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[Fwd: Re: [Freesurfer] annotation file and labels for fsaverage]
by carl＠nmr.mgh.harvard.edu 31 Jan '09

31 Jan '09

Hi Jeff - read the thread below starting with my Sept 8 2008 email. Bruce - what is the status on the insula label for aparc? carl > Hello all, > > Thank you for your quick replies to my previous posts. One more question. I am wondering what the difference is and if I should be taking average thickness measurements for cortical regions from lh.aparc.a2005s.stats or lh.aparc.stats. I think the main difference is that lh.aparc.a2005s.stats was made with ?h.atlas2005_simple.gcs and lh.aparc.stats was made with ?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs. Which one is more accurate? I am using freesurfer 3.0.5. > > Thank you, > Jeff Sadino Bruce Fischl fischl at nmr.mgh.harvard.edu Tue Sep 9 10:03:31 EDT 2008 Previous message: [Freesurfer] annotation file and labels for fsaverage Next message: [Freesurfer] dicom image viewer Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] great, thanks Ron. Bruce On Tue, 9 Sep 2008, Ron Killiany wrote: > I believe Sarah will be over at MGH on friday to begin finalizing this. > > --ron > > On Mon, Sep 8, 2008 at 9:31 PM, Bruce Fischl <fischl at nmr.mgh.harvard.edu>wrote: > >> Hi Dara, >> >> there is an insula label in the works (*lots* of people have asked this >> question). Ron: any updates on the insula label? >> >> thanks >> Bruce >> >> On Mon, 8 Sep 2008, Dara Manoach wrote: >> >> Thanks very much for the detailed info Karl (and Doug and Bruce)! >>> >>> My primary ROI is ACC, so we'll probably use Aparc with the cingulate >>> divisions. I'll have to review the paper to see if the anatomic bases of >>> the divisions are described. I'm surprised, though, that there is not an >>> insula label, and I'm wondering why it would not be possible to use ROI >>> labels from the two annotation schemes to examine activation in group data >>> (i.e., ACC labels from aparc and insula from aparc2005). >>> >>> best, >>> dara >>> >>> On Sep 8, 2008, at 8:18 PM, Bruce Fischl wrote: >>> >>> for what it's worth we label the cc now explicitly in the aseg, which is >>>> certainly more accurate than the aparc used to be. >>>> >>>> Thanks for the detailed answer though Carl! >>>> >>>> Bruce >>>> On Mon, 8 Sep 2008 carl at nmr.mgh.harvard.edu wrote: >>>> >>>> >>>>> Hi Dara, >>>>> >>>>> You can certainly use either one as Doug says, but depending on your >>>>> purposes, one or the other may have some virtues. 2005 consists of >>>>> discrete sulcal and gyral labels with traditional anatomical names so >>>>> there are a lot more labels (which is why Doug describes it as very >>>>> detailed), whereas aparc in general collapses these into summary >>>>> regions. >>>>> >>>>> But it is not a a simple case of lumper vs splitter....For instance it >>>>> seems that >>>>> >>>>> Aparc divides the cingulate into rostral anterior, caudal anterior, >>>>> posterior cingulate whereas in aparc 2005 it is lumped into one >>>>> cingulate >>>>> label >>>>> >>>>> Aparc shows the corpus c. nicely (I think there may even be a >>>>> subparcellation available in development) whereas the cc is lost in the >>>>> medial wall in 2005. >>>>> >>>>> Aparc differentiates the pars orbitalis nicely on the orbital surface >>>>> from >>>>> the rest of the ofc, aparc 2005 does not ? possibly of interest to >>>>> someone >>>>> who is looking at ventrolateral pfc and its neighbors >>>>> >>>>> Aparc includes in its lateral ofc label everything lateral to the rectus >>>>> gyrus, including the central ofc and the (unlabeled) transverse sulcus >>>>> neither of which would be understood as being in the lateral ofc as that >>>>> term is typically used today. >>>>> >>>>> Aparc 2005 shows a view that nicely differentiates the rectus gyrus on >>>>> sagital section from the adjoining, whereas aparc lumps a broad >>>>> territory >>>>> into ?medial OFC? >>>>> >>>>> Aparc 2005 includes parcellation of the Insula, aparc does not and it is >>>>> lost in the unknown medial wall (there has been talk of fixing this but >>>>> is >>>>> this real, Bruce or Doug?) >>>>> >>>>> Perhaps what we need is a ?best of aparc and aparc 2005?. >>>>> >>>>> For surfing purposes you can also ?fool? tksurfer into showing you the >>>>> names of the (typically more more detailed) 2005 parcellations while >>>>> viewing the brain labeled with the aparc labels which at times have more >>>>> detail ? though I have never asked Doug if this will always work >>>>> correctly. >>>>> >>>>> If others have discovered pros and cons in other regions, please share. >>>>> >>>>> Best, >>>>> >>>>> >>>>> Carl >>>>> >>>>>

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lh.aparc.a2005s.stats and lh.aparc.stats differences
by Jeff Sadino 30 Jan '09

30 Jan '09

Hello all, Thank you for your quick replies to my previous posts. One more question. I am wondering what the difference is and if I should be taking average thickness measurements for cortical regions from lh.aparc.a2005s.stats or lh.aparc.stats. I think the main difference is that lh.aparc.a2005s.stats was made with ?h.atlas2005_simple.gcs and lh.aparc.stats was made with ?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs. Which one is more accurate? I am using freesurfer 3.0.5. Thank you, Jeff Sadino _________________________________________________________________ Windows Live™ Hotmail®…more than just e-mail. http://windowslive.com/howitworks?ocid=TXT_TAGLM_WL_t2_hm_justgotbetter_how…

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difficulty readings DICOM files from CD
by Sam Enumah 30 Jan '09

30 Jan '09

Hello, My name is Sam Enumah and I am an undergraduate working in the A.A. Martinos Imaging Center at MGH Navy Yard. I have become familiar with Freesurfer's tkmedit function and I am able to analyze my data once I am given a set of 144 MR dicom files. While the mri_convert tool works for the dicom files that are on the local machine, I cannot seem to get it to work for the files I have tried to retrieve from a CD. The files on my local host machine all display the extension ".dcm" while the files from the CD do not display a file extension and are files with names that consist of 8 unique numbers (e.g 48480095) As you may know, when running mri_convert, the user need only input one of the files in a series and it recognizes all the other files and creates the desired output (in this case the ".nii" file type to be read by tkmedit). However, when I tried to input these 8 digit file names into mri_convert, I received the following error: [gordo:12250000] (nmr-std-env) mri_convert 48480995.dcm adc.nii mri_convert 48480995.dcm adc.nii $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from 48480995.dcm... Starting DICOMRead2() dcmfile = /autofs/homes/014/xmlentz/Desktop/dicom/08110217/12250000/48480995.dcmdcmdir = /autofs/homes/014/xmlentz/Desktop/dicom/08110217/12250000 Ref Series No = 805 ERROR: bits = 8 not supported. Send email to freesurfer(a)nmr.mgh.harvard.edu I tried "mri_convert <filename> --in_type ge adc.nii" but kept getting the error: genesisRead(): can't determine file name format Essentially, my problem is that I have roughly 1000 dicom files (as evidenced by command "file" in terminal) without an identifiable extension and I need to find a way to change these into one of any of the set MR001.dcm - MR144.dcm to be read by mri_convert. As it stands now, I don't know what series (average DC, isotropic, FA, etc.) these 8 digit numbers correspond to so I'm unsure of how to proceed. Suggestions? Thanks for your time. -Sam -- Sam Enumah Harvard College Class of 2010 Concentrator in Neurobiology senumah(a)fas.harvard.edu

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mri_divide_parcellation
by Diana Wotruba 30 Jan '09

30 Jan '09

Dear FS experts I divided the fsaverage parcellations (aparc.a2005s) into about 1000 smaller parcellations, using mri_divide_parcellation. What would be the easiest way to get the cortical thickness in these areas for each subject? Is it reasonable to copy the new .annot file from fsaverage into each subjects label folder ensuing mris_anatomical_stats? Any help would be appreciated Regards Diana

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research assistant position in intracranial EEG
by Thomas Thesen 29 Jan '09

29 Jan '09

Research Assistant Position in Cognitive Neuroscience Department of Neurology, School of Medicine, New York University We are seeking a full-time Research Assistant to assist with cognitive neuroscience experiments involving human intracranial EEG. Main topics of investigation are language, memory, multisensory, brain-computer interface, seizures and others. Responsibilities include, but are not limited to, recruiting and scheduling of control subjects and patients, testing and recording from intracranial patients, maintenance of equipment, databases and files, as well as data analysis and manuscript preparation. Candidates who have experience with neuroimaging data collection and analysis are especially encouraged to apply. Other neuroimaging methods employed by the lab include fMRI and MEG. The laboratory provides a unique exposure to both basic research and clinical neuroscience. The position requires interaction with patients and hospital staff and therefore excellent verbal and interpersonal skills are required. Must be well-organized and detail oriented; extensive computer experience strongly preferred, with programming highly desirable. B.A. or B.S. required, such as in neuroscience, psychology, biology, computer science or biomedical engineering. The position is ideal for exceptional candidates seeking to pursue an advanced research degree in neuroscience or a related field. Likely start date is June 2009. Please visit our web lab page for more information: http://mmil.ucsd.edu/thomas/group Please send resume and cover letter to: Thomas Thesen, Ph.D.Assistant Professor of Neurology New York University School of Medicine thomas.thesen(a)med.nyu.edu

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Measuring regional cortical thickness
by Jeff Sadino 29 Jan '09

29 Jan '09

Hello, I would like to measure the cortical thickness for each region. All I can find is how to do it for user-defined ROI's, but not for each auto-segmented region. Can anyone point me in the right direction? Also, can you manually add and subtract pixels from region labels from the surface in tksurfer in a similar way that you can in tkmedit? Thank you very much. Jeff Sadino _________________________________________________________________ Windows Live™ Hotmail®…more than just e-mail. http://windowslive.com/howitworks?ocid=TXT_TAGLM_WL_t2_hm_justgotbetter_how…

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sulc & curv
by Juranek, Jenifer 29 Jan '09

29 Jan '09

Rudolph, many thanks for the additional details. Just a follow-up question (or two): 1. Short stubby gyri might have the following morphometric properties? a) Short feature: shallow sulcal depths would be expected to have sulc values hovering around the mean surface (e.g. around 0) in negative curvature areas b) Stubby feature: increased GM volume, increased surface area, and perhaps increased cortical thickness depending on how the WM behaved Thanks so much, Jenifer

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Graphical problems or more
by Jürgen Hänggi 29 Jan '09

29 Jan '09

Dear FS experts We parcellated the aparc.a2005s of fsaverage into parcellations of 300 mm^2 (attached file FinerParcells_fsaverage). When I overlaid this new parcellations on a single subject, there seems to be something wrong (attached file FinerParcells_individual). Because I use this new finer parcellations with the command mris_anatomical_stats to get cortical thickness of these finer parcellations across subjects, I am wondering whether there is only a graphical problem. When I have a look at the resulted thickness values and the reported number and names of parcellations, everything seems to be OK. Any ideas? I use FS 4.2.0 Mac Intel. Thanks in advance Regards Jürgen ---------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) 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) ----------------------------------------------------------

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Re: [Freesurfer] --fsgd file
by Siddharth Srivastava 29 Jan '09

29 Jan '09

Hi Jurgen, Thanks for the response. Seems like a feasible idea. I can do it for my "Normals", but the atypicals have a large variability in the measure. And only the atypicals have missing data. Thanks for the idea though... sid. On Thu, Jan 29, 2009 at 11:02 AM, Jürgen Hänggi < j.haenggi(a)psychologie.uzh.ch> wrote: > Hi Siddharth > > If there are not too many missing values, you can fill the missing values > by the mean of the values you have and hope that the subjects who completed > all tasks did not systematically deviate from the subjects who did not > complete the tasks. > > Regards > Jürgen > > > > On 28.1.2009 20:46 Uhr, "Siddharth Srivastava" <siddys(a)gmail.com> wrote: > > Hi everyone, > I was wondering if it is possible to flag missing > entries in > the covariates corresponding to subjects, in the construction of the file > passed > through --fsgd to mri_glmfit ? Not all my subjects completed all the > tasks, > and i need to code them in the file, somehow. > thanks, > sid. > > ------------------------------ > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ---------------------------------------------------------- > Juergen Haenggi > Ph.D. (Dr. des.) > 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) > ---------------------------------------------------------- > >

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--fsgd file
by Siddharth Srivastava 29 Jan '09

29 Jan '09

Hi everyone, I was wondering if it is possible to flag missing entries in the covariates corresponding to subjects, in the construction of the file passed through --fsgd to mri_glmfit ? Not all my subjects completed all the tasks, and i need to code them in the file, somehow. thanks, sid.

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