Re: [Freesurfer] Task-based connectivity

External Email - Use Caution Hi Kazuhisa, I believe that I included a wrapper for FSFAST to run gPPI. Please download the toolbox and take a look. If it's not there or your having issues, please let me know and I can help troubleshoot. Best Regards, Donald McLaren, PhD On

Re: [Freesurfer] GLM - covariate question

Pedro, Instead of saying that you want to include the covariate in the analysis, it's better to consider why you want to include the covariate and how it changes the interpretation. You don't necessarily want to regress out covariates, especially when the covariate is different between groups.

[Freesurfer] Minc File Error

Zeke and others, I recently installed Freesurfer v6 ( freesurfer-Darwin-OSX-stable-v6-beta-20151015.dmg , MacOS 10.9.5, XQuartz 2.7.8), and Freeview always closes whenever I try to

Re: [Freesurfer] Checking optseq efficiency of a custom par file.

You need to build a wrapper that creates all possible combinations of the three sets of par files. Then use this to build a design matrix for each one. Then estimate the efficiency (eff) and VRF (vrf) for the contrasts of interest. M = C*inv(X'*X)*C'; eff = 1/trace(M); vrf =

Re: [Freesurfer] Questions about the correction methods in Surfstat

>The output figure is attached. In the colorbar of the figure, left represents cluster corrected p value and right one represents the vertex >corrected p value, right? Right. >So, the warm color region in the figure can be survived by the RFT vertex correction, and the cool color region in the

Re: [Freesurfer] registering NHP data

-- *From:* MCLAREN, Donald [mclaren.don...@gmail.com] *Sent:* Tuesday, August 04, 2015 9:36 AM *To:* Borzello, Mia *Subject:* Re: [Freesurfer] registering NHP data Mia, You could use the 112RM-SL atlas for normalization and then use the Saleem-Logothetis Atlas

Re: [Freesurfer] help with using optseq2

This type of design is not suitable for optseq2. Furthermore, you only have 100s of task and almost 300s of scan time. This will lead to lots of empty space. You really need more than 2 conditions per event type. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow,

Re: [Freesurfer] Dynamic causal modeling

SPM does not make any distinction about the source of the data. For SPM to work, all you need is .nii files for your data and you'd need a VOI.mat that corresponds to the .nii file size. If you take a look at the gPPI toolbox on the NITRC website, there are commands/tools that convert FS-FAST 1st

Re: [Freesurfer] finding local extrema in surface data

Not the fastest approach, but for each vertex, you could find the neighbors and then test if the vertex is the maximum. There are matlab functions for getting the list of neighboring vertices. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of

[Freesurfer] Label to Nii Conversion

I have a label file on the surface, but want to be able to use it to extract surface data that is already in nifti format (dimensions: [2737 1 6]). Is there a way to convert a label to nifti? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of

[Freesurfer] Brainhack EDT - Boston Updates and Registration Details

*October 18th and 19th, Boston* *McGovern Institute for Brain Research @ MIT - * *http://whereis.mit.edu/?go=46* http://whereis.mit.edu/?go=46 *3rd floor Atrium * *Doors will be locked, so we will have to let you in. If you are the door, please call 4-3544 or (617-324-3544) or send a chat

[Freesurfer] Brainhack Eastern Standard Time - Boston October 18-19, 2014

*Do you have a great idea for collaboration or want to collaborate on great ideas?* *THEN BRAINHACK IS THE PLACE FOR YOU* Brainhack is a unique conference that convenes researchers, artists, and members of industry from across the globe and a myriad of disciplines to work together on

Re: [Freesurfer] Correlation coeffecient

Lars, Yes. You could use that equation. Here are some more conversions: http://www.soph.uab.edu/Statgenetics/People/MBeasley/Courses/EffectSizeConversion.pdf Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General

[Freesurfer] Surface Label to Nifti File

I'm trying to convert a surface label to a nifti file to use with functional surface data that is already in nifti format. The ultimate goal is to be able to use the converted surface label as a seed in gPPI analyses that is run in MATLAB. I've been able to use volume based seeds for the MNI305

Re: [Freesurfer] comparing two conditions with disproportionate number of trials

For the contrast AB, the number of trials is not considered. When you contrast A and B, you are assessing the mean response to trials of condition A to the mean response to trials of condition B. You wouldn't want to weight this by the number of trials as then the contrast would not make sense.

[Freesurfer] gPPI Toolbox Version 13.1 for SPM has now been released

Version 13.1 of the gPPI toolbox (previously released versions were 7.12 and 13) is now available at http://www.nitrc.org/projects/gppi Version 13.1 now supports task-models from FSFAST and can read the model structure directly from your FSFAST analysis. Version 13.1 now support robust weighted

Re: [Freesurfer] A question regarding DODS or DOSS

You might also want to read about mean centering and same or different slopes here: *http://mumford http://mumford*.fmripower.org/*mean*_*centering*/ Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and

Re: [Freesurfer] Power analysis for Qdec

One comment on power calculations. You cannot do the power calculations after you have completed the study. Any reviewer/referee asking you to compute the power should be politely informed that post-hoc power analyses are not valid and are biased (because you would be computing the power of the

Re: [Freesurfer] Power analysis for Qdec

. On Tue, Oct 29, 2013 at 10:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Good point Donald. Where can one get G*Power? doug On 10/29/2013 10:38 AM, MCLAREN, Donald wrote: One comment on power calculations. You cannot do the power calculations after you have completed the study

[Freesurfer] Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST OCTOBER 3rd, 2013)

Dear Colleagues, The Neurobureau is excited to announce a stipend program for Brainhack 2013. The stipend program was created following a generous grant from Siemens Healthcare to assist young investigators in attending Brainhack 2013. Without their support, the stipend program would not exist.

[Freesurfer] UPDATES on Brainhack 2013 (including stipend application extension)

Dear All, Brainhack 2013 will be taking place in just under a month outside of Paris, France. A welcome reception will be held on the evening of October 23rd to be followed by the hackathon on October 24th, 25th, and 26th. Brainhack 2013 will be highlighted by Ignite talks by: - *Yves

[Freesurfer] Brainhack Registration and Payment

Brainhack.org is currently offline due to technical issues. We hope to have the website back up and running shortly. Here are the details to register (if you have not already) and to complete the payment process (if you pre-registered). The cost for the entire workshop and lodging for 4 nights is

[Freesurfer] Fwd: Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST TONIGHT)

Dear Colleagues, The Neurobureau is excited to announce a stipend program for Brainhack 2013. The stipend program was created following a generous grant from Siemens Healthcare to assist young investigators in attending Brainhack 2013. Without their support, the stipend program would not exist.

[Freesurfer] Fwd: Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST SEPTEMBER 27, 2013)

Dear Colleagues, The Neurobureau is excited to announce a stipend program for Brainhack 2013. The stipend program was created following a generous grant from Siemens Healthcare to assist young investigators in attending Brainhack 2013. Without their support, the stipend program would not exist.

[Freesurfer] Fwd: Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST SEPTEMBER 27, 2013)

Dear Colleagues, The Neurobureau http://www.neurobureau.org is excited to announce a stipend program for Brainhack 2013 http://www.brainhack.org (October 23-26 in Sevres, France (just outside of Paris). The stipend program was created following a generous grant from Siemens Healthcare to assist

Re: [Freesurfer] Ploting convolved stimuli with actual stimuli

Aser, If you you put your custom sequence into SPM, you can get the graphs above. The key variables are: SPM.Sess.U.u, time variable is 0:TR/#oftimebins:TR/#oftimebins*size(SPM.Sess.U.u,1) SPM.xX.X, time variable is 0:TR:TR*size(SPM.xX.X,1), this is the convolved data., this is the stick function

Re: [Freesurfer] Getting around a design matrix with zero columns

Ye, If you use the DOSS model as Doug suggested, you have will not have a column of 0s in the matrix. However, the group columns become the covariate-adjusted thickness in each group (e.g. thickness at the mean years of meditation across everyone) - which doesn't make sense as non-meditators

Re: [Freesurfer] [martinos-tech]

Suzanne, p0.005 is the same whether its voxels or vertices. The liberal nature of 20 voxels is vague to begin with as there is two things contributing to how liberal 20 voxels are: (1) voxel size - 20 1mm isotropic voxels is quite different from 20 3mm isotropic voxels; (2) The number of voxels

[Freesurfer] Brainhack 2013 Update - Registration is open, Stipend program announced

Dear colleagues, I wanted to draw your attention on the upcoming Brainhack 2013, which is being held from October 23-26 at the Centre International d'Études Pédagogiques, Sèvres, France (just outside of Paris). Registration is limited, please register to guarantee a spot (http://www.

[Freesurfer] Brainhack 2013 Invitation and Registration Link

Dear colleagues, I wanted to draw your attention on the upcoming Brainhack 2013, which is being held from October 23-26 at the Centre International d'Études Pédagogiques, Sèvres, France (just outside of Paris). Brainhack 2013 is a unique workshop with the goals of fostering interdisciplinary

Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing

This raises an interesting question. Given that the longitudinal process is more reliable, if we collect 2 scans on the same day, should we average those scans and then submit to Freesurfer or apply Freesurfer first and then create an average of the metrics from the longitudinal pipeline? Best

[Freesurfer] Mean Regional Thickness

Has anyone published the mean cortical thickness of healthy older adults for all the Freesurfer ROI? I've only been able to find papers that report a of subset of the ROIs. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts

[Freesurfer] Cross-sectional v5.1 vs. Longitudinal v4.4

Dear All, If I had to choose between longitudinal processing v4.4 or cross-sectional processing v5.1 for analyzing longitudinal data, what processing stream should I choose? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts

Re: [Freesurfer] p-value visualization

Here is an example regionaldata file. (File with script and dependency is being held for moderator approval) Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research

[Freesurfer] T2/FLAIR images longitudinal stream

Martin and others, As the T2/FLAIR image is only available for cross-sectional processing; if we are doing a longitudinal study, is there any advantage of using the T2/FLAIR image? Will the improved pial surface can transferred to the base and long surfaces? Best Regards, Donald McLaren

[Freesurfer] Fwd: [FSL] Neuro Bureau Announces the BRAIN-ART COMPETITION 2013

In order to recognize the beauty and creativity of artistic renderings emerging from the neuroimaging community, we are launching the third annual Brain-Art Competition. Countless hours are devoted to the creation of informative visualizations for communicating neuroscientific findings. The

Re: [Freesurfer] Permutation doubts

An alternative approach would be to use bootstrapping to determine the significance as was done by Gross et al. 2012. *Cortical signatures of cognition and their relationship to Alzheimer's disease.* Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of

Re: [Freesurfer] How to get surface-based AAL template {Disarmed}

I believe that someone has created the AAL labels on the Colin 27 brain. These should be able to be transformed to the fsaverage brain. I've contacted the person who said they had the files and will let you know if I get the files and am able to transform the files. Best Regards, Donald McLaren

Re: [Freesurfer] slice timing

If you are using ASL, you do not want to use Slice timing. You must compute the CBF maps and keep the slice timing intact. Removing the time delay between slices will lead to the wrong CBF values as the CBF equations have the time delay in the equation. Best Regards, Donald McLaren

Re: [Freesurfer] Correlation with cortical thickness

. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Wed, Mar 27, 2013 at 3:46 PM, MCLAREN, Donald mclaren.don...@gmail.comwrote: Here is a link describing the difference in the methods: http

Re: [Freesurfer] Linear Mixed modal

Contrast creation is the same in all programs. It is based on the design matrix. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA

Re: [Freesurfer] contrast matrix

. is correct? thank you very much! look forward for your reply! Bo Xiang At 2012-11-21 04:07:37,MCLAREN, Donald mclaren.don...@gmail.com wrote: On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Thanks Donald. Is this the standard way to do this? I

Re: [Freesurfer] Correlation with cortical thickness

Here is a link describing the difference in the methods: http://onlinelibrary.wiley.com/store/10.1046/j.1365-2656.2002.00618.x/asset/j.1365-2656.2002.00618.x.pdf?v=1t=heswinwbs=dce1a222e16e861d105340fd919c65fb43dc39ac Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research

Re: [Freesurfer] help with contrasts

a statistician - which I am not. Laura. On Thu, Mar 21, 2013 at 5:51 PM, MCLAREN, Donald mclaren.don...@gmail.com wrote: Please include the list of the column labels. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts

Re: [Freesurfer] help with contrasts

group, as you suggested - I just want to make sure I am understanding the weights correctly first... LT On Fri, Mar 22, 2013 at 8:23 AM, MCLAREN, Donald mclaren.don...@gmail.com wrote: On Thu, Mar 21, 2013 at 8:59 PM, Laura M. Tully tully.la...@googlemail.com wrote: oops sorry! (I

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

For many non-human primate species, volume templates already exist. I would recommend using them and aligning your surface templates to them to aid in the ability to compare studies across laboratories in the same space. For rhesus, see the 112RM-SL atlas. Best Regards, Donald McLaren

Re: [Freesurfer] preparing NHP data for whole brain analysis

I would recommend using the volume space initially until you can get more surfaces to create your group surface. The one issue with the 112RM_SL is that there is no EPI template. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology,

Re: [Freesurfer] preparing NHP data for whole brain analysis

the missing high quality anatomy. Doug, I did not get from the documentation how to use preproc-sess to align data to an NHP atlas in volume space (that is not in human MNI space). Please advise. Thanks! Caspar 2013/2/12 MCLAREN, Donald mclaren.don...@gmail.com I would recommend using

Re: [Freesurfer] L-R Volume Flipping

When we added the --spm-nii option, the problem disappears. The following thread is also relevant: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017981.html On Tue, Dec 18, 2012 at 8:26 PM, MCLAREN, Donald mclaren.don...@gmail.com wrote: Thanks, that's what I thought might

Re: [Freesurfer] L-R Volume Flipping

that does not read in and act on the geometry, then things can appear to flip around. doug On 12/18/12 8:47 PM, MCLAREN, Donald wrote: Dear All, I've noticed something strange with some data I'm helping to process: When looking at the L/R asymmetry in the brains (attached), the images

Re: [Freesurfer] Reference for clusterwise correction for multiple comparisons

For volumes, I usually cite: Forman, S.D., Cohen, J.D., Fitzgerald, M., Eddy, W.F., Mintun, M.A., Noll, D.C., 1995. Improved assessment of significant activation in functional magnetic resonance imaging (fMRI): use of a cluster-size threshold. Magn. Reson. Med. 33, 636–647. It's also referenced

Re: [Freesurfer] Subgroup analysis

On Tue, Nov 27, 2012 at 1:28 PM, Mahinda Yogarajah y.mahi...@gmail.com wrote: Hi, Thanks for the reference and explanation of the subtle statistical inferences. It was very useful. You are right in what i am trying to show (c- controls, p1 to p4 patients with varying levels of endogenous

Re: [Freesurfer] How to design the contrast matrix with 12 regressors?

I assume that your 12 columns are: your 6 groups followed by 6 columns representing your covariate. You must first test that the slopes are not different with an F-test: 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 If you don't find any

Re: [Freesurfer] How to design the contrast matrix with 12 regressors?

: mha...@wustl.edu On 11/26/12 4:32 PM, MCLAREN, Donald mclaren.don...@gmail.com wrote: I assume that your 12 columns are: your 6 groups followed by 6 columns representing your covariate. You must first test that the slopes are not different with an F-test: 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0

Re: [Freesurfer] contrast matrix

/2012 01:50 PM, MCLAREN, Donald wrote: Bo, Doug asked me to chime in on your issue. Here are some points that you (and others) will hopefully find useful. (1) Inferences are two-step process. First, you create and estimate the design matrix. Every column in the design matrix

Re: [Freesurfer] contrast matrix

Bo, Doug asked me to chime in on your issue. Here are some points that you (and others) will hopefully find useful. (1) Inferences are two-step process. First, you create and estimate the design matrix. Every column in the design matrix accounts can account for some of the variance in the data.

Re: [Freesurfer] Subgroup analysis

On Mon, Nov 19, 2012 at 12:36 PM, Mahinda Yogarajah y.mahi...@gmail.com wrote: Hi Donald and Doug, Thanks for advice. Can I be a little bit clearer as I suspect I need a little more guidance. When comparing controls (gp c) and whole patient group (gp p) I see interesting differences in

Re: [Freesurfer] contrast matrix

:)? Nope. You are right. If the male and female effects are different, then they could cancel each other out. If you suspect this to be the case, then you should be able to demonstrate a three-way interaction. thanks! doug On 11/20/2012 01:50 PM, MCLAREN, Donald wrote: Bo, Doug asked me

[Freesurfer] bbregister

Doug, I received this question from a colleague, Exactly which segmentation file from recon -all is being used in the bbregister command? Thanks, Donald ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] bbregister

Which surfaces does it use? On Tue, Nov 20, 2012 at 2:21 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Donald, It does not use any of the segmentations. In fact, it does not use any of the anatomical volumes. It only uses the surfaces. doug On 11/20/2012 03:19 PM, MCLAREN, Donald

Re: [Freesurfer] Subgroup analysis

Doug and Mahinda, Since the assumption is that the slope is the same across all subjects, I would demean once. I would use one model with 1 control group and N patient group. The model will then test whether or not the covariate-adjusted group means are the same or different. By doing it in a

[Freesurfer] AAL labels

Has anyone created an AAL label file for Freesurfer? I've done some ROI analysis using AAL regions and want to display regional values on the freesurfer surface. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General

[Freesurfer] Brainhack 2012

Dear colleagues, I wanted to draw your attention on the upcoming 2012 Brainhack, 1st edition, to be held from September 1-4 at the Max Plank Institute for Human Cognitive and Brain Sciences, Leipzig, Germany. Brainhack is not a conference or a workshop. It should be closer to one of those

Re: [Freesurfer] FA (DTI) statistical analysis: 3 covariates

I don't believe that Freesurfer has the tools to use non-imaging data as the dependent variable. The GLM in freesurfer is setup to use the imaging data at the dependent variable. For your question, I'd recommend SAS, STATA, SPSS, or another standard statistical package. Best Regards, Donald

Re: [Freesurfer] DODS, DOSS, and interactions

If the covariates are collinear, then you can't properly estimate the model. They are collinear if they explain the variance of each other. I would first test for the relationship of your covariates before putting them into the model as you don't want the covariates to be collinear. Best

[Freesurfer] Allen Brain Institute to Freesurfer Labels

Does anyone have a mapping of the Allen Brain Institute labels to the freesurfer parcellations? Just the labels would be sufficient for these purposes. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of

Re: [Freesurfer] treatment of missing values in mri_glmfit

Kristine/Doug, Are you missing Dependent Variable values or Independent Variable Values? If you are missing some IV values, there are two potential solutions: (1) Drop the subject; (2) Impute the value of that subject given other variables and relationships of those variables and the variable

Re: [Freesurfer] Problem with covariates in design for surface based analysis

Charlotte, There is no difference, from a statistical perspective, of nuisance factors and covariates. The key questions are: (1) Do any of these covariates have a differential effect on thickness between groups? (2) Do you want to compare the actual group means or the covariate-adjusted group

[Freesurfer] Reliability and accuracy of Freesurfer

I've looked through a number of freesurfer papers, but haven't been able to find the answer to what I am looking for and was hoping someone had the references easily available. (1) What is the reliability of regional volumes generated from freesurfer over time? (2) What is the accuracy of labels

[Freesurfer] Surface Area from mri_surfcluster versus mri_segstats

I've noticed that if I run mri_surfcluster to produce a label file, then merge the labels into a single label using mri_mergelabels, then mri_segstats with the slabel option with the fsaverage subject; I get different surface areas from mri_surfcluster (summed all the cluster areas) and

[Freesurfer] Image Filtering

Bruce and others, Are there any spatial filters applied during the segmentation process other than a bias field correction? For example, a spatially adaptive non-linear means filter (e.g VBM8)? If not, do you think denoising filters will improve the accuracy and/or reduce manual editting?

[Freesurfer] Concatenate surfaces

Is there a way to concatenate surfaces for use with mri_segstats? The surfaces are already in fsaverage space. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General

[Freesurfer] mri_mcsim and mri_glmfit-sim

I am trying to figure out how to cluster some data on the cortical surface; however, I've run into a few issues: (1) I can't seem to find a description or examples for running mri_mcsim and mri_glmfit-sim won't work because I'm not using FSFAST to create my statistical maps. (2) A previous email

Re: [Freesurfer] two questions regarding qdec and conjunction analysis is FS

See inline responses.On Wed, Aug 24, 2011 at 7:35 AM, Tetiana Dadakova tetian...@gmail.com wrote: Dear FS experts, I have two questions: 1. In qdec.table.dat file I am specifying several continuous factors, e.g factor1 and factor2. For some subjects factor2 is missing, therefore I leave

Re: [Freesurfer] DOSS or DODS

For question #3; #4. #3 Any good stastistical textbook will be useful. The two that come to mind are: (a) Meyers and Wells. Research Design and Statistical A nalysis (b) Keppel and Wickens. Design and Analysis: A Researcher's Handbook (4th Edition) #4 SPM uses the General Linear Model for all

Re: [Freesurfer] statistical question

Just a couple of thoughts. It depends on what you want to control for AND how you want to control for it. For example, if the relationship of ICV to X differs between boys and girls, you might want to control ICV separately for each group. The results after controlling for ICV are those brain

[Freesurfer] Non-human primate surface template

Dear all, Does anyone have or is perhaps working on a surface template for the rhesus macaque brain? -- Best Regards, Donald McLaren = Support the Alzheimer's Association Memory Walk 2009 ~~~ Join the Wisconsin Alzheimer's Disease Research Center team or make a donation.