >> (212) 543-6155 >> >> > > > 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.

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Re: [Freesurfer] green layer in coronal view
by Louis Nicholas Vinke 19 Sep '13

19 Sep '13

Hi Francesco, I have never seen that before. Maybe Ruopeng knows what might be causing this? What's the exact command line you are using and does it appear right when freeview opens? -Louis On Wed, 18 Sep 2013, Francesco Siciliano wrote: > Hi Louis, > I have a quick question when you have a chance. One of the brains that I am > attempting to edit in freeview has a strange > green layer that overlays the volumes in coronal view. I attached a screen > shot. Any ideas what this is or how to get rid > of it? It is only present in coronal view. > > Thanks! > -Francesco >

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Freesurfer September 2013