Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

mri_mask problem
by Gabriel Go.Es. 09 Mar '11

09 Mar '11

Hello, I'm making some manual segmentation changes in the brainmask.mgz and using mri_vol2vol and mri_mask commands to apply these changes to the rawavg.mgz, the output from the mri_vol2vol looks perfectly normal,and retains all changed made by me, but when I use the mri_mask command over the rawavg.mgz no segmentation seems to be donne in the final output file. Does any one has an idea of what could be wrong? the commands after manual corrections are: mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheadermri_mask rawavg.mgz brain2raw.mgz outbrain.mgz Thanks in advanced,Gabriel

2 2

Re: [Freesurfer] glm question
by Douglas N Greve 09 Mar '11

09 Mar '11

Gabriel Go.Es. wrote: > > Thank you so much, Doug > > I've check at your update and saw that this contrast has to be /2, > wich I guess means 0.5 instead of one to keep the scale right? Yes. > > and the contrast for me, would be something like: > Let's suppose > group1_males > group1_females > group2_males > group2_females > group3_males > group3_females > for differences between males and females (males > females) > regreessing the efects of group would be: > [0.333 -0.333 0.333 -0.333 0.333 -0.333] Correct > differences between group1 & group 3 regressing the effects of gender: > [0.5 0.5 0 0 -0.5 -0.5] Correct > and the differences between males and females for a single group can be: > [1 -1 0 0 0 0] > am I right??? Yes > but I don't yet figure out how to set a difference from 0 in any of > the group means (to meassure the effect of group), nor the interaction > between group and gender, and that's because my model is not like the > one from the example, Try using [1 -1 -1 1 0 0] [1 0 0 0 -1 1] This is a single matrix with two rows. The first row tests for an interaction between G1/2 and M/F. The second row tests for G1/3 and M/F. Note that you don't need a third row. > > > > > > > Date: Wed, 9 Mar 2011 14:52:37 -0500 > > From: greve(a)nmr.mgh.harvard.edu > > To: gabriellbk(a)hotmail.com > > CC: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] glm question > > > > That contrast is wrong. I've updated this page with the correct contrast > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf6G0V > > which is: > > > > |+1 -1 0 -1 +1 0| > > |+1 0 -1 -1 0 +1| > > > > This is an F-contrast (two rows). The first row looks for a difference > > between L and R for M and F (ie, a simple interaction between LR and > > MF). The second row looks for a difference between L and A for M and F. > > If either of these subcontrasts shows an effect, then there is an > > interaction. > > > > doug > > > > > > Gabriel Go.Es. wrote: > > > > > > Dear FreeSurfer experts, > > > > > > > > > > > > I'm doing some group analyses and I'm a little stocked with this: > > > > > > I have Six Groups (2 Factors, one with three levels and the other one > > > with two levels), and one covariate. I don't know the rule for > setting > > > the contrasts for an ANOVA and for the interaction between the two > > > factors regressing out the covariate. I've checked at the FS wiki and > > > found the following contrast for six groups (two factors) and zero > > > covariates. > > > > > > > > > > > > Contrast 6 gender-x-handedness.mtx (interaction between gender and > > > handedness) > > > > > > [0.333 -0.333 -0.333 0.333 0.000 0.000 0.000 0.000 0.000] > > > > > > [0.000 0.000 0.000 0.000 0.000 0.333 -0.333 -0.333 0.333] > > > > > > > > > > > > I don’t understand the rule that has been followed. > > > > > > Can any one help me with this? > > > > > > > > > > > > Bests, > > > > > > Gabriel > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > 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. > > -- 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

1 0

2 questions on folding index, local gyrification index
by Chris Hyatt 09 Mar '11

09 Mar '11

I had asked the Listserv a week or so ago if there was a way to get the Folding Index measurement for each subject and ROI using aparcstats2table, similar to area, thickness, gray volume etc.. The data are in the ?h.aparc.stats files for each subject, along with thickness, thickness std, surface area, gray volume, mean curv, gauss curv and curv index. Can this be done, or the feature added to aparcstats2table? If not, I'll write my own code to do this. Also, I'm calculating the local Gyrification Index (lGI) for my subjects. It works well, but our group currently has only one Image Processing Toolbox license. It appears Freesurfer calls the toolbox only briefly. Does anyone know which toolbox functions are called? I know that fspecial() is one of the functions called, and if that is the only function, it probably can be replaced with a custom function to eliminate the need for the toolbox. Thanks! Chris

2 1

Original Brain Surface Transparent
by Allie Rosen 09 Mar '11

09 Mar '11

Hi Everyone Again, I thought I'd re-state my question more clearly: I managed to make an annotation with 2 parts: one, of interest, and the other, not. On the color table file, the "not of interest" part has 0 0 0 0 for Red, Green, Blue, and Opacity. However, when I load the annotation in TkSurfer, the "not of interest" part of the brain is the original grey. So, here is my question: is there a way to make the original brain surface transparent? If not, then it is pointless for me to have the "not of interest" part in my annotation at all. Thanks very much, Allie Rosen, MSc Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

1 0

intracranial EEG position at NYU
by Thesen, Thomas 09 Mar '11

09 Mar '11

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. The position is available for 2-4 years and includes benefits. Start date can be immediately or later upon agreement. Please visit our web lab page for more information: http://www.med.nyu.edu/thesenlab 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 </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE>

1 0

Aparc Cutting?
by Allie Rosen 09 Mar '11

09 Mar '11

Hi Everyone, I'm wondering if it is possible to use the "cut" function in TkSurfer to delete specific atlas annotations. For example, can I create a label of my specific area of interest, inverse the label to highlight the rest of the brain, and then either cut out these regions or make them transparent? Can anyone help me out? Thank you, Allie Rosen, MSc Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

4 12

Re: [Freesurfer] Whole brain gray matter image
by Douglas N Greve 09 Mar '11

09 Mar '11

For mni152 space, you'll need to register your anatomical to the 152 brain. You can do this with the freesurfer mni152reg program (might only be in the new version). Then use mri_vol2vol specifying this reg and also making sure that you use nearest neighbor interpolation. One problem is that this does not rotate the directions, so it might not be useful to you. doug caoaize wrote: > Hi, Doug, > > If I want to use the generated gray matter for VBM analysis, I need to > put them into the same space (MNI, or Talariach). Do you know where or > how I can get that ? Thanks. > > Aize > > > > > Date: Tue, 1 Mar 2011 16:31:52 -0500 > > From: greve(a)nmr.mgh.harvard.edu > > To: caoaize(a)hotmail.com > > Subject: Re: [Freesurfer] Whole brain gray matter image > > > > You'll probably have to go to 255 or so (255 is corpus callosum). Also, > > for aparc+aseg, everything above 1000 will be GM. > > doug > > > > caoaize wrote: > > > I am saying just look through 1to 98, and remove the IDs that relate > > > with WM,vent, etc. No need to look at the the ID more than 100, > right? > > > Thanks. > > > > > > Aize > > > > > > > Date: Tue, 1 Mar 2011 15:42:28 -0500 > > > > From: greve(a)nmr.mgh.harvard.edu > > > > To: caoaize(a)hotmail.com > > > > Subject: Re: [Freesurfer] Whole brain gray matter image > > > > > > > > No, that will give you both WM and GM. > > > > > > > > caoaize wrote: > > > > > Hi, Doug, > > > > > > > > > > Should I just check the IDs from 1 to 98 in > FreesurferColorLUT.txt? > > > > > > > > > > Aize > > > > > > > > > > > Date: Wed, 9 Feb 2011 14:27:08 -0500 > > > > > > From: greve(a)nmr.mgh.harvard.edu > > > > > > To: caoaize(a)hotmail.com > > > > > > Subject: Re: [Freesurfer] Whole brain gray matter image > > > > > > > > > > > > Yea, though I think I'd use aparc+aseg for this since the cortex > > > > > > boundaries in the aseg are not great. The easiest way to do it > > > is to use > > > > > > mri_binarize with the --match option. You could list all of the > > > IDs that > > > > > > correspond to gray matter structures, but it is probably easier > > > to list > > > > > > all the stuff that you don't want (eg, cerebral and > cerebellar white > > > > > > matter, CC, hypointensit ies, CSF, etc, (and 0)), then use the > > > --inv to > > > > > > invert it. > > > > > > > > > > > > doug > > > > > > > > > > > > caoaize wrote: > > > > > > > I need both cortical and subcortical. As I understand, I can > > > extract > > > > > > > them from aseg.mgz, right? ribbon.mgz gives some information > > > too, any > > > > > > > idea? Thanks. > > > > > > > > > > > > > > Aize > > > > > > > > > > > > > > > Date: Wed, 9 Feb 2011 11:44:15 -0500 > > > > > > > > From: greve(a)nmr.mgh.harvard.edu > > > > > > > > To: caoaize(a)hotmail.com > > > > > > > > CC: freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > Subject: Re: [Freesurfer] Whole brain gray matter image > > > > > > > > > > > > > > > > > > > > > > > > Do you want cortical and subcortical or just cortical? > > > > > > > > doug > > > > > > > > > > > > > > > > > > > > > > > > caoaize wrote: > > > > > > > > > Hello FS Experts, > > > > > > > > > > > > > > > > > > I am trying to generate the whole brain gray matter > image, > > > I use > > > > > > > > > aparc_aseg.mgz - wm.mgz for gray matter mask, then use > this > > > > > mask for > > > > > > > > > gray matter. Is it correct? What is the difference between > > > > > aseg.mgz > > > > > > > > > and ribbon.mgz? Hope your help. Thanks. > > > > > > > > > > > > > > > > > > Aize > > > > > > > > > > & gt; > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > 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 > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > Freesurfer mailing list > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > 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 th e e-mail. > > > > > > > > > > > > > > > > > > > > -- > > > > > > 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 > > > > > > > > > > > > > > -- > > > > 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 > > > > > > > > -- > > 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 > > > > * -- 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

1 0

glm question
by Gabriel Go.Es. 09 Mar '11

09 Mar '11

Dear FreeSurfer experts, I'm doing some group analyses and I'm a little stocked with this: I have Six Groups (2 Factors, one with three levels and the other one with two levels), and one covariate. I don't know the rule for setting the contrasts for an ANOVA and for the interaction between the two factors regressing out the covariate. I've checked at the FS wiki and found the following contrast for six groups (two factors) and zero covariates. Contrast 6 gender-x-handedness.mtx (interaction between gender and handedness) [0.333 -0.333 -0.333 0.333 0.000 0.000 0.000 0.000 0.000] [0.000 0.000 0.000 0.000 0.000 0.333 -0.333 -0.333 0.333] I don’t understand the rule that has been followed. Can any one help me with this? Bests, Gabriel

2 1

qdec problems
by 汪贵宏 09 Mar '11

09 Mar '11

Hi,all: I have several problems about the qdec in freesurfer 5.0. Firstly,can somebody explain the function of the buttons in the qdec's third step (display),such as Set using FDR in the False Discovery Rate ,Monte Carlo Null-Z simulation.If I just let these buttons as the default ,is it right ? Secondly, what does the "MAX" and "VtxMAX" and "NVtxs"mean just as follows,which is output from the teminal. Generating cluster stats using min threshold of 2... Found 5 clusters Contrast: 'rh-Diff-Yes-No-Intercept-thickness', 10fwhm, DOF: 21 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -3.4159 8928 51.50 31.9 -34.9 46.8 146 postcentral 2 -2.6111 120796 42.30 30.5 -6.5 -32.9 79 entorhinal 3 -2.5302 122287 22.28 35.4 -68.1 43.1 41 inferiorparietal 4 2.3762 145773 21.24 40.3 22.6 20.6 46 parsopercularis 5 2.1491 24852 19.94 4.8 -40.1 71.5 55 paracentral ============================================================ Thanks, Wang

3 2

Resampling Question
by Jeff Sadino 09 Mar '11

09 Mar '11

Hello, I have a question about the effects of FreeSurfer's resampling algorithms. The way our pipeline goes is that we convert our DICOM images into .nii.gz format using FSL tools. One of the commands we use is FSLCPGEOM. I was never sure why, but our script would always break without it. Looking into it in more detail now, I see that it is replacing the voxel size information in the Nifti header with the voxel size in the template that FSLCPGEOM is copying from. This is causing all of our data to show isovolumetric 1x1x1 information in the header, even if the voxels really are non-isovolumetric. I have been having a difficult time combining FreeSurfer results across our different studies and I am wondering if this might be the reason why. All of our studies have voxels acquired near 1x1x1 isovolumetric, usually no more than .3mm away in any direction. What would the effect be of pushing data through the FreeSurfer reconstruction pipeline that is not really 1x1x1 isovolumetric? Thank you, Jeff Sadino

2 2

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