Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

corpus intrudes into other structures
by Keefe, Helen L 21 Jan '11

21 Jan '11

Hi Everyone, I have frequent cases of the corpus callosum intruding into other structures. I followed directions for "Expand the boundary of an existing region" at https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit#Alternateediti… without success, Then I heard that version 5.0 might solve the problem of structures intruding into others. However, when I used the new version, the entire corpus area was labeled as "none" I returned to the previous version and to "Expand the boundary of an existing region" but am still not able to make it work. I got the path drawn between the two structures, but when I choose "remove from label" on the "Custom Fill" box, the entire brain is labeled as the structure I want to expand. I simply want to relabel the part of the caudalantriorcingulate that has been labeled corpus. Thanks, Helen

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Errors with the "Cut Plane" feature in tksurfer
by Iris.steinmann 21 Jan '11

21 Jan '11

Hello freesurfers, I installed 'freesurfer-Linux-centos4-stable-pub-v5.0.0.tar.gz' on my ubuntu 10.10 mashine. First I had a little trouble but now it works (thank you Doug!!!), except one little problem: I tried to cut a plane in tksurfer to get a patch. I marked a closed area, pressed the 'cut closed line' button, than click into my area and press the 'fill uncut area' button ….than tksurfer crashed and the following error appears tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. Abort I found the same question in the mailing list , but no answer. Is there a solution? Did i made something wrong? Kind regards Iris

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Different sequences in one evaluation
by Gergely Orsi 21 Jan '11

21 Jan '11

Hi Freesurfers, I have a quick question: I have two groups, both measured on the same scanner, with the same sequence (3D MPRAGE), and with almost the same parameters. TR/TE/TI/BW/MATRIX/FOV/FOV-phase/Flip angle/Slice thickness/in-plane resolution... everything is the same, but the number of slices. Total measurement time was also the same. One group was measured with 160 slices, the other with 176. Can I compare the two groups in freesurfer? Thanx, -- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi(a)gmail.com

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Sig.mgh to annotation
by Jürgen Hänggi 20 Jan '11

20 Jan '11

Dear FS experts We would like to transform the sig.mgh file to an annotation file in order to extract the thickness value in each individual brain. The problem is that we have 3 clusters in the sig.mgh file and we would like to split these 3 clusters into annotations in order to compute cortical thickness within each single cluster. How to do it? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Job postings
by XJ Kang 20 Jan '11

20 Jan '11

*POSTDOCTORAL POSITION* *IMAGING HUMAN AUDITORY CORTEX*** The Human Cognitive Neurophysiology Laboratory (www.ebire.org/hcnlab <http://www.ebire.org/hcnlab>) affiliated with UC Davis and the Department of Veterans Affairs Northern California is searching for a postdoctoral fellow to study human auditory cortex in normal adult, elderly, and hearing loss populations using a new 3.0T Siemens Verio scanner. The structure of human auditory cortical fields will be investigated using cortical surface mapping of multimodal structural brain imaging data (including high-resolution T1, 30-direction diffusion tensor imaging, FLAIR and magnetization transfer imaging). Functional organization is studied with fMRI in intermodal selective attention tasks. Functional activations to speech and non-speech stimuli will be studied. The job involves close collaboration with international scientists, graduate students, and post-docs. */Job Availability:/* Immediate. */Job duration:/* 2-3 years. Salary: $50,000-$70,000 depending on experience. */QUALIFICATIONS. /*Successful candidates should have a strong background in auditory perception, physiology and/or anatomy (PhD or MD required), an excellent publication record, familiarity with Windows and Linux operating systems, and some programming experience. Knowledge of psychophysics, neuropsychology, hearing science, and familiarity with neuroimaging methods including fMRI, ERPs, or TMS is desirable. US citizenship preferred. Interested candidates should email a C.V., letter of intent, and the names of three references to: David L. Woods, Dept. of Neurology, UC Davis and VANCHCS (127E), 150 Muir Rd., Martinez CA 94553. Email: dlwoods(a)ucdavis.edu. HCNLAB is located in Martinez, CA. on the San Francisco Bay. *POSTDOCTORAL POSITION:* *QUANTITATIVE AUTOMATED LESION DETECTION OF BRAIN INJURY*** The Human Cognitive Neurophysiology Laboratory (www.ebire.org/hcnlab <http://www.ebire.org/hcnlab>, affiliated with UC Davis and the Department of Veterans Affairs Northern California) is searching for a postdoctoral fellow to assist in the study the structural and functional consequences of traumatic brain injury. Brain structure will be imaged on a 3.0T Siemens Verio using multimodal structural brain imaging (including high-resolution T1, diffusion tensor, FLAIR, and magnetization transfer imaging). Results are analyzed using both Freesurfer-based cortical surface mapping and additional automated parcellation techniques to quantify tissue properties in subcortical structures and white matter tracts. MRI structure will be correlated with cognitive performance on PC-based cognitive test batteries. The job involves close collaboration with international scientists, graduate students, and post-docs. */Job Availability:/* Immediate. */Job duration:/* 2-4 years. Salary: $50,000-$70,000 depending on experience. */QUALIFICATIONS./* A PhD or MD degree is required. Candidates should have a strong background in cognitive neuroscience, computational neuroscience, image processing and/or neuroanatomy (as well as an interest in all of these areas) and an excellent publication record. Desirable candidates will have some of the following attributes: familiarity with Windows and Linux operating systems, and some MATLAB programming experience and knowledge of neuroanatomy, neuropsychology, MRI/fMRI, and other neuroimaging methods including ERPs, or TMS. US citizenship preferred. Interested candidates should email a C.V., letter of intent, and the names of three references to David L. Woods, Dept. of Neurology, UC Davis and VANCHCS (127E), 150 Muir Rd., Martinez CA 94553. Email: dlwoods(a)ucdavis.edu <mailto:dlwoods@ucdavis.edu>. HCNLAB is located in Martinez, CA. on the San Francisco Bay.

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mkanalysis-sess in Stable 5
by Adam Nitenson 20 Jan '11

20 Jan '11

Hi Freesurfers, I'm trying to update our analysis for Stable 5, and I'm having some trouble trying to recreate our current Stable 4 version (espcially since I have not yet made a gui-less analysis). The command I used was: mkanalysis-sess -analysis fmcsm5_functionals_Stable5 -TR 2 -paradigm paradigm -event-related -funcstem fmcsm5 -motioncor -inorm -polyfit 2 -mcextreg -nconditions 9 -timewindow 24 -prestim 4 -TER 2 -autostimdur However, it's not accepting the -motioncor flag, and I'm not sure what the correct replacement is. For reference, I'm trying to replicate the analysis as close to the original, which has the following analysis.info file: analysis fmcsm5_functionals TR 2.000000 fsd bold funcstem fmcsm5 inorm 100.000000 runlistfile tpexclude parname paradigm designtype event-related nconditions 9 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 Condition 6 Condition06 Condition 7 Condition07 Condition 8 Condition08 Condition 9 Condition09 and analysis.cfg text -extreg mcextreg -nextreg 3 -delay 0.000000 -TER 2.000000 -polyfit 2 -gammafit 2.250000 1.250000 -gammaexp 2.000000 -timewindow 24.000000 -prestim 4.000000 -autostimdur Thank you, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Beginner Question on registration process
by Gabriele Arnulfo 20 Jan '11

20 Jan '11

Hi all, I'm a new freesurfer user and I've a small question for you all. Which the faster and reliable way to map a list of points into the freesurfer geometrical space? I've already read the pdf/ppt but there's no suggestion in there about which command should be used (if any). I've read about matlab tools that could be used for this purpose is it right? My task is really simple but i cannot figure out which is the best way. I've got a list of points (basically intra-cerebral electrodes coordinates segmented from MRI) in the MRI space and I'd like to calculate the respective points in the freesurfer space. Cheers, gabriele -- In a world without wall, how needs WINDOWS??

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Re: [Freesurfer] How to make a surface overlay? - repost
by Ed Gronenschild 20 Jan '11

20 Jan '11

Hi Bruce, I managed to do what I wanted: by linking the ?.aparc.annot file with ?thickness file and FreeSurferColorLUT.txt I get a list of thickness value, segID and structure name. Now I can change each thickness into whatever value I want and save it as a curve file which I can then overlay on the pial surface. Thank you for your suggestions. Ed On 19 Jan 2011, at 17:31, Bruce Fischl wrote: > it's 'curv' format (read_curv.m I think) > On Wed, 19 Jan 2011, Ed > Gronenschild wrote: > >> What is the format of ?.thickness files? >> >> On 19 Jan 2011, at 15:43, Bruce Fischl wrote: >> >>> read_annotation.m will load a .annot file. We'll try to digup the >>> tksurfer >>> bit that did this >>> >>> >>> On Wed, 19 Jan 2011, Ed >>> Gronenschild wrote: >>> >>>> Hi Bruce, >>>> >>>> I'm not familar with matlab but I can read the matlab scripts to >>>> understand >>>> what they are doing. I can then convert the code into C code. >>>> Which matlab script can I use to load the parcellation? >>>> >>>> My suggestion would be to load the ?.thickness and replace the >>>> thickness >>>> values with the corresponding -log(p) values. However, I don't know >>>> which >>>> thickness in this file belongs to which segID? >>>> >>>> Ed >>>> >>>> On 19 Jan 2011, at 14:28, Bruce Fischl wrote: >>>> >>>>> Hi Ed, >>>>> >>>>> sorry, I keep hoping someone else will respond as we did put >>>>> something >>>>> together to do this once upon a time, but apparently it's faded >>>>> from all >>>>> of our memories. You could do it in matlab by loading the >>>>> parcellation and >>>>> just setting every vertex with the parcellation value to the same >>>>> scalar. >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> On Tue, 18 Jan 2011, Ed Gronenschild wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I've done some statistics on thickness and volume >>>>>> of the default cortical regions (segIDs 1000 - 1035 >>>>>> and 2000 - 2035) for a number of subjects. >>>>>> How can I show for instance the p values >>>>>> (expressed as -log(p)) as an overlay on the pial >>>>>> surface of fsaverage? >>>>>> >>>>>> Ed >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> >>>> >>>> >> >> >>

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error message in mri_concat: fp==0
by Lars M. Rimol 20 Jan '11

20 Jan '11

Hi, I got this error message when attempting to use mri_concat. Number or inputs, frames etc. seems ok, but when it is about to write the output file, this happens: Writing to /home/lmr/test.mgh , -1): could not open file: fp==0 (I use v.4.5.0) Any suggestions? Thank you! yours, LMR -- yours, Dr. Lars M. Rimol

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overlaping in aparc+aseg
by LAOUCHEDI MAKHLOUF 19 Jan '11

19 Jan '11

hi everyone after running recon-all i noticed (on somme normal patients) overlaping in some labels: part of image with 11165 and 11113 wich correspond to p { margin-bottom: 0.21cm; } - ctx_lh_G_front_inf-Orbital p { margin-bottom: 0.21cm; } - ctx_lh_S_orbital-H_Shaped at the same time (verified with fslview) thanks p { margin-bottom: 0.21cm; }

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