Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

wm volume
by Lars Tjelta Westlye 05 May '05

05 May '05

Hi all, is there a way I can attain the total wm volume for each of the hemispheres? And is it possible to estimate the wm volume of certain gross anatomical areas, like the different lobes? Thanks! Best wishes, Lars Tjelta Westlye

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Aligning in the command line
by Fornito, Alexander 05 May '05

05 May '05

Hi all, I've noticed you can set expert preferences to align before averaging in the GUI, but how do you do it from the command line? My understanding of the following from the usage is that it assumes that the transform already exists in the /transforms dir, but how do I create this? "The volume can be resampled into another space by supplying a transform using the --apply_transform flag. This reads the transform file and applies the transform (when --apply_inverse_transform is used, the transform is inverted and then applied). An example of a transform file is talairach.xfm as found in subjectid/mri/transforms." Do you create it separately through the MNI tools before proceeding with freesurfer, or is there some way to do it through Fressurfer? Thanks, Alex

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Re: [Freesurfer] Manual editing tips?
by evelina＠nmr.mgh.harvard.edu 04 May '05

04 May '05

Hello Alex, A helpful approach when editing the lateral ventricles is to view the sagittal plane; usually the filling should not extend anterior to the point where the posterior fornix is erased. The axial plane is also useful. The tutorial focuses on the coronal plane, which isn't optimal for determining when to stop the edits (moving anteriorly). Smoothness of the surface -- the aim of manual editing is chiefly to eliminate the defects that the subsequent automated topology fixer cannot likely handle, whether or not they are easily visible on the surface. The large defects outlined in the manual are pretty safe bets for editing in this respect, and there are other anatomical idiosyncrasies that you'll find in normal or other populations which you can anticipate having to edit in order to "force" a topologically correct surface, e.g. brain lesions resulting in large gaps of white matter voxels. It's hard to predict what will need to be edited without having done quite a few brains, but in general your choice is to either: a) err on the side of caution and edit whatever corresponds with a visible defect on the inflated surface, or; b) run the topology fixer first to see how/whether it could handle the remaining visible defects, with the risk that you might need to edit the extra defects afterward, anyway. And of course the Euler number calculation can give you precise information about a hemisphere's topological defect index. I'd recommend routinely editing the standard areas that lead to topological defects (as per the tutorial), then running the automated topology fixer, unless it is a structurally unusual brain with quite large visible defects. The automated topology fixer by and large works, and it's usually a better use of operator time to wait on this 5-hour process rather than spend an hour or so, perhaps pointlesssly, doing extra edits first. The surfaces are generated using the normalized brain volume and not strictly the segmented white matter volume, so edits on the WM volume do not arbitrarily affect the cortical thickness measures. Hope this helps, if not, ask more - > Hi all, > I've noticed that the tutorial's instructions for manual editing of the ventricles stops at about slice 92 (for Bert's data). Does this mean only the posterior portion of the lateral ventricles need to be filled, and that there is no need to continue to fill in the ventricles up to the anterior horns as well? > Also, a couple more queries re: manual editing: > - Sometimes I can see handles emanating from the surface that are not in the areas listed in the manual. Are there any guidelines re: what should be deleted as opposed to what should be filled? > - Are there any guidelines for just how smooth the brain surface should be before moving on to create the final surface? Some of my surfaces appear quite smooth (ie., no obvious handles), although somewhat bumpy, esp. around the posterior-dorsal areas. > - Am I correct in assuming that what is tissue is edited or not will affect surface generation and hence estimates of cortical thickness? In this case, is it advisable to carry out some kind of reliability analysis for morphmoteric studies? > > Thanks for your help, > Alex > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Manual editing tips?
by Fornito, Alexander 03 May '05

03 May '05

Hi all, I've noticed that the tutorial's instructions for manual editing of the ventricles stops at about slice 92 (for Bert's data). Does this mean only the posterior portion of the lateral ventricles need to be filled, and that there is no need to continue to fill in the ventricles up to the anterior horns as well? Also, a couple more queries re: manual editing: - Sometimes I can see handles emanating from the surface that are not in the areas listed in the manual. Are there any guidelines re: what should be deleted as opposed to what should be filled? - Are there any guidelines for just how smooth the brain surface should be before moving on to create the final surface? Some of my surfaces appear quite smooth (ie., no obvious handles), although somewhat bumpy, esp. around the posterior-dorsal areas. - Am I correct in assuming that what is tissue is edited or not will affect surface generation and hence estimates of cortical thickness? In this case, is it advisable to carry out some kind of reliability analysis for morphmoteric studies? Thanks for your help, Alex

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mask to label
by Stephanie McMains 03 May '05

03 May '05

I was wondering if there was a script that allowed me to convert a mask back into a label. I was looking at mri_vol2roi, but it seems to want the input in bshort format. Thanks for any help, Stephanie McMains

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rh.qsphere = rh.orig
by Keyma Prince 03 May '05

03 May '05

Hi, When I run check_subject on one of my subject I get the following message: WARN: rh.qsphere is same size as rh.orig. I am not sure when the rh.qsphere is generated but can you let me know how to correct this problem so i can continue with parcellate_subject. thanks, Keyma Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

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Alignment for cutting planes
by Fornito, Alexander 03 May '05

03 May '05

Hi, I've been working with some images in their native space, and some of them are tilted with respect to the superior-inferior axis. Consequently, when I attempt to manually edit the cutting planes, the plane through the corups callosum does not neatly cleanly separate the two hemispheres (ie., some of the RH may get include with the LH or vice versa). Should all my images be aligned to a template (eg., the MNI brain) via DOF registration before I start creating surfaces in freesurfer, or is there some other solution to the problem? Thanks for your help, Alex

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Vacancy: FreeSurfer Expert
by Moo K. Chung 01 May '05

01 May '05

Sorry to use this email list for job ad. UNIVERSITY OF WISCONSIN-MADISON Position Vacancy Listing PVL# 50206 http://www.ohr.wisc.edu/pvl/pv_050206.html Working title: Information Processing Consultant Official title: SR INFORM PROC CONSLT(S44BN) or INFORM PROCESS CONSLT(S44DN) or ASSOC INF PROC CONSLT(S44FN) Degree and area of specialization: BS in Computer Science, Electrical Engineering or related areas required. MS preferred. Minimum number of years and type of relevant work experience: Minimum 1 year experience working in the methodological aspect of neuroimaging and familiarity with SPM, FreeSurfer, AIR, AFNI and other neuroimage processing/analysis softwares. Demonstrated experience with JAVA, C, MATLAB, VTK, and Unix/Linux required. Principal duties: The Information Processing Consultant will investigate the functional and neuroanatomical correlates using neuroimaging modalities such as MRI, fMRI and DTI. This will be done by performing data analysis correlating neuroanatomical measures (cortical thickness, gray and white matter tissue density) computed from MRI with functional measures (fMRI activation, IQ and face recognition task scores). Under the supervision of faculty members, the person will be expected (i) to perform image processing on MRI using SPM, FreeSurfer, AIR or other available softwares in the lab; (ii) to write computer codes in JAVA, C or MATLAB to perform a specific image processing tasks; (iii) to write Unix/Linux scripts to automate the procedures (iv) to visualize 2D surface and 3D volume images with VTK; (v) to write technical reports; and (vi) advise faculty, staff and students on the use of statistical analysis tools for fMRI protocols. This person will supervise 1 -2 undergraduate students. A period of evaluation will be required ************************* Appointment type: Academic Staff Department(s): GRAD/WAISMAN CENTER Full time salary rate: Minimum $32,895 ANNUAL (12 months) Depending on Qualifications Term: This is a renewable appointment. Appointment percent: 100% Anticipated begin date: MAY 03, 2005 Number of positions: 1 TO INSURE CONSIDERATION Application must be received by: APRIL 28, 2005 HOW TO APPLY: Send resume and cover letter referring to Position Vacancy Listing #50206 to Donna Cole Phone: 608-265-8107 UW-Madison, Waisman Center TTY: 608-263-2473 Waisman Center for Brain Imaging and Behavior Fax: 608-262-9440 1500 Highland Avenue Email: dmcole(a)wisc.edu Madison WI 53705-2280 NOTE: Unless confidentiality is requested in writing, information regarding the names of applicants must be released upon request. Finalists cannot be guaranteed confidentiality. UW-Madison is an equal opportunity/affirmative action employer. We promote excellence through diversity and encourage all qualified individuals to apply. For more academic job opportunities at the University of Wisconsin- Madison please click on PVL Home For more information on the University of Wisconsin-Madison Office of Human Resources please click on http://www.ohr.wisc.edu For more information on the University of Wisconsin-Madison see our home page at http://www.wisc.edu For UW Madison Campus Safety Information see http://www.wisc.edu/Students/Campus_Safety.htm ---------------- MOo K. Chung http://www.stat.wisc.edu/~mchung Assistant Professor 608-262-1287 Department of Statistics Department of Biostatistics and Medical Informatics W.M. Keck Laboratory for Functional Brain Imaging and Behavior University of Wisconsin-Madison

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Brodman areas on cortical sheet
by Darren Weber 30 Apr '05

30 Apr '05

Hi Bruce et al., do you have Brodmann regions defined for the surface template (average7)? If so, how are they defined and what is the practical implementation? Best, Darren -- Darren L. Weber, Ph.D. Visiting Postdoctoral Scholar Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." --Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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Re: [Freesurfer] Dicom
by Joongnam Yang 29 Apr '05

29 Apr '05

Thanks Doug, When I used mri_convert to convert *.dcm to *.hdr, the resulting *.hdr has anterior and posterior reversed. The top was posterior and the bottom was anterior. Is there any way to change, so that the top is anterior and the bottom is posterior? Nam. >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 04/28/05 6:09 PM >>> It will transform all of them that belong to the same series into one file. If they don't all belong to the same series, then you're on your own. doug Joongnam Yang wrote: > > Thanks Doug, > > Is there a way of transforming all the *.dcm files into one-volume > {img,hdr,mat} file? > > Nam. > > >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 04/28/05 2:56 PM >>> > > Try > > mri_convert file.dcm f -ot spm > > where file.dcm is a dicom file in the series you want to convert (there > is no special naming requirements -- in fact the file names can be > random). The output will be > > f001.{img,hdr,mat} > f002.{img,hdr,mat} > > doug > > Joongnam Yang wrote: > > > > Hi all, > > > > I am sorry, since I might have missed the answer. > > My question is, the following question by Mr. Ajay Pillai has been > answered? > > If yes, would someone forward me the answer please? > > > > Thanks. > > Nam. > > > > >>> Ajay Pillai <pillai(a)ccs.fau.edu> 04/27/05 2:26 PM >>> > > Hi, > > I am trying to convert my dicom funcional scan images into SPM analyze > > (or even AFNI BRIK) format. > > > > I have about 320 functional volumes of 30 slices each. So basically I > > have 9600 .dcm files which I have renamed sequentially for each > > subject.The first 30 constitute one volume the next 30 next volume and > > so on. > > > > Can mri_convert do this? If so could some one please tell me how? > > > > Thank you > > > > Ajay > > > > _______________________________________________ > > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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Freesurfer