Re: [Freesurfer] How to visualize the result with mri_glmfit and --table aparc flag

Dear Doug >From what you instructed me is the data of its voxels on the whole brain? Because I analyze on the whole brain. I would like to interpret the result by know the result like beta 1's value, beta 2's value and beta N's value from the file beta.mgh for the formula Y = X*b so I can write ou

[Freesurfer] mri_annotation2label No such file or directory

Dear FreeSurfer experts I am trying to extract the label using standard aparc.annot and will be using mri_mergelabels to create my own lobes to do GLM fit later on for ROI analysis. However, it shows me the error like this when I check there are the files aparc.annot and the file from surf folder.

[Freesurfer] create symmetric mask on surface

Dear freesurfer experts I created a binary mask on fsaverage4(eg: lh.mask.fs4.mgh) with 30 vertices included in the mask on the left hemisphere, how can i obtain a symmetric mask on the right hemisphere that covered the same regions like the mask on the left hemisphere? Thanks! Meiling __

Re: [Freesurfer] mri_glmfit-sim output error

Did you name one of your contrasts "lh-Avg-thickness-Gender*Age-Inter.mtx"? If so, then remove the star ("*") as that has special meaning to the shell On 5/26/17 2:11 AM, Duy Nguyen wrote: Dear Doug After I add --debug like this: mri_glmfit-sim --debug --glmdir lh.gender_age.glmdir --cache

Re: [Freesurfer] How to visualize the result with mri_glmfit and --table aparc flag

I don't know how he extracted those exact numbers. If I were doing it I would load it into matlab as I said before. beta = MRIread('beta.mgh'); betamat = fast_vol2mat(beta); Then betamat will be a matrix of Nbetas by Nvoxels. Decide which beta and which voxel you want and print out the volume.

Re: [Freesurfer] mri_annotation2label No such file or directory

Do you have write permission into that folder? The surface is just the surface that the annotation is on. Once you have your label, you can use it for thickness On 5/26/17 3:54 AM, Duy Nguyen wrote: Dear FreeSurfer experts I am trying to extract the label using standard aparc.annot and will

Re: [Freesurfer] Segmentation fault (core dumped) error

No idea. Can you upload the subject so I can take a closer look? https://gate.nmr.mgh.harvard.edu/filedrop2 On 5/26/17 9:35 AM, Devin Sodums wrote: Hello FreeSurfer developers, I’m attempting to run recon-all on a T1 image and keep getting the same error message: Segmentation fault (core d

[Freesurfer] white mater parcellation

Dear Freesurfer expert; I'm new to Freesurfer. I have used wmpar to analyze white matter. So, Is there another tool to parcellation just deep white matter ? Thanks. -- Cleudiana Lima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:/

Re: [Freesurfer] Segmentation fault (core dumped) error

Sure thing, I'll send it in a few. Thanks, Devin From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Friday, May 26, 2017 9:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation fault (core dumped)

Re: [Freesurfer] create symmetric mask on surface

Try running cd $FREESURFER_HOME/subjects/fsaverage4/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere lh.sphere.left_right I'm not 100% sure that this will do the right t

Re: [Freesurfer] white mater parcellation

what do you mean by deep white matter? On 5/26/17 9:50 AM, Cleudiana Lima wrote: Dear Freesurfer expert; I'm new to Freesurfer. I have used wmpar to analyze white matter. So, Is there another tool to parcellation just deep white matter ? Thanks. -- Cleudiana Lima

[Freesurfer] UPDATE: error in long_mris_slopes

Hi everyone, it seems the error isn't hemisphere specific after all. It shows up on 1 subject in the left hemisphere, too (just later in the subject list). Weirdly the subjects that produce the error on the right hemisphere are different one than those producing the error when working on the l

Re: [Freesurfer] [EXTERNAL] Re: Haskins Pediatric Atlas use in FS

Hi Peter, Thank you so much for picking up on this. Yes, I guess I mean template - I am still new to FS and get some of the terms/procedures mixed up. Jenni Pacheco at NIH (copied) is helping to bring our group up to speed. Hopefully she can clarify further. I would appreciate being able to us

Re: [Freesurfer] Contrast matrix format {Disarmed}

I was trying to follow along with the suggestion you provided someone else here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32951.html I'm not sure how relevant that solution is to my problem though, and I'm pulling values from the "cache.th40.neg.y.ocn.dat" file which is out

Re: [Freesurfer] Contrast matrix format {Disarmed}

It does not matter whether you used the maxvox or the mean of the cluster. The two p-values are measuring fundamentally different phenomena. The cluster pvalue is measuring the likelihood of seeing a cluster of that size by chance. The p-value you have computed is the likelihood of seeing a mea

Re: [Freesurfer] Haskins Pediatric Atlas use in FS

Hi Jack, We do not have such an automated option at the moment. Lilla On Thu, 25 May 2017, John Hettema wrote: To FreeSurfer team,   I have child MRI data for which it would be best to use a pediatric atlas/template for warping, alignment, and labeling. I am aware of the Haskins Pediatric

Re: [Freesurfer] 7T recon

Hi Matt yes, that means there was a topological defect that was incorrectly fixed. If you load the wm.mgz over the lh.orig.nofix, then in the orig.nofix load the file defect_labels as an overlay and change the overlay settings to that the min is 1 and click the "use overlay color" button it w

Re: [Freesurfer] 7T recon

Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then re-run the recon from autorecon2-wm? Thanks, Matt From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvar

Re: [Freesurfer] 7T recon

yes, and autorecon3 On Fri, 26 May 2017, Hibert, Matthew Louis wrote: > Thanks Bruce. After I remove the problem voxels in wm.mgz, do I then re-run > the recon from autorecon2-wm? > > Thanks, > Matt > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [fre

Re: [Freesurfer] Contrast matrix format {Disarmed}

Okay but if we run a simple regression analysis on the mean values between groups for the clusters which mri_glmfit-sim found significant between groups, why isn't that significant? Are we leaving a covariate out? From: freesurfer-boun...@nmr.mgh.harvard.edu o

Re: [Freesurfer] Contrast matrix format {Disarmed}

Aren't your p-values sig? They are both in the range of .0001 On 05/26/2017 02:23 PM, Hilton, Benjamin Taylor wrote: > > Okay but if we run a simple regression analysis on the mean values > between groups for the clusters which mri_glmfit-sim found significant > between groups, why isn't that s

Re: [Freesurfer] mri_annotation2label No such file or directory

Dear Doug Thank you for your quick response. I got the data from oasis website. How can I get the permission to continue my analysis? Thanks Duy On Fri, May 26, 2017 at 8:46 PM Douglas Greve wrote: > Do you have write permission into that folder? > > The surface is just the surface that the anno