Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions
by Douglas N Greve 24 Apr '13

24 Apr '13

You don't generate a negative coefficient. The sign and magnitude of the coefficient is determined by the fitting procedure. It may be the case that a positive coef fits the data better than a negative. You should not change the gamma parameters. doug On 04/24/2013 04:06 PM, SHAHIN NASR wrote: > > I know but how can we generate negative coefficient? To clarify, we > use alpha=2, delta=2.25 tau=1.25 to generate default HRF. Using > negative values for alpha, delta or tau, does not invert the shape of > the curve (HRF). > > > On Wed, Apr 24, 2013 at 3:12 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > What do you mean the gamma function generates positive values? It > will create a regressor with a positive-going HRF. However, the > regression coefficient can be negative which would invert the > shape. The reg coef is fit to the data, so the data will tell you > whether there is an undershoot or not. > doug > > > > On 04/24/2013 03:02 PM, SHAHIN NASR wrote: > > Hi Doug, > Sorry to follow this topic with a delay but we tried to > model BOLD signal undershoot with a gamma function and we > failed. The problem is, gamma function generates positive > values and we can NOT use "inverse gamma function" (or > otherfunction similar to that) as a part of mkanalysis-sess > (for modeling BOLD signal undershoot). We even used matlab > gammafit to estimate parameters and it said that values should > be positive otherwise gammafit function fails. > Do you have any suggestion? > > > > On Wed, Apr 10, 2013 at 6:46 PM, Douglas N 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: > > > yes, that is what you want. The only other way that comes > to mind > is to model each event type as two event types one delayed > relative to the other. Then model the responseto each as a > gamma. > If the delay is right, then the first gamma should model > the main > positive response and the second gamma will model the negative > response. both will be independent from the other. > > doug > > > On 04/10/2013 05:00 PM, shahin(a)nmr.mgh.harvard.edu > <mailto:shahin@nmr.mgh.harvard.edu> > <mailto:shahin@nmr.mgh.harvard.edu > <mailto:shahin@nmr.mgh.harvard.edu>> wrote: > > I think I figured it out but I want to double check. I am > generating > group-average map for my subjects using isxconcat-sess > command > which > generates ces maps for each time frame. I think these > maps are > what I > wanted. Right? > If you still have other solutions that you think may > generate more > reliable results, I am eager to know. For instance, is > there > anyway to > fit a model as we do for spmhrf or fslhrf, but just > for the > negative > peak? > > Regards > > That's the problem Doug. I have already generated > the FIR > model but how > can > I show the sig MAP for one "particulat time > point". What > are the other > ways? > > > On Wed, Apr 10, 2013 at 4:05 PM, Douglas N 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 Shahin, there are several ways that you > could do > it. The one that > immediately comes to mind is to use an FIR and > then > test for a > difference > at a particular post stimulus time point. > doug > > > > > On 04/10/2013 03:54 PM, SHAHIN NASR wrote: > > Hi, > I want to generate a map to show the > significant difference > between > HRF undershoot (negative peak of activity) > between two conditions > independent from the positive peak. Is there > anyway, to generate this > map? > > P.S.: Please note that I need a map and > not a time > course graph. > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting><http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/**facility/filedrop/index.html> > > <http://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/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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/ > > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > -- > 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/ > > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School -- 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/

1 0

Fwd: Comparing HRF undershoots between conditions
by SHAHIN NASR 24 Apr '13

24 Apr '13

That's the problem Doug. I have already generated the FIR model but how can I show the sig MAP for one "particulat time point". What are the other ways? On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > Hi Shahin, there are several ways that you could do it. The one that > immediately comes to mind is to use an FIR and then test for a difference > at a particular post stimulus time point. > doug > > > > > On 04/10/2013 03:54 PM, SHAHIN NASR wrote: > >> Hi, >> I want to generate a map to show the significant difference between >> HRF undershoot (negative peak of activity) between two conditions >> independent from the positive peak. Is there anyway, to generate this map? >> >> P.S.: Please note that I need a map and not a time course graph. >> >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> > > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: 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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

3 6

smooth overlay
by Thomas Janssens 24 Apr '13

24 Apr '13

Dear Freesurfers, During the display of my data in tksurfer I smoothed my overlay with 1 smoothing step (Tools > Surface > Smooth Overlay... ). All I could figure out was that this is done by sclv_smooth but what is exactly happening mathematically in this case? What does 1 smoothing step correspond to? Thanks a lot for your help! Regards, Thomas Janssens Thomas Janssens, PhD student FWO Laboratorium voor Neuro- en Psychofysiologie K.U.Leuven Medical School Herestraat 49, B-3000 Leuven (Belgium) phone +32 16 33 00 35 cell phone +32 494 115 509 thomasj(a)nmr.mgh.harvard.edu thomas.janssens(a)med.kuleuven.be

2 1

Re: [Freesurfer] cwpvalthresh not specified
by Jeni Chen 23 Apr '13

23 Apr '13

Phew! Thanks! jeni

1 0

cwpvalthresh not specified
by Jeni Chen 23 Apr '13

23 Apr '13

Hello, Just a quick question, if the 'cwpvalthresh' flag wasn't specified when running mri_glmfit-sim, the script will use the default .05 value, correct? Thanks for clairfying. Jeni Chen

2 1

merging dti data
by Jon Wieser 23 Apr '13

23 Apr '13

we captured some dti data. there were 2 runs. we acquired in the axial plane, 2mm slice thickness the first run captured the lower half of the brain, slice locations: I56-S20, and the second run captured the upper half of the brain S16-S92. i have made briks from each of these runs. I can convert the briks to nifti files I want to merge the nifti files together to analyze the data in tracula In the past i have merged data from two dti runs, but each run have covered the entire brain, with the following commands mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz would it work to concat the two half brain niftis into one file and analyze that with tracula? (I will concat the bvec and bvals files too) would this cause problems doing it this way? Thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145

3 8

transformation between cvs and native space
by Kami Koldewyn 23 Apr '13

23 Apr '13

Hi All, We have contiguous ROIs in cvs template (volume) space. We need to move this to each individual subject's surface. What's the best way of doing this? We tried going from template volume to individual volume to individual surface, but these rois were not all contiguous on the surface -- in some cases they were split nearly in half (most likely because they were placed on either side of a sulcus). We could try to correct for this problem in each individual, but that would be very labor-intensive and pretty subjective across individuals. We're thinking that it would be better to go from template volume to template surface and then from template surface to individual surface -- this way we can make all of our corrections on the template surface, which would make ad hoc corrections not different across subjects. But we're not sure what the best way to do this is as the cvs transform that allows us to get back to subject-specific native space is a volume transform: 1. Do people think that going to template surface rather than individual volume is the better intermediate step? 2. If yes, do you think it's best to move to the CVS surface and then use spherical surface alignment transform to move from the template surface to each individual surface - or is there a better way to do this? Any pointers on how to do this with the smallest number of transformations and/or steps that require morphing or interpolation would be greatly appreciated. sorry for the long email, and thanks in advance! -kami --------------------------------------------------------------- Kami Koldewyn, PhD. McGovern Institute for Brain Research MIT, Building 46 Room 4141 (Kanwisher Lab) Cambridge, MA 02139 kamik(a)mit.edu

1 0

GLM | group comparison and correlation on surface with whole-brain DTI/tractography results | How to setup fsgd and contrast matrix?
by Robert Schulz 23 Apr '13

23 Apr '13

Hi Freesurfers, I managed to project tractography results (seed-based whole-brain tractography performed in FSL) onto the surface of each individual subject (19 OLD, 19 YOUNG). Each individual surface (including the results) has been transferred to fsaverage to allow statistical group comparison on the group surface level: mri_surf2surf --srcsubject SUBJ --srcsurfval ${main}/${study}/voxelnum_IN_STRUCT_fs_DILF.mgh --trgsubject fsaverage --trgsurfval ${main}/${study}/voxelnum_IN_STRUCT_fs_DILF_average.mgh --hemi ${side[$i]}h I concatenated all the subjects (first 19 old, then 19 young) and smoothed it with fwhm of 10 using the following commands: mri_concat ${main}/${study}/*voxelnum_IN_STRUCT_fs_DILF_average.mgh --o ${main}/${study}/all.mgh mri_surf2surf --srcsubject fsaverage --srcsurfval ${main}/${study}/all.mgh --fwhm 10 --trgsubject fsaverage --hemi ${side[$i]}h --trgsurfval ${main}/${study}/all_smooth.mgh My questions: 1) To answer the question where the "tractograophy_results_on_surface" are higher in OLD then in YOUNG I used the follwong command mri_glmfit --glmdir ${main}/${study}/fs/glmout --y ${main}/${study}/all_smooth.mgh --fsgd ${main}/${study}/fs/glmout/glmout/glm.fsgd --C ${main}/${study}//fs/glmout/omy.mtx --surf fsaverage ${side[$i]}h --cortex with glm.fsdg GroupDescriptorFile 1 Class Old Class Young Input co_001 Old Input co_002 Old Input co_003 Old Input co_004 Old Input co_005 Old Input co_006 Old Input co_007 Old Input co_008 Old Input co_009 Old Input co_010 Old Input co_011 Old Input co_012 Old Input co_013 Old Input co_014 Old Input co_015 Old Input co_016 Old Input co_017 Old Input co_018 Old Input co_019 Old Input cy_001 Young Input cy_002 Young Input cy_003 Young Input cy_004 Young Input cy_005 Young Input cy_006 Young Input cy_007 Young Input cy_008 Young Input cy_009 Young Input cy_012 Young Input cy_016 Young Input cy_019 Young Input cy_020 Young Input cy_021 Young Input cy_022 Young Input cy_024 Young Input cy_014 Young Input cy_025 Young Input cy_028 Young and the contrast file omy.mtx 1 -1 This approach gave me plausible results compared to my pilot FSL analysis. 2) Second I'd like to perform a simple correlation analysis correlating the result_on_surface in OLD with another behavioural measure (e.g. performance in a motor task). Therefore I concatenated the surfaces of all OLD subjects. I wonder how the fsgd file and the contrast file would look like for the GLM_FIT? If I put GroupDescriptorFile 1 Class Old Variables Learning Input co_001 Old x Input co_002 Old x Input co_003 Old x Input co_004 Old x Input co_005 Old x Input co_006 Old x Input co_007 Old x Input co_008 Old x Input co_009 Old x Input co_010 Old x Input co_011 Old x Input co_012 Old x Input co_013 Old x Input co_014 Old x Input co_015 Old x Input co_016 Old x Input co_017 Old x Input co_018 Old x Input co_019 Old x in the fsdg with x = behavioural result and " 0 1 " in the contrast file corr.mtx (looking for positive correlation between surface_result and behaviour), I don't get any significant results. And I am not sure whether I performed the analysis correctly. Can anybody tell me whether the GLM, fsgd and contrast files are set up correctly, both for the group comparison in 1) and for the correlation analysis in 2). Thank you very much! Kind regards, Robert -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus

1 0

Research Assistant position
by Olivier Coulon 23 Apr '13

23 Apr '13

Dear All, please find below an announcement for a research assistant position. ----------------------------------------------------------------------------------- Neuroimaging Research Engineer - Centre IRMf de La Timone, Marseille, France *Recruitment date:* May 2013 *Application closing date:* May 15th, 2013 *Contract duration:* 30 months *Salary*: 19.000 -- 24.000 Euros / year, depending on experience *Context* The La Timone fMRI Centre (http://irmfmrs.free.fr/) of the Institut des Neurosciences de La Timone (http://www.int.univ-amu.fr/) in Marseille provides neuroscientists, medical researchers, and psychologists from the Aix - Marseilles area and beyond with Magnetic Resonance Imaging (MRI) services. The Centre operates a 3 Tesla MR system fully dedicated to neuroscience and psychology research in human and non-human primates and equipped with high-end stimulation and recording systems. The Centre, affiliated to CNRS and Aix-Marseille University, is involved in clinical, fundamental and methodological research and technical development through collaboration with local, national and international research groups and with a strong involvement in training and teaching. *Mission* The post holder will have for mission to assist the user community with basic and advanced analysis of cerebral MRI data (functional and structural). Specifically, tasks include: - Advise and help users with standard analysis of brain MR data - Help users with advanced analyses such as functional connectivity, diffusion tensor imaging, tractography, multivariate analysis, morphometry, ... - Develop and optimize software pipelines - Assist with the design and set-up of new studies - Contribute to education and training of the users *Profile of the candidate* Background in neuroimaging essential Experience with brain image analysis packages (e.g., SPM, Freesurfer, BrainVISA or FSL) Experience with development of brain image analysis methods or/and their application to neuroimaging studies desirable Good knowledge of statistical methods and tools Expertise with one or several programming languages (Matlab, Python, C/C++) Autonomy, initiative, ability to work at the interface between multidisciplinary teams *Information requests and applications should be addressed to **Jean-Luc.Anton(a)univ-amu.fr**, **Patricia.Romaiguere(a)univ-amu.fr**, and **Pascal.Belin(a)univ-amu.fr* -- signatureMail2011 Olivier Coulon, CNRS research Fellow, Head of the Images&Models team olivier.coulon(a)univ-amu.fr <mailto:olivier.coulon@univmed.fr> Tel: +33491828527 fax: +33491828550 http://olivier.coulon.perso.esil.univmed.fr <http://olivier.coulon.perso.esil.univmed.fr/> LSIS Laboratory, I&M Team ESIL, Campus de Luminy, Case 925, 13288 Marseille cedex 09, FRANCE BrainMorph logo http://www.lsis.org/brainmorph

1 0

Where does a sulcus end and a gyrus begin in FreeSurfer?
by Yang, Daniel 23 Apr '13

23 Apr '13

Dear FreeSurfer Experts and Users, This is probably a basic question, so please bear with me. I'm looking at the Coronal view in tkmedit, and I am wondering how does FreeSurfer knows where a gyrus ends and a sulcus begins (and vice versa). For example, I'm looking at the superior temporal sulcus. But I'm not sure how FS figures out which part is superior temporal gyrus, middle temporal gyrus, or superior temporal sulcus? Thanks! Daniel

3 3

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