Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

Dear Douglas N Greve, FreeSurfer Team, Thank you for your clear explanation. Best Wishes, Han On Wed, Jun 1, 2016 at 3:55 PM, Douglas N Greve wrote: > Column 5 is completely redundant with column 1 (and highly colinear with > column 3). Column 6 is nearly identical

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

Column 5 is completely redundant with column 1 (and highly colinear with column 3). Column 6 is nearly identical to column 2 (and highly colinear with column 4). This is causing your matrix to be ill-conditioned On 05/26/2016 02:12 PM, Hanbyul Cho wrote: > Dear Douglas N Greve, > > > I sent

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

Dear FreeSurfer Team, I wonder you could not read an previous attached file. Thank you, Han On Thu, May 26, 2016 at 12:12 PM, Hanbyul Cho wrote: > Dear Douglas N Greve, > > > I sent again this design matrix (= Xg.dat) by attached. > > Thank you. > > Han. > > On Thu,

Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses

Are you using selxavg-sess or selxavg3-sess. you should be using selxavg3-sess On 06/01/2016 03:45 PM, Raney, Talia L. wrote: > Okay, the thing is that when I remove the no-con flag I get this error > "ERROR: the design type of this analysis is notask >selxavg-sess can only be used to

Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg

This worked! Thanks very much for your help! On 2016-05-23, at 11:25 AM, Douglas N Greve wrote: > Try it without the --reshape option in mri_surf2surf > > On 05/20/2016 05:51 PM, Kari Parsons wrote: >> Hi, >> >> I'm trying to get some cortical thickness

Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses

Okay, the thing is that when I remove the no-con flag I get this error "ERROR: the design type of this analysis is notask selxavg-sess can only be used to analyse event-related and blocked", which means I have to change the analysis.info using mkanalysis-sess,correct? Which flag would I use

[Freesurfer] Masking in functional connectivity pipeline

Hi FreeSurfer experts, I have a question about two specific steps in my fc pipeline. Since my seed is a single vertex, I convert the seed label to a mask, which I then smooth and binarize, and then convert to a volume file for fcseed-sess. 1) Is there way to directly convert a label into a

Re: [Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses

Don't include the -no-con-ok flag. For resting state, you don't need to run mkcontrast-sess because a contrast will automatically be created for you. On 06/01/2016 02:24 PM, Raney, Talia L. wrote: > Hi FreeSurfer users, > I have some resting state data that I preprocessed and conducted first

[Freesurfer] Selxavg3-sess with no-con-ok and ROI analyses

Hi FreeSurfer users, I have some resting state data that I preprocessed and conducted first level analyses using the flag -no-con-ok. Since no ces.nii.gz or sig.nii.gz is createdcomes up because there is no contrast, I'm wondering if it's possible to conduct functional ROI analyses with the

Re: [Freesurfer] Coordinates in TRACULA group analysis

Thanks, Anri. So the previous steps seem to have run fine. Are there any .log files created in the stats/ folder, which is created by trac-all -stat? On Wed, 1 Jun 2016, Anri WATANABE wrote: Hi Anastasia, This is a /scripts/trac-all.log of one subject of the group. Thanks, Anri

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

Ok, sorry: wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_COVARIATES_AGE_GENDER/OWNDESIGNED_Alex_covariates_design_matrix_surfstat_version$ mri_glmfit \ > --glmdir lh.AD_CN_COVARIAETS_AGE_GENDER.glmdir ERROR: must specify an input X

Re: [Freesurfer] Using customized stats code for mass-univariate approach in freesurfer for structural data

Sorry about that. I attached the previous conversation below. Yes - I am interested in applying the monte carlo sim to my own model fit. Doug can you walk me through the steps I need to get this part done? When you say residuals, I am assuming that I need to supply a vector file of residuals

Re: [Freesurfer] Using customized stats code for mass-univariate approach in freesurfer for structural data

Please include previous correspondence On 06/01/2016 11:39 AM, Chung, Yoonho wrote: > > Yes - I am interested in applying the monte carlo sim to my own model > fit. Doug can you walk me through the steps I need to get this part > done? When you say residuals, I am assuming that I need to supply

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

Can you send me just the terminal output from mri_glmfit? On 06/01/2016 12:45 PM, Hao wen wrote: > Hi, thanks for your reply, here is the output of the terminal in txt > file, hope to hear from you soon > Merci > Hao > >

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

Hi, thanks for your reply, here is the output of the terminal in txt file, hope to hear from you soon Merci Hao De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Douglas Greve Envoyé :

Re: [Freesurfer] Using customized stats code for mass-univariate approach in freesurfer for structural data

Yes - I am interested in applying the monte carlo sim to my own model fit. Doug can you walk me through the steps I need to get this part done? When you say residuals, I am assuming that I need to supply a vector file of residuals after I fit my model to the smoothed data (eg. using

Re: [Freesurfer] FC from resting-state

You should first check your func-anat registration with tkregister-sess On 6/1/16 11:20 AM, Martin Juneja wrote: Hello FreeSurfer experts, I am working on resting-state functional connectivity using freesurfer by following the instructions from:

Re: [Freesurfer] mris_preproc - srcsubjreg

I would not expect the glm to change much, but the activation might shift around a little depending upon your new target. On 6/1/16 11:18 AM, Makaretz, Sara Johanna wrote: > Thank you! Does this mean that an older glm would have still used fsaverage > for the "common surf" but then the output

[Freesurfer] FC from resting-state

Hello FreeSurfer experts, I am working on resting-state functional connectivity using freesurfer by following the instructions from: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough I made sure that the seed region (for ever subject) I am using is at the correct

Re: [Freesurfer] mris_preproc - srcsubjreg

Thank you! Does this mean that an older glm would have still used fsaverage for the "common surf" but then the output is mapped to the target? Outputs from older glms load no problem on the targets, and look "as expected" Aka would you expect a major difference in glmfit outputs with old

Re: [Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

please send the terminal output that includes the error On 6/1/16 8:10 AM, Hao wen wrote: Hello, freesurfers: I am doing group analysis, with two diff groups, so I want to know that how to create my own Contrast and Design matrix, because that I know in QDEC and CMline, in the freesurfer

Re: [Freesurfer] Questions about fsgd file & contrast

1) You don't include sex as a covariate. Include it as a class (ie, Class Male and Class Female rather than Class Main). 2) You need to include Minutes in your null hypothesis. 3) Include minutes as a covariate as you have done, then create the proper contrast matrix. The contrast matrix will

[Freesurfer] Postdoctoral Fellow in Pediatric MRI - NYC

*The Cognitive Development and Neuroimaging Lab* in the *Division of Child and Adolescent Psychiatry in the Department of Psychiatry, Columbia University Medical Center and the New York State Psychiatric Institute* invites applications for a post-doctoral associate in the area of developmental

Re: [Freesurfer] correct thinking?

Hi Bruce, Thanks for your answer and all your help, I only want to look at cortical thickness for now. Best, Marja On Wed, Jun 1, 2016 at 11:11 PM, Bruce Fischl wrote: > Hi Marja > > yes, if you want to compare measures averaged over our predefined ROIs > that is

Re: [Freesurfer] correct thinking?

Hi Marja yes, if you want to compare measures averaged over our predefined ROIs that is all you need to do. Note that for volumes you probably want to include ICT/eTIV as a regressor cheers Bruce On Wed, 1 Jun 2016, Marja Caverlé wrote: Hi guys, I just wanted to make sure I am

[Freesurfer] Questions about fsgd file & contrast

Dear list, We have a question about the set up of the FSGD file. We have 1 group, 2 continued covariates (age & mintues), 1 discontinued covariate (sex) GroupDescriptorFile 1 Title G1V3 Class Main Variables Age Sex Minutes Input subject1 Main 30 0 1200 Input subject2 Main 40 1 180 My

[Freesurfer] CM_Group_analysis_Create tha contrast and design matrix by myself

Hello, freesurfers: I am doing group analysis, with two diff groups, so I want to know that how to create my own Contrast and Design matrix, because that I know in QDEC and CMline, in the freesurfer wiki, You just give the example for the DODS & DOSS, but it is not so flexible! I know that