Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Re: [Freesurfer] R: Re: correction on question: offset in qdec GUI
by Hamza Alshuft 01 Nov '13

01 Nov '13

Hi Freesurfers! Has any one got an answer to this query asked sometime ago: > "Hi list, > I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And > what I can do using it? Hi Bruce, I'm referring to "offset" in qdec/Display threshold line, near Min/Mid/Max. For example, I'm noting that if set +1 as offset the red statistical area is more larger. Stefano" What the OFFSET next to the threshold max. is for? Kind regards Hamza This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

1 0

PhD position: Neuroimaging (MRI) in Epilepsy, University of Liverpool
by Keller, Simon 01 Nov '13

01 Nov '13

PhD Studentship in Specialised MRI in Medically Refractory Epilepsy £13,726 pa Stipend Department of Molecular & Clinical Pharmacology, Institute of Translational Medicine Location: University Campus Ref: PhD-MRI-refractory-epilepsy/WWW Closing date for receipt of applications: Thu, 07 Nov 2013 17:00:00 GMT A PhD Studentship is available in the Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine at the University of Liverpool, supervised jointly between Dr. Simon Keller and Professor Tony Marson. This is an exciting project that involves collaboration with the Walton Centre NHS Foundation Trust (WCFT), which is a specialist neurosciences NHS hospital providing a high quality, integrated, multidisciplinary neurosciences service to the northwest of England and North Wales. The multidisciplinary Epilepsy Research Group at the University of Liverpool and WCFT has a long-standing international reputation for assessing outcomes in people with epilepsy. People with medically refractory epilepsy who do not have a discernable brain abnormality on routine magnetic resonance imaging (MRI) pose a significant challenge in the clinical management of their disorder. Neurosurgeons are more hesitant to operate on people without an identifiable structural abnormality, and for people who do undergo surgery, postsurgical outcome is significantly poorer compared to people with a focal brain abnormality (e.g. hippocampal sclerosis). The focus of this project will be to use specialised MRI approaches with sophisticated image analysis techniques for people with refractory epilepsy who were found to be MRI-negative during routine clinical imaging in an attempt to identify brain alterations that may underlie the epilepsy disorder. You will perform manual and automated quantitative MRI (e.g. high resolution hippocampal measurements, analysis of cortical thickness), diffusion tensor imaging (DTI) and resting-state functional MRI analyses on data prospectively acquired for people with epilepsy and healthy controls. There is also the opportunity to analyse neuroimaging data that has been previously acquired. You will be expected to present your work at internal departmental meetings, national and international conferences, and as peer-reviewed manuscripts in internationally renowned journals. Applications are sought from graduates (First or Upper Second) in Neuroscience, Biomedical Science, Psychology, Medicine, or an equivalent discipline. Experience with MRI analysis techniques, particularly in context of a postgraduate qualification, is desirable. This studentship includes PhD tuition fees (UK/EU students only) and is available for three years. To apply please send a copy of your CV with covering letter to: Dr. Simon Keller (simon.keller(a)liv.ac.uk<mailto:simon.keller@liv.ac.uk>). -- Dr. Simon S. Keller Lecturer and Senior Scientist Neuroimaging The Department of Molecular and Clinical Pharmacology Institute of Translational Medicine University of Liverpool 2nd Floor, Neurological Science Clinical Sciences Centre Aintree University Hospitals and The Walton Centre NHS Foundation Trusts Lower Lane Liverpool L9 7LJ Tel: +44 (0)151 529 5943 Simon.Keller(a)liverpool.ac.uk<mailto:Simon.Keller@liverpool.ac.uk> www.liv.ac.uk/translational-medicine/staff/simon-keller/

1 0

mri_glmfit-sim with conjunction maps but without pre-cached data
by Caspar M. Schwiedrzik 01 Nov '13

01 Nov '13

Hi, I have a question regarding cluster size thresholding using mri_glmfit-sim. Namely, I have a sig.nii conjunction map that I made with mri_concat. The analyses that serve as input to the conjunction map are done on a custom surface template. If I want to run mri_glmfit-sim, how would that work? I obviously do not have precached data. Thanks, Caspar

2 10

recon-all scripts w/ new GCA atlas
by Mark Plantz 31 Oct '13

31 Oct '13

Hello freesurfers, I am currently attempting to run recon-all on infant subjects with a newly created 'gca' atlas. I e-mailed the listserv a while back about a strange memory allocation error that occurred right at the beginning of the "subcortical segmentation" pipeline. For a while, we thought that it was an issue with the actual atlas. However, after talking with someone who created canine atlases, it seems like it is a particular bug in the recon-all scripts themselves. It appears as though the default recon-all script needs to be altered to accept the new gca atlas. I was wondering if anyone has had success getting Freesurfer to accept their gca atlas? Thank you! Best, Mark

1 0

Volumes in native or normalized space, and eTIV
by Dorian P. 31 Oct '13

31 Oct '13

Dear all, Excuse if these are simple questions but I am a bit confused on the significance of the volume measures. 1. Are the volumes of ROIs calculated after normalization? 2. If volumes are calculated post-normalization, why is correction for eTIV needed? 3. What is the quickest way to correct for eTIV? Thank you. Dorian TJU

3 5

improvement of segmentation qualitiy by setting control points
by Annemarie Brandhofe 31 Oct '13

31 Oct '13

Dear freesurfer community, we are conducting cortical-thickness analysis and we have encountered some problems with setting control points to improve segmentation quality. Mainly, white matter was classified as grey matter after completion of the first run that incorporated control points. Now we have several questions, we would be very thankful for your comments: 1. According to your expereince, how many control points for the overall brain are usually necessary to obtain good segmentation results? 2. Are control points necessary at all? Is there a way to control the segmentation quality? 3. Is there any visual example on how to best set control points? Thank you for your help, Annemarie

1 0

Re: [Freesurfer] [martinos-tech] parametric modulation
by Douglas N Greve 31 Oct '13

31 Oct '13

For condition 4 (posslope), the weight is always 0. You can't compute a slope if all the values are the same. doug On 10/29/2013 10:44 AM, Suzanne Oosterwijk wrote: > Hi Doug, > > Attached is the Xtmp.mat file for the analysis that gets the error. > > Thanks for your response on the second question. I am not sure what > you mean with demeaning, so I guess that I am not doing that :-) I > just wanted to make sure that not getting the same results does not > indicate a fundamental problem in my paradigm files. > > Thanks! > Suzanne > > > On Tue, Oct 29, 2013 at 3:31 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Suzanne, can you send me the Xtmp.mat file that gets created? > > On your second question, the answer might be a little tricky. > First, are you demeaning the modulation value? If not, then you > can certainly get different maps. The other part is that you can > get unpredicatable results because the design matrix is not > orthogonalbecause you have several event types. > > doug > > > > On 10/28/2013 12:30 PM, Suzanne Oosterwijk wrote: > > Hi Doug, > > I am running parametric modulation analyses in which I am > modeling 5 different ratings given by participants in response > to images. To model these ratings I made paradigm files > defining both the onset and the slope for each trial (see > email exchange below). Since I have 5 different ratings, I > made 5 different paradigm files per participant, per run. > These paradigm files hold the exact same trial sequence, only > with different numbers for the slope condition. When running > selxavg3-sess I get the following error: > > Input to SVD must not contain NaN or Inf. > > Error in cond (line 36) > s = svd(A); > > Error in fast_selxavg3 (line 279) > XCond = cond(XtX); > > The strange thing is that selxavg3-sess stops running at a > particular participant when I am trying to model one > particular rating, whereas the exact same analysis for the > other three ratings I have run so far (for the same > participant) does not result in an error. I checked the > paradigm files over and over but I cannot find the mistake. > The paradigm files are all the same in terms of timing and > condition codes etc., the only thing that is different between > the files are the specific ratings per trial. So I really > don't understand why I get this error. I attached the paradigm > files for the erroneous analysis and also for the analysis > that runs successfully. I also attached the selxavg3-sess > logfile for the an erroneous analysis and for the successful > one. Maybe I am missing something here, but I just don't see it. > > Also, I have one other question concerning the parametric > modulation. As I understand it modeling the onset is the same > analysis as a normal contrast comparing a particular condition > against baseline. I compared the onset significance maps > (comparing onset to baseline) for each separate rating, and to > my surprise they are not the same. Since only the ratings > differ between the different analyses, and not the onset times > of the stimuli, I expected those maps to be completely > identical. Am I right in this assumption, or is there a reason > they can be different? > > Thanks! > Suzanne > > > > On Thu, Aug 15, 2013 at 4:28 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Suzanne, that is fine > doug > > > > On 8/14/13 7:13 AM, Suzanne Oosterwijk wrote: > > Hi Doug, > > Just a follow-up question. The ratings that I > collected for the > parametric modulation analysis have a range from 0 to > 1. This > means that the weights for some stimuli will have the > value 0. Is > this a problem? I am asking just to make sure that a > weight of 0 > does not exclude the corresponding data-point. > > Thanks, > Suzanne > > > On Fri, Jul 26, 2013 at 7:14 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Suzanne, yes that looks correct. > doug > > > > On 7/26/13 9:27 AM, Suzanne Oosterwijk wrote: > > Hello all, > > I want to perform a parametric modulation > analysis in > Freesurfer and I have a question about how to > adapt my > paradigm file. I understand how to code the > offset and the > slope (by adding the individual ratings as the > slope > weight), but I just want to check whether I am > correctly > modelling the trials of no interest. > > I have presented people with negative, > positive and neutral > images all preceded by a fixation cross. I > have individual > ratings for the negative images that I want to > use for the > parametric modulation analysis, but I don't > have any ratings > for the positive and neutral images. I do want > to model > these images and the fixation cross, however, > to make sure > that do not become part of the null. Based on > the wiki I > adapted my paradigm file like this: > > (1 = offset for the negative image; 2 = slope > for the > negative image; 3 = neu/pos image of no > interest; 4 = fixation) > > 00121NULL > 12431fix > 15131negoffset > 1523.79negslope > 18431fix > 21331neu/pos > 24431fix > 27131negoffset > 27231.00negslope > 30431fix > 33131negoffset > 3323.49negslope > 36091NULL > etc. > > Is this correct? > > Thanks so much for responding! > Suzanne > > > > -- > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>>va.nl <http://va.nl> > <http://va.nl> > > > https://sites.google.com/site/suzanneoosterwijk/ > > __._,_.___ > Reply via web post > > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwM2ltbGk0BF9TA…> > Reply to sender > <mailto:suzanne.oosterwijk@gmail.com > <mailto:suzanne.oosterwijk@gmail.com>?subject=Re%3A%20parametric%20modulation> > Reply to group > <mailto:martinos-tech@yahoogroups.com > <mailto:martinos-tech@yahoogroups.com>?subject=Re%3A%20parametric%20modulation> > Start a New Topic > > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJlMGwxMWZ1BF9TA…> > Messages in this topic > > <http://groups.yahoo.com/group/martinos-tech/message/5830;_ylc=X3oDMTM0bWtjc…> > > > (1) > > Recent Activity: > > Visit Your Group > > <http://groups.yahoo.com/group/martinos-tech;_ylc=X3oDMTJlNWFnMGY0BF9TAzk3Mz…> > > Yahoo! Groups > > <http://groups.yahoo.com/;_ylc=X3oDMTJkNzk1aW9nBF9TAzk3NDc2NTkwBGdycElkAzQ5O…> > > Switch to: Text-Only > > <mailto:martinos-tech-traditional@yahoogroups.com > <mailto:martinos-tech-traditional@yahoogroups.com>?subject=Change%20Delivery%20Format:%20Traditional>, > Daily Digest > <mailto:martinos-tech-digest@yahoogroups.com > <mailto:martinos-tech-digest@yahoogroups.com>?subject=Email%20Delivery:%20Digest> > • Unsubscribe > > <mailto:martinos-tech-unsubscribe@yahoogroups.com > <mailto:martinos-tech-unsubscribe@yahoogroups.com>?subject=Unsubscribe> > • Terms of Use > <http://docs.yahoo.com/info/terms/> • Send us > Feedback > <mailto:ygroupsnotifications@yahoogroups.com > <mailto:ygroupsnotifications@yahoogroups.com>?subject=Feedback%20on%20the%20redesigned%20individual%20mail%20v1> > . > > __,_._,___ > > > 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. > > > > > -- > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>>va.nl <http://va.nl> > <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > > > > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>>va.nl <http://va.nl> <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu>va.nl <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 1

tracula bvec flipped sign
by Cat Chong 30 Oct '13

30 Oct '13

Dear Experts, I was hoping you could help me with the following problem. Tracula failed when I attempted to use Siemens (Skyra) dicoms as input for the configuration file, so I converted the dicoms to niftii format using dcm2nii. I used the gradient information of the bvec file created by dcm2nii ( after re-assembling it into the appropriate 3 column format) and specified it as the bvec.txt file to run Tracula. All post- processing worked fine and the fiber paths look ‘ok’ as far as I can tell. Here is the conundrum: When I compared the bvec gradients from the dcm2nii conversion to the SIEMENS hardwired protocol, the sign of the ‘z’ direction appears to have been flipped? I am not sure why this happened and whether to choose the “hardwired” Siemens scanner bvecs or the ones created by the niftii conversion. Which ones are correct to use? Very best regards, Catherine

2 1

-autorecon2 -cp vs -autorecon2 without -cp
by Adam Mezher 30 Oct '13

30 Oct '13

Hi all, Just curious to know what would happen to the image if, after making control point edits, I do not include the -cp flag to the run command? Conversely, what would happen if I include the -cp flag without having made edits? Thanks, Adam *Adam Mezher* Staff Research Associate Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center 4150 Clement St. (114M) San Francisco, CA 94121 Tel: 415-221-4810 Ext. 4629 Fax: 415-668-2864

2 1

-openmp
by Jared Tanner 30 Oct '13

30 Oct '13

Hi, This might be answered somewhere but does -openmp work in 5.3 for OS X 10.8.x devices (I know online with the 5.2 release notes it says CENTOS only)? I ran recon-all with the -openmp flag and it finished without errors but did the flag actually do anything? Thank you, Jared

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