Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

Question about inferior temporal lobe topological/control points anomalies
by pietro de rossi 11 Oct '12

11 Oct '12

Dear FreeSurfer users and developers, I'm getting very frequently some bilateral inferior temporal lobe topological/control points anomalies. I attach an example with and without segmentation on. It seems to me that they are not affecting the pial surface's shape (inferior aspect of right temporal lobe attached in first picture. Should I edit and rerun recon? Thank you very much Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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TRACULA trac-all -path ERROR
by Fernando Ventrice 11 Oct '12

11 Oct '12

Dear Freesurfer-Tracula users, I'm trying to use Tracula to analyze some DTI images. I already used Freesurfer and FSL without problems. First of all, my system is the following: Linux Xubuntu 12.04 LTS x86_64 - Intel i7 - 8Gb RAM - Nvidia GeForce GT 520 1GB Freesurfer version 5.1.0 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz) FSL version 5.0.1 (from Neurodebian) The first problem I had was with the first command: "trac-all -prep -c dmrirc_file" gave an error about not finding the 'job' command. This was solved (thanks to Anastasia Yendiki) using: "set runlist=(1)" in the 'dmrirc_file'. Then, I had some problems with the second command: "trac-all -bedp -c dmrirc_file", which gave this error: Queuing preprocessing stages /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 263: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [: xbedpostx_pre: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 472: [: -le: argument expected Queuing parallel processing stage /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [: xbedpostx: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x43: unexpected operator 0 slices processed Queuing post processing stage /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 263: [: NONE: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [: xbedpostx_post: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x: unexpected operator /home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 472: [: -le: argument expected Reading about this on the freesurfer mailing-list I got to the conclusion of running directly: bedpostx /home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dmri (in the middle I learned how to use condor!) It finished without errors. So I went to the last command: "trac-all -path -c dmrirc_file" which complained about not finding the following file: ERROR: Could not open /home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt These files were at "/home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dlabel/mni"... should I copy them to the diff folder?? I send as attachments the error output from "trac-all -path -c dmrirc_file" and the "dmrirc_file" I used. Best regards and thanks a lot! Fernando Ventrice El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar

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TRACULA: multiple bvecs files in one configuration file
by Loi 11 Oct '12

11 Oct '12

Hello, I see in the message thread that as of July 2011 there was no support for multiple bvecs files in one configuration file. Have any changes been made regarding this? And if so, how can I include multiple paths to bvecs files? Thank you, Joy-Loi

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Which atlas to use for optimal parcellation of the auditory cortex (HG and of the PT )?
by Narly Golestani 11 Oct '12

11 Oct '12

Dear all, dear Christophe Destrieux, 1. I would like to know which is the best version of freesurfer to use, or rather regarding the best atlas to call (using a flag) in order to ensure that our parcellation of the auditory cortex, and of the first transverse temporal gyrus and of the planum temporale in particular, are optimal. I see in an email dated Jan 3rd of this year that it was suggested to use the 2009 atlas for this. Is this still the best option to use? 2. and..: Can I invoke this by using the ‘--annot aparc.a2009s’ flag when writing the results to a table after having run recon-all –all using freesurfer version 4.4? If I’m not mistaken, version 4.4 does not generate the 2009 atlas, and I will need to instead run a more recent version of freesurfer. Thanks in advance for any input that you may have, Best wishes, Narly.

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basic comparison
by Jacobs H (NP) 11 Oct '12

11 Oct '12

Hi FreeSurfers, I am preparing a simple presentation, to show some basic stuff in my lab and therefore I would like to compare the cortical thickness of two subjects. Is there a way to do this? For the GLM, I probably have not enough degrees of freedom? Is there a way that I could subtract the two thickness overlays? Thanks Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

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Cognitive Neuroscientist Position, University of Nebraska, Lincoln (fwd)
by Louis Nicholas Vinke 11 Oct '12

11 Oct '12

---------- Forwarded message ---------- Date: Thu, 11 Oct 2012 13:29:03 +0000 From: Nicole Earnest <nearnest2(a)unl.edu> To: "freesurfer-owner(a)nmr.mgh.harvard.edu" <freesurfer-owner(a)nmr.mgh.harvard.edu> Subject: Cognitive Neuroscientist Position, University of Nebraska, Lincoln Please forward the following job ad to your listserv. Thank you. Cognitive Neuroscientist Center for Brain, Biology and Behavior The Center for Brain, Biology and Behavior at the University of Nebraska–Lincoln is recruiting a cognitive neuroscientist with fMRI expertise at the Associate or Full Professor rank. The successful candidate is expected to demonstrate excellence in research including an established record of grant funding. We have preference for candidates who can create and connect to initiatives in traumatic head injury and related areas. The interdisciplinary Center engages a broad spectrum of investigators, including a unique research collaboration with University Athletics, and ishoused within a new 26,000 square foot building. The facility’scenterpiece is a new Skyra 3 Tesla Siemens scanner, as well as 12 high-density EEG/ERP, NIRS and TMS systems. The Skyra is integrated with a 256-electrodehigh-density EEG system and an eye tracker that enable simultaneous recordings. The Center is adjacent to the University’s Holland Computing Center with supercomputer resources and support. The tenure home for the successful candidate will be based on a match between candidate background, preferences and departmental interest. Candidate must have an earned Ph.D. Review of applications will begin December 2, 2012 and continue until the position isfilled. To be considered for the position, please go to http://employment.unl.edu, requisition #120845 and complete the Faculty/Academic Administrative Form. Interested applicants should then submit a letter of application, curriculum vitae, research and teaching statement, pdfs of completed research, and letters of recommendation sent directly from three referees to: Dr. Dennis L. Molfese,Director, The Center for Brain, Biology and Behavior, 238 Burnett Hall, University of Nebraska, Lincoln, NE 68588-0308. Lincoln, Nebraska is a vibrant collegetown of approximately 260,000 that combines the cultural richness of a large university with the affordability of a Midwestern city. The University of Nebraska has an active National Science Foundation ADVANCE gender equity program, and is committed to a pluralistic campus community through affirmative action, equal opportunity, work-life balance, and dual careers. Sincerely, Nikki Nicole Earnest Senior Assistant, Center for Brain, Biology, & Behavior Editorial Assistant-Developmental Neuropsychology University of Nebraska-Lincoln/Psychology Department 324A Burnett Hall Lincoln, NE 68588-0308 Phone: (402)472-0168 Fax: (402)472-4637

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MR Physicist/Scientist Position, University of Nebraska, Lincoln (fwd)
by Louis Nicholas Vinke 11 Oct '12

11 Oct '12

---------- Forwarded message ---------- Date: Thu, 11 Oct 2012 13:28:06 +0000 From: Nicole Earnest <nearnest2(a)unl.edu> To: "freesurfer-owner(a)nmr.mgh.harvard.edu" <freesurfer-owner(a)nmr.mgh.harvard.edu> Subject: MR Physicist/Scientist Position, University of Nebraska, Lincoln Please forward the following job ad to your listserv. Thank you. MR Physicist/Scientist Research Assistant Professor University of Nebraska-Lincoln The University of Nebraska - Lincoln is seeking to hire a MR Physicist/Scientist at the Research Assistant professor level to oversee a new state-of-the-art fMRI facility that includes a new Skyra 3T Siemens fMRI scanner within the Center for Brain, Biology and Behavior at the University of Nebraska, Lincoln. This interdisciplinary Center engages a broad spectrum of investigators and occupies a new 26,000 sq. ft.building. In addition to the Skyra scanner, Center facilities include 12 high-density EEG/ERP and NIRS systems, genetics and endocrine labs, as well as 256-electrode high density EEG/ERP and eye tracker systems integrated with the fMRI that enable simultaneous recordings within test sessions. The Center is adjacent to the University’s Holland Computing Center with supercomputer resources and support. The position will include responsibility for ensuring smooth day-to-day operation of the scanner as well as development of new pulse sequences and hardware to support neuroimaging research conducted on the scanner. The successful candidate will have a Ph.D. in physics, chemistry, biomedical engineering, electrical engineering, or a related field, with at least five years of experience in pulse sequence development, MRI hardware, image reconstruction neuroimaging, or a combination of these fields. Previous experience on Siemens scanners is preferred. The candidate will be expected to develop his or her own successful research and grant-funded programs in neuroimaging, pulse sequence development, image reconstruction, or related academic domains. There will also be opportunities to mentor graduate students and teach courses on MR Physics and other topics of interest to the candidate. In support of these goals, collaboration with Siemens and other research groups/institutions will be encouraged. Compensation is dependent on experience. The successful candidate will be affiliated with an academic department based on a match between candidate background, preferences and departmental interest. Review of applications will begin December 2, 2012 and continue until the position is filled. The start date for this position is July 1, 2013. To be considered for the position, please go to http://employment.unl.edu, requisition #120842 and complete the Faculty/Academic Administrative Form. Interested applicants should then submit a letter of application, curriculum vitae, a research statement, pdfs of completed research papers, and letters of recommendationsent directly from three referees to Dr. Dennis L. Molfese, Director, The Center for Brain, Biology and Behavior, 238 Burnett Hall, University of Nebraska, Lincoln, NE. 68588-0308. Lincoln, Nebraska is a vibrant college town of approximately 260,000 that combines the cultural richness of a large university with the affordability of a Midwestern city. The University of Nebraska has an active National Science Foundation ADVANCE gender equity program, and is committed to a pluralistic campus community through affirmative action, equal opportunity, work-life balance, and dual careers. Inquiries should be sent to Nicole Earnest <nearnest2(a)unl.edu>. Sincerely, Nikki Nicole Earnest Senior Assistant, Center for Brain, Biology, & Behavior Editorial Assistant-Developmental Neuropsychology University of Nebraska-Lincoln/Psychology Department 324A Burnett Hall Lincoln, NE 68588-0308 Phone: (402)472-0168 Fax: (402)472-4637

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Control point edits adversely affect cortical surfaces using FS 5.1
by Vanessa Louise Cropley 11 Oct '12

11 Oct '12

Hi all, I have seen others post a similar problem on the freesurfer mailing list but I could not find a solution. When I edit a volume using control points, I am noticing that the use of CP edits adversely effects the wm/gm surfaces in the resulting re-processed image. Like others have reported, the surfaces are adversely affected in locations distant from the CP edits. The temporal lobes are particularly affected. We are using freesurfer 5.1. I have noticed the following things: 1. The problem occurs irrespective of the number of control points added, i.e. whether >100 or <10 control points added 2. The problem occurred when only one CP was added in a voxel that was clearly wm 3. The problem did not occur after reprocessing with FS 4.5 4. I have tried the flag to disable mri_ca_normalize when reprocessing with –autorecon2. This did not seem to help. I used the command: recon-all –nocanorm –autorecon2-cp –subjid $SUBJ I have screenshots available that illustrate the changes in the surfaces after reprocessing. Could anyone help with this problem? Thank-you, Vanessa

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Boundary problem
by youngmin huh 11 Oct '12

11 Oct '12

Dear all, I'm working with some 3T images and got some bad segmentation problem. I ran recon1 with nuintensitycor-3T, recon2, and recon2-cp after adding some control points. I attached an example. As you can see, it has kind of scrambled white matter boundaries. I wonder how I could fix this. Thanks, youngmin Huh

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Re: [Freesurfer] cortical parcellation question
by Bruce Fischl 11 Oct '12

11 Oct '12

Hi Daniel, no, sorry. The gca is not a cortical atlas. Those labels are stored in the .gcas file and aren't in the same space (in fact, they are in a surface-based spherical coordinate system and not in the volume at all, so not easily combinable). Bruce On Thu, 11 Oct 2012, Daniel Ferreira wrote: > Thanks for the detailed information. > > The mean intensity image (mean_intensity.nii) generated from frame #1 is > almost exactly what I need. This image has all the sub-cortical regions > assigned a discrete integer number (i.e. all the voxels in the left > cerebelllar grey matter = 8 and right = 47). However the whole of the > neocortex is defined as left (intensity = 3) and right (intensity = 42) > only, there are no cortical sub-divisions. > > Is it possible to have the individual neocortical regions assigned a > discrete integer number; (obviously not one already assigned to the other > regions in the mean_intensity.nii image)? For example all inferior temporal > voxels = 9; middle temporal voxels = 10; superior temporal voxels = 11. So > each of the regions defined in the "colortable_desikan_killiany.txt" file > found in the FREESURFER_HOME/average/ directory are also defined in the > mean_intensity.nii image? > > Thanks > > > 2012/10/6 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Daniel > > it's in .gca format, and includes information that wouldn't fit > in a nifti file (e.g. markov relationships). You can use > mri_convert to extract some of the basic info though (e.g. the > most likely class at each location and the mean intensity of the > most likely class) using mri_convert. For example: > > mri_convert $FREESURFER_HOME/average/RB_all_2008-03-26.gca#0 > ./labels.nii > mri_convert $FREESURFER_HOME/average/RB_all_2008-03-26.gca#1 > ./mean_intensity.nii > > > where the #<n> syntax mean extract the nth frame from the 4D gca > volume. Frame 0 is the most likely label and frame 1 is the mean > intensity. Note however that there is lots more info in the .gca > that this doesn't capture such as the MRF parameters I mentioned > above, class variances, other class probabilities, etc.... > cheers > Bruce > > > > > On Thu, 4 Oct 2012, Daniel Ferreira wrote: > > Thanks Bruce, > When you say the atlas itself is included in the > Freesurfer distribution, do > you mean there is a 3D version of it available in > the download? > Also, I am not looking for the individual subjects' > images, I just want a > copy of the final atlas as a 3D image in > analyze/nifti format. (i.e. in the > same format as the Harvard-Oxford atlas that is > downloaded with FSL). > > Thanks a lot. > > Daniel Ferreira > > > > 2012/10/3 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Daniel, > > 1. Do you mean the atlas or the parcellation > of your subjects? > We cannot distribute the individual subjects > in the atlas as the > data was collected under an IRB long ago that > didn't include > this. The atlas itself (summary statistics > derived from those > subjects) is included in the FreeSurfer > distribution. > > 2. The subcortical areas are the same, but not > the cortical > ones. That cortical parcellation is quite > coarse, and while we > did implement it we were never given > permission to distribute > the automated version, so it is not part of > FreeSurfer. The > boundaries that we define are thus different > than that one (and > since the Harvard-Oxford one is based on > volumetric labeling of > folding patterns we found that it contained a > bunch of errors in > which e.g. the wrong side of a sulcus was > labeled) > > cheers > Bruce > > > On Wed, 3 Oct 2012, Daniel Ferreira wrote: > > Dear experts, > I have a couple of questions regarding > the cortical > parcellation atlas that > is used in Freesurfer: > > 1) I would like to know if it is > possible to obtain > the Desikan-Killiany > atlas in 3D analyze/nifti format. With > each region > of the brain assigned a > discrete integer number (for example the > all of the > voxels of the left > inferior temporal lobe have an intensity > = 1, or > the whole of the left > hippocampus = 2). > > 2) Are the Harvard-Oxford cortical and > subcortical > atlases that can be > downloaded with FSL the same as the > cortical > parcellation atlas that is used > in Freesurfer? (i.e. are the > neuroanatomical > boundaries the same; does the > left inferior temporal cortex in the > Freesurfer > cortical parcellation = the > left inferior temporal cortex in the > Harvard-Oxford > atlas downloaded with > FSL) > > Many thanks > > Daniel Ferreira > > > > > > > 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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Freesurfer October 2012