Freesurfer June 2010

freesurfer@nmr.mgh.harvard.edu

97 participants
138 discussions

MMIL postdoctoral position
by Don Hagler 14 Jun '10

14 Jun '10

Postdoctoral Research Scholar Position, Multimodal Imaging Laboratory, University of California, San Diego The Multimodal Imaging Laboratory (MMIL) at the University of California, San Diego invites applications for a postdoctoral research scholar position under the direction of Drs. Donald Hagler and Anders Dale. The successful candidate will join a multi-disciplinary team of scientists, programmers, and support staff addressing a variety of neuroscience questions using multimodal brain imaging, electrophysiology, behavior, and genetics. An important component of the work done at MMIL, and an integral role of the currently announced position, is the development and improvement of methods for the analysis of neuroimaging data. This will include extending our recent work on a white matter fiber tract atlas (Hagler et al., HBM 2009) to encompass a more diverse population of subjects, additional fiber tracts, and a larger age range, including infants. The postdoctoral researcher will receive training in brain imaging and methods development, and will be encouraged to develop his or her own research projects. 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. Proficiency in the following areas is required: 1. computer programming (e.g. MATLAB, C/C++) 2. scientific writing Experience and/or interest in the following areas is desired: 1. structural MRI, diffusion MRI 2. neuroimaging analysis software (e.g. FreeSurfer, FSL) 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 dhaglerjr(a)hotmail.com with the subject line "MMIL postdoctoral position". Letters of reference will be required before final approval of hiring. Informal inquiries for more details are welcome. _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28…

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Calc stats on ROI in qdec
by Jeff Sadino 14 Jun '10

14 Jun '10

Hello, I am wondering if it is possible to calculate t-values and significance of a whole ROI in qdec, version 1.2. Right now, I have no problem doing it on a point-by-point basis, but I want to do whole ROI analysis within qdec. For example, I want to know the p-value of the whole lh_superiorparietal region for the "Does the average thickness differ between HIV and Control?" contrast. Your help is always appreciated! Mahalo, Jeff

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Re: [Freesurfer] make_average_subject with large cohorts
by Nick Schmansky 14 Jun '10

14 Jun '10

Marie, I fixed the memory leak that was causing your out-of-memory error when running mris_make_average_surface. A new mris_make_average_surface for Mac Intel Leopard is posted here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-int… I'm still looking into the mri_average failure. I dont know what to say about the license error, as the code that handles the license hasnt changed since v2.0. As an aside, I'm skeptical of the utility of a volume or surface composed of 400+ subjects. The volume will be too blurry to be of use, and the surface will have lost any group-specific patterns that might have existed. If retaining the unique morphometric properties of your subject set is important, you might want to consider using just 20 or so randomly chosen subjects. Perhaps Bruce or others can comment. Nick On Wed, 2010-06-02 at 18:53 +0200, Marie Schaer wrote: > Hi Nick, > > Thank you for your response. I added the flag --debug, please find in > attachment the log. I am working on a Mac Intel Quad-Core Intel Xeon, > Processor 3 GHz, RAM 5GB. I also tried with another similar machine > which 9GB, but it exited with the same error exactly at the same > point. Even using the -no-aseg option it stops exactly at the same > point. I also provide you a screenshot with the top command running, a > few minutes before the error, and just after the error. > > As for the license error, I just had this problem using the Freesurfer > version 4.5, and you are right, it may be a connection problem because > our data are on a server (mounted with afp). It is however strange > that it exits always at exactly the same point... Anyway, no license > problem with version 4.4 or 4.3. > > Many thanks for your help, > > Marie > > On 1 juin 10, at 16:54, Nick Schmansky wrote: > > > can you try adding the flag --debug to make_average_volume? it will > > output a lot of stuff, but will pinpoint at which stage it is running > > out of memory. also, try running 'top' in another terminal to monitor > > the amount of memory it's consuming while running. > > > > as for the license error, that is bizarre, i can't think of a reason > > for > > that, unless your subjects are located on an NFS drive (a network). > > we've seen lots of problems with NFS and the Mac OS, where the > > connection drops for a couple seconds. > > > > n. > > > > > > On Mon, 2010-05-31 at 22:39 +0200, Marie Schaer wrote: > >> Hi everyone, > >> > >> I did not find a solution to my problem yet: how to launch > >> make_average_subject / make_average_volume / make_average_surface > >> on a > >> large number of subjects on a Mac Intel? Did someone encounter this > >> error before? > >> > >> Many thanks in advance for your help, > >> > >> Marie > >> > >> On 29 mai 10, at 20:07, Marie Schaer wrote: > >> > >>> > >>> Hi Nick, > >>> > >>> Sorry for disturbing again. As advised, I tried to launch separately > >>> make_average_volume and make_average_surface. Even with the --no- > >>> aseg > >>> option with make_average_volume I got the "cannot allocate memory" > >>> error. And with the make_average_surface I got the "license error" > >>> in > >>> the middle of one subject processing... Any idea? > >>> > >>> Thank you very much, > >>> > >>> Marie > >>> > >>> > >>> On 28 mai 10, at 21:37, Nick Schmansky wrote: > >>> > >>>> try adding --no-aseg to the command line. that out-of-memory error > >>>> seems to originate with creation of the average aseg.mgz file > >>>> (hopefully > >>>> you wont need it for your subject set, typically you dont need > >>>> aseg.mgz > >>>> since aseg stats are usually gathered from a set of aseg.stats > >>>> files, > >>>> not from an average aseg.mgz). > >>>> > >>>> doug: maybe we should make --no-aseg the default? > >>>> > >>>> n. > >>>> > >>>> > >>>> On Fri, 2010-05-28 at 21:31 +0200, Marie Schaer wrote: > >>>>> Hello everybody, > >>>>> > >>>>> I have a problem running make_average_subject for a large number > >>>>> of > >>>>> subjects (>400) on a Mac Intel. I tried with different Freesurfer > >>>>> versions (all the log outputs are attached). Using the freesurfer > >>>>> version 4.3 and 4.4 the make_average_subject script always stop at > >>>>> the > >>>>> 297th subject with the error "Cannot allocate memory". I already > >>>>> tried > >>>>> to uncomment the line "limit descriptors unlimited" or to set it > >>>>> to > >>>>> various values, as proposed in the mailing list, but without > >>>>> success > >>>>> (it always stop at the 297th subject). Then I tried with the > >>>>> Freesurfer version 4.5 (therefore I had to recompute the > >>>>> lh.inflated.H > >>>>> and lh.inflated.K which are not automatically produced in previous > >>>>> versions), but with the 4.5 version I got a strange "license > >>>>> error" > >>>>> message in the middle of the script (and my licence is certainly > >>>>> fine > >>>>> as I can run any other script without problems). > >>>>> > >>>>> Does anyone have an idea? Many thanks in advance for your precious > >>>>> help, > >>>>> > >>>>> Marie > >>>>> > >>>>> _______________________________________________ > >>>>> 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 > >>>> > >>>> > >>>> 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(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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Depth of sulci from ?h.sulc
by Lena Palaniyappan 13 Jun '10

13 Jun '10

I located some discussions but could noit figure out how can I obtain numerical depth values from ?h.sulc files. I need to find the sulcal dept of certain sulci as defined in aparc.a2009 Thanks in advance Lena This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Re: [Freesurfer] R: R: How means all the output file from a segmentation?
by Bruce Fischl 13 Jun '10

13 Jun '10

vol2surf won't work - that's for scalar maps. You need a tesselation I guess, which you can generate with mri_tesselate or mri_mc. If it's just for visualization though you could probably just load it into freeview and look at it as an isosurface of the volume. cheers Bruce On Sun, 13 Jun 2010, Leonardo Chesi wrote: > Hi bruce, > my goal is to obtain a 3D surface of the hippocampal region for a visual > comparison with a manual segmentation made by a neuroradiologist. Today I > managed to extract the volume with mri_binarize but I can't transform it in > a surface that tkurfer can visualize. For that I try to use mri_vol2surf but > I obtain a surface with 0 vertices. Can you help me?? > Cheers > Leonardo > > -----Messaggio originale----- > Da: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Inviato: domenica 13 giugno 2010 14.29 > A: Leonardo Chesi > Cc: freesurfer(a)nmr.mgh.harvard.edu; Ruopeng Wang > Oggetto: Re: R: [Freesurfer] How means all the output file from a > segmentation? > > Hi Leonardo, > > you just want to visualize it? Can you explain your goals a bit better? > You could view it in freeview as an isosurface if you wanted. Ruopeng: is > there wiki documentation for this? > > > cheers > Bruce > > > On Sun, 13 Jun 2010, Leonardo Chesi wrote: > >> >> Hi Bruce, Thanks for your attention, >> Can you write for me a sample line where I want to compute a 3D volume of >> the hippocampal? And I can show it with tksurfer? Thanks >> Leonardo >> >> -----Messaggio originale----- >> Da: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Inviato: sabato 12 giugno 2010 20.22 >> A: Leonardo Chesi >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Oggetto: Re: [Freesurfer] How means all the output file from a > segmentation? >> >> Hi Leonardo, >> >> the outputs are listed on our wiki. If you want to extract a single >> structure you can use mri_binarize using the indices in the >> $FREESURFER_HOME/FreeSurferColorLUT.txt file. >> >> cheers >> Bruce >> On Sat, 12 Jun 2010, Leonardo >> Chesi wrote: >> >>> Hi, after the segmentation process, we obtain a lots of file that I can't >>> understand what they represent. Infact I know the mean of the file >> aseg.mgz >>> (that is a mask of the segmentation) and norm.mgz but for example I can't >>> understand the difference between brainmask.mgz and brainmask_auto.mgz. >> Can >>> you help me with a list of the output? And can I obtain the volume >> rendering >>> of only one part of the segmented structure? (es. Hippocampal)?? >>> >>> Thanks for your help >>> >>> Leonardo >>> >>> >> >> >> 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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standard deviation map
by Michael Scheel 13 Jun '10

13 Jun '10

Dear FS experts, I have a anatomical scan of a subject with a rare neurogenetical disorder. I'd like to compare this with a age matched control group. How can I visualize a z-score transform map of the cortical thickness, i.e. how would I compute and vizualize the number/amount of standard deviations that my subjects differs from the mean of the control group at each vertex? Thanks, Michael

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Re: [Freesurfer] R: How means all the output file from a segmentation?
by Bruce Fischl 13 Jun '10

13 Jun '10

Hi Leonardo, you just want to visualize it? Can you explain your goals a bit better? You could view it in freeview as an isosurface if you wanted. Ruopeng: is there wiki documentation for this? cheers Bruce On Sun, 13 Jun 2010, Leonardo Chesi wrote: > > Hi Bruce, Thanks for your attention, > Can you write for me a sample line where I want to compute a 3D volume of > the hippocampal? And I can show it with tksurfer? Thanks > Leonardo > > -----Messaggio originale----- > Da: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Inviato: sabato 12 giugno 2010 20.22 > A: Leonardo Chesi > Cc: freesurfer(a)nmr.mgh.harvard.edu > Oggetto: Re: [Freesurfer] How means all the output file from a segmentation? > > Hi Leonardo, > > the outputs are listed on our wiki. If you want to extract a single > structure you can use mri_binarize using the indices in the > $FREESURFER_HOME/FreeSurferColorLUT.txt file. > > cheers > Bruce > On Sat, 12 Jun 2010, Leonardo > Chesi wrote: > >> Hi, after the segmentation process, we obtain a lots of file that I can't >> understand what they represent. Infact I know the mean of the file > aseg.mgz >> (that is a mask of the segmentation) and norm.mgz but for example I can't >> understand the difference between brainmask.mgz and brainmask_auto.mgz. > Can >> you help me with a list of the output? And can I obtain the volume > rendering >> of only one part of the segmented structure? (es. Hippocampal)?? >> >> Thanks for your help >> >> Leonardo >> >> > > > 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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Processing need more time using freesurfer
by Zhangyuanchao 13 Jun '10

13 Jun '10

Hi, expert, I used freesurfer on a 32bit ubuntu operation system some days ago. For one subject, the "recon-all -s $filename -all" command need 30 hours or less. I changed it to 64bit Centos operation system, however, the precessing time needed for one subject seems longer than on 32bit system, It needs nearly 40 hours. I do not know what the matter is. Thanks!

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Re: [Freesurfer] How means all the output file from a segmentation?
by Bruce Fischl 13 Jun '10

13 Jun '10

Hi Leonardo, the outputs are listed on our wiki. If you want to extract a single structure you can use mri_binarize using the indices in the $FREESURFER_HOME/FreeSurferColorLUT.txt file. cheers Bruce On Sat, 12 Jun 2010, Leonardo Chesi wrote: > Hi, after the segmentation process, we obtain a lots of file that I can't > understand what they represent. Infact I know the mean of the file aseg.mgz > (that is a mask of the segmentation) and norm.mgz but for example I can't > understand the difference between brainmask.mgz and brainmask_auto.mgz. Can > you help me with a list of the output? And can I obtain the volume rendering > of only one part of the segmented structure? (es. Hippocampal)?? > > Thanks for your help > > Leonardo > >

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manual entry for mri_concat
by Michael Scheel 13 Jun '10

13 Jun '10

Dear FS experts, I recognized that there is no manual entry for mri_concat and fslcalc.fsl. Although there is an extensive help text just typing the command I would find a manual entry (man mri_concat) including exmaples very helpful (or an entry on the freesurfer command site). Thanks, Michael

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Freesurfer June 2010