Freesurfer

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Re: [Freesurfer] volumes per lobe
by MAHINDA YOGARAJAH 12 Oct '12

12 Oct '12

Dear Experts, As an addendum to the last post I made here are the commands I propose to use to extract lobar measures for GM and WM. I would be grateful for input. GM Lobar Values (1) mri_annotation2label --subject subject1 --hemi ?h --lobesStrict lobesfile (2) mri_anatomical_stats –mgz –cortex ../label/?h.cortex.label –f ../stats/?h.lobesfiles.stats –b –a ../label/?h.lobesfile.annot subject1 ?h white Q: Is this valid? Q:Do I need to include that part of the command in italics - is it not redundant given the use of the ?h.lobesfile.annot - using one or the other does give a different result at the top of the stats file (namely NumVert, WhiteSurfArea, and mean thickness which disappears if ?h.cortex.label is not passed) - why is this ? WM Lobar Values (1) mri_annotation2label --subject subject1 –hemi ?h --lobesStrict lobesfile (2) mri_aparc2seg --s subject1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.lobar.mgz --ctxseg aparc+aseg.mgz --annot ?h.lobesfile.annot Q: Is this valid ? Q: Do I need all the items in italics - they are present in the recon-all logfile but not in some forum posts on similar topics. (3a) mri_segstats --seg mri/wmparc.lobar.mgz --sum stats/wmparc.lobar.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject1 --surf-wm-vol --surf-ctx-vol --totalgray --ctab newcolourtable --etiv OR (3b) mri_segstats --seg mri/wmparc.lobar.mgz --sum stats/wmparc.lobar.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/norm.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject1 --surf-wm-vol --ctab newcolourtable --etiv Q: Which of these should I be using - the latter is based on the recon-all log file, while the former is based on forum posts - what are the differences (as highlighted in italics). Thanks. Mahinda

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mri_ms_fitparms?
by dgw 12 Oct '12

12 Oct '12

Hi, >From the wiki (http://www.freesurfer.net/fswiki/mri_ms_fitparms) I can see that mri_ms_fitparms can accept and afi map. Can someone tell me what assumptions the -afi subcommand makes about the position of the afi map relative to the flash volumes? does it calculate everything in scanner coordinates, or do I need to register them to one another? Thanks, D

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Re: [Freesurfer] volumes per lobe
by MAHINDA YOGARAJAH 12 Oct '12

12 Oct '12

Dear FreeSurfer Experts, I write in regard to the posting on calculating GM measures on a lobar basis. I had a couple of quick questions: 1) Having derived a lobesfile using mri_annotation2label --subject <name> --hemi lh --lobesStrict lobesfile one uses mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.lobesfile.stats -b -a ../label/lh.lobesfile.annot subject lh white a) Why is the -cortex ../label/lh.cortex.label option needed ? I thought this is needed if one wants to pass cortical label for computing statisitcs across all of the cortex ? When I repeat the command without it the stats at the bottom of the lobar stats file are the same. However the total number of vertices and white surface area total at the top of the stats file are different and without the -cortex option the average thickness at the top disappears - why is this ? Should the cortex flag be included or not for lobar GM volumes b) Does the flag white refer to areas based on white matter in which case if one wants areas based on pial surface should pial flag be used ? 2) What would the approach be to get lobar measures as above but for white matter instead ? Thanks. Mahinda

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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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