Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Importing Freesurfer output into "R" - Data Dictionaries, etc.
by Max Gunther 14 May '10

14 May '10

Dear Freesurfers, I am new to Freesurfer and I am wondering if there is a relatively painless way to import Freesurfer raw output data (e.g. .cvs or .xls files) into R? I mostly wondering if anyone has created data dictionaries to label and create the variables in a way that is formatted for R (or SPSS or SAS or whatnot). I.e., this must have already been done by someone? Any shortcuts? Any suggestions or help would be much appreciated (and would save us a lot of time!) Cheers, Max Max Gunther, PhD Vanderbilt University Medical Center Departments of Psychiatry and Medicine Center for Health Services Research Nashville, TN www.ICUdelirium.org

1 0

Postdoctoral Research Scholar Position, Multimodal Imaging Laboratory, University of California, San Diego
by Don Hagler 14 May '10

14 May '10

Postdoctoral Research Scholar Position, Multimodal Imaging Laboratory, University of California, San Diego The Multimodal Imaging Laboratory (MMIL) at the University of California, San Diego invites applications for a postdoctoral research scholar position under the direction of Drs. Donald Hagler and Anders Dale. The successful candidate will join a multi-disciplinary team of scientists, programmers, and support staff addressing a variety of neuroscience questions using multimodal brain imaging, electrophysiology, behavior, and genetics. An important component of the work done at MMIL, and an integral role of the currently announced position, is the development and improvement of methods for the analysis of neuroimaging data. This will include extending our recent work on a white matter fiber tract atlas (Hagler et al., HBM 2009) to encompass a more diverse population of subjects, additional fiber tracts, and a larger age range, including infants. The postdoctoral researcher will receive training in brain imaging and methods development, and will be encouraged to develop his or her own research projects. Applicants for the position must have completed relevant Ph.D. research activities within the past five years. Applications from many disciplines may be considered, and the position is open to qualified international applicants. Experience or expertise in the following areas is highly desired: 1. computer programming (e.g. MATLAB, C/C++). 2. structural MRI, diffusion MRI 3. neuroimaging analysis software (e.g. FreeSurfer, FSL) 4. scientific writing This posting is for a 2-year appointment beginning immediately. Salary will be consistent with the NIH/NRSA levels in accordance with the University of California, San Diego policies for Postdoctoral trainees. Compensation includes full staff benefits, including health insurance, and vacation time. Review of applications will begin immediately and will continue until the position is filled. To apply, please send your CV, a brief statement of research interests and goals, and any selected reprints to dhaglerjr(a)hotmail.com with the subject line "MMIL postdoctoral position". Letters of reference will be required before final approval of hiring. Informal inquiries for more details are welcome. _________________________________________________________________ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:…

1 0

correlation between thickness and volume
by Rajagopalan, Venkateswaran 14 May '10

14 May '10

Dear All, I ran group comparison between control and patients independently on thickness, area and volume. I found significant difference between the two groups on volume and thickness, now i am wondering it is possible to run a correlation between the volume and thickness results to see how good they are related. How to do this using mri_glm command line version and what should be the contrast for this comparison. Any help would be appreciated. Thanks venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

1 0

Question concerning Fractional Anisotropy
by Weisinger, Brian (NIH/OD) [E] 14 May '10

14 May '10

Hello, I am trying to run the dt_recon with the fractional anisotropy to do a project with white matter. I am running into a problem actually getting the command to work. I am trying to follow the example online dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals f.bvecs --s M87102113 --o dti But I am not sure where/what I am supposed to put after the -i. The other stuff I am pretty sure I know, --s = the subject folder --o = the folder I want the output to go in Can you fill me in on what I'm missing, I looked in the subjects output files and could not find anything that ended with .dcm. Thank you, Brian Weisinger

2 1

How to make the thickness of different subjects into one MGH file?
by liyari5018 14 May '10

14 May '10

Hi Freesurfer experts, i want to know how to make different subjects'(suppose I have 10 subjects) lh.thickness.fsaverge.mgh (1*163842) into one mgh file(10*163842)? Thanks! LJ

3 2

version number
by Hoptman, Matthew 14 May '10

14 May '10

Hi, I have a relatively old version of Freesurfer, and I'm not sure how to get the version number. Could anyone please advise? It's from back in the day when we used csurf. Best, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _________________________________________ Conserve resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

2 1

Error of fsaverage unknown during mri_glmfit
by newfei＠nmr.mgh.harvard.edu 13 May '10

13 May '10

Hi, I encountered the error of 'option fsaverage unknown' when running the mri_glmfit. Any idea on what I have missed during the steps leading to this? [audrey:newfeiGLM] (nmr-std-env) mri_glmfit --y lh.Vis_schiz.thickness.10.mgh --fsgd Vis_schiz.fsgd dods --C age.mtx -surf fsaverage lh --cortex --glmdir lh.Vis_schiz.glmdir gdfReadHeader: reading Vis_schiz.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 41.2941 1 PremorbidIQ 107.942 2 BDI 5.41176 Class Means of each Continuous Variable 1 Control 41.3333 113.6880 2.4000 2 Schiz 41.2632 103.4053 7.7895 INFO: gd2mtx_method is dods ERROR: Option fsaverage unknown Thanks in advance, Newfei

2 1

Fwd: problems with tksurfer
by Krish Subramaniam 13 May '10

13 May '10

FYI.. Begin forwarded message: > From: iacono(a)nmr.mgh.harvard.edu > Date: May 13, 2010 3:11:09 PM EDT > To: "Krish Subramaniam" <krish(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] problems with tksurfer > > Thanks Krish! > you solved my problem. > I mean, I made just a small error in typing the SUBJECT_DIR and with > ls > $SUBECTS_DIR I realized it! > Sorry for the trivial question and thanks for your help! > Maria > > >> Hi Maria >> >> The SUBJECTS_DIR is one directory above the my_subj_name. Sorry if >> this is a trivial point, but worth a check. >> >> can you give me the output of following commands >> >> echo $SUBJECTS_DIR >> ls $SUBJECTS_DIR >> >> On May 12, 2010, at 7:03 PM, iacono(a)nmr.mgh.harvard.edu wrote: >> >>> Hi all! >>> I have some problems to visualize surfaces by tksurfer. When I try >>> to load >>> a surface with the command tksurfer my_subj_name lh inflated I >>> receive the >>> following error: >>> ERROR: could not read header info from T1 or orig in >>> homes/..../my_subj_name/mri >>> The SUBJECTS_DIR is the correct one and in my mri folder there are >>> both >>> T1.mgz and orig.mgz. >>> Any suggestion? Could the headers of those files be corrupted? How >>> can I >>> check it? >>> Thanks in advance for any help! >>> Maria >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> >> > >

1 0

problems with tksurfer
by iacono＠nmr.mgh.harvard.edu 13 May '10

13 May '10

Hi all! I have some problems to visualize surfaces by tksurfer. When I try to load a surface with the command tksurfer my_subj_name lh inflated I receive the following error: ERROR: could not read header info from T1 or orig in homes/..../my_subj_name/mri The SUBJECTS_DIR is the correct one and in my mri folder there are both T1.mgz and orig.mgz. Any suggestion? Could the headers of those files be corrupted? How can I check it? Thanks in advance for any help! Maria

3 2

talairach to native space
by Tina Jeon 13 May '10

13 May '10

Hello freesurfers, I am trying to align my T1W image in native space to the surface files (?h.pial, ?h.white, ?h.inflated, ?h.base) but it seems that they do no align perfectly. I thought the labeling information is in native space? However this does not seem to be the case because in the ascii files for the surfaces we found -120 in the coordinates but native space is [0,240] (i.e., without negatives). Is using tkregister2 the solution? Or using an affine registration matrix to transform the coordinates? Thanks in advance. Your help would be greatly appreciated. Tina Jeon

2 1

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