Freesurfer January 2011

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

statistical question
by Ilana Hairston 24 Jan '11

24 Jan '11

Hi there, This is a bit outside the pure technical questions. My subject pool has both boys and girls, with the boys having larger intracranial volume. My results when controlling for gender and intracranial volume however are not the same (obviously, one is a dichotomous variable, the other continuous). Looking at the results, i prefer the latter over the former, more consistent with the literature, and more internally consistent (i.e., brain regions associated with intenalizing sub-scales and the internalizing total scale). But it could be argued that I am removing important variance - maybe stressed out kids have smaller heads? Any recommendation? thanks -- ******************************* peligro! flaca pero mala! ******************************

2 1

fixing cortical parcellations
by Kerstin Pannek 23 Jan '11

23 Jan '11

Dear freesurfer experts I am having some trouble with inaccurate cortical parcellation after autorecon3. Cortical regions seem to be "spilling over" into neighbouring regions (for example supramarginal in inferior parietal as seen in the attachment). How can I manually adjust these errors? Thanks! Cheers Kerstin

1 0

Aseg tables
by Ilana Hairston 22 Jan '11

22 Jan '11

Hi there, I have been using QDEC to create data tables, which i then analyze in SPSS. Mainly because I have missing values on some of my variables, and QDEC doesn't seem to like that. and it has limited statistic capabilities. Anyways... I want to do a sanity check to verify that the regions that are labeled as hippocampus or such, is labeled correctly, but i can't seem to find an annotation table that contains aseg.volume. thx ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** What might have been is an abstraction Remaining a perpetual possibility Only in a world of speculation T.S. Eliot

3 2

Re: [Freesurfer] Beginner Question on registration process
by Gabriele Arnulfo 22 Jan '11

22 Jan '11

Hi again I've finally found the exact transformation which is ... gather from the original nifti the qfrom matrix (say Qf) and then collect with mri_info vox2ras-tkr orig.mgz , the transformation matrix (say T) to map ras to index in the freesurfer space. I've finally matched the points. Why mri_info -vox2ras 001.mgz is different (signs mismatch and also qoffset values are different) from the original qform matrix ... they do not suppose, as U have said, to share the same space? Thanks for any support and for your hints. g. 2011/1/21 Douglas Greve <greve(a)nmr.mgh.harvard.edu> > yes, 001.mgz and the DICOM share the same space. > > doug > > > On 1/21/11 9:08 AM, Gabriele Arnulfo wrote: > > Hi all, > > MRI, in this context, i was considering the original DICOM T1 MRI space > before the conversion to 001.mgz file. Is your suggestion still the right > way to solve my task? > > > > 2011/1/20 Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> >> I don't know of another way to map control points. By MRI space I assume >>> that you mean the scanner RAS space? Eg, the space defined by the nifti >>> qform? I think this matrix will be >>> >>> L = inv(T)*Q >>> >>> where Q is the scanner vox2ras of the orig volume and T is the tkregister >>> vox2ras of the orig volume. >>> You can get both of these matrices using mri_info. >>> >>> doug >>> >>> >>> Martin Reuter wrote: >>> >>>> Hi Gabriele, >>>> >>>> not sure if there is an easy way (probably Doug knows). But if there >>>> isn't, I wrote a tool mri_map_cpdat to map control points from one space >>>> to another. A control points dat file is a txt file containing >>>> coordinates. The tool will be available in 5.1 where it is used to >>>> transfer manual edits in the longitudinal stream. I could send a copy of >>>> it before. >>>> So you can: >>>> - create a control.dat file with your coordinates >>>> - map it using a lta file. >>>> I am not sure how you can get the lta that you need (from native to >>>> freesurfer conform space) but probably someone else can help with that. >>>> This probably has been discussed before. >>>> >>>> Here is the format of the control.dat: >>>> >>>> xcoord1 ycoord1 zcoord2 >>>> xcoord2 ycoord2 zcoord2 >>>> xcoord3 ycoord3 zcoord3 >>>> info >>>> numpoints 3 >>>> useRealRAS 0 >>>> >>>> >>>> So instead of the coords put your numbers, of course you can have more >>>> than three points. >>>> >>>> Best, Martin >>>> >>>> On Thu, 2011-01-20 at 17:26 +0200, Gabriele Arnulfo wrote: >>>> >>>> >>>>> 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?? >>>>> _______________________________________________ >>>>> 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 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >>> >>> 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. >>> >>> >> >> >> -- >> In a world without wall, how needs WINDOWS?? >> > > > > -- > In a world without wall, how needs WINDOWS?? > > -- In a world without wall, how needs WINDOWS??

3 2

two issues with the processing stream
by Ilana Hairston 22 Jan '11

22 Jan '11

Hi there, we are having two unrelated problems with a couple of files: 1. A brain running extremely slow, after initial processing. i.e. we ran recon-all, made some edits (control points etc.) and now for some reason the second round is taking days. 2. An error message*: ERROR: _FindFacePath: could not find path! *We looked it up on the freesurfer wiki and there is an entry about this error, but the answer perhaps was not posted. thanks ilana -- ******************************* peligro! flaca pero mala! ******************************

3 4

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

2 1

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

1 0

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

3 4

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. ----------------------------------------------------------------------------

3 2

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.

1 0

← Newer
1
2
3
4
5
6
7
8
...
15
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer January 2011