[Freesurfer] mri_glmfit-sim output error

Dear FreeSurfer experts, When I try to run mri_glmfit-sim, the output came out like this: cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd lh.gender-age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C lh-Avg-thickness-FemaleMale.intercept.mtx --C lh-Avg-thickness-Gender.diff.mtx

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

Thank you for you quick response Doug Please instruct me how I can read out the output file beta.mgh to get the values from the mri_glmfit output on FreeSurfer. Thank you for your help and warmest regards, Duy Nguyen *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC*

[Freesurfer] Error in hippocampal subfield segmentation

Hello FreeSurfer Developers, I'm attempting to compute hippocampal subfield segmentation. Unfortunatelty I found following errors. Segmentation violation detected at Sat May 20 10:45:37 2017 --

[Freesurfer] Extracting fMRI mean time series from Desikan ROIs

Hello Freesurfer Experts, I have a question to ask about extracting the mean time series from resting-state fMRI (239 volumes). I have used bbregister to bring the 4D fMRI data into T1 space. My next objective is to project the data onto the fsaverage surface, and then extract the mean time se

Re: [Freesurfer] fix topology issue

I edited the brainmask not the wm.mgz. Best, Paul On Fri, May 19, 2017 at 11:49 AM, Bruce Fischl wrote: > it depends what you do. If you edit the wm.mgz to remove the connection > you only need to run autorecon2-wm and autorecon3, which is a lot faster > > > cheers > Bruce > > On Fri, 19 May 201

Re: [Freesurfer] fix topology issue

it depends what you do. If you edit the wm.mgz to remove the connection you only need to run autorecon2-wm and autorecon3, which is a lot faster cheers Bruce On Fri, 19 May 2017, miracle ozzoude wrote: Hello Bruce, Thank you. Also, I don't need to run the entire pipeline again just autoreco

Re: [Freesurfer] fix topology issue

Hello Bruce, Thank you. Also, I don't need to run the entire pipeline again just autorecon2 and autorecon3 Best, Paul On Fri, May 19, 2017 at 11:41 AM, Bruce Fischl wrote: > it depends on how many connections there are > > On Fri, 19 May 2017, miracle ozzoude wrote: > > Hello Bruce, Is 2 or 3 sl

Re: [Freesurfer] fix topology issue

it depends on how many connections there are On Fri, 19 May 2017, miracle ozzoude wrote: Hello Bruce, Is 2 or 3 slices ok? Also, after that I should run the rest of recon-all stage from autorecon2.  Best,  Paul On Fri, May 19, 2017 at 11:32 AM, Bruce Fischl wrote: yes, or try rerunning

Re: [Freesurfer] fix topology issue

Hello Bruce, Is 2 or 3 slices ok? Also, after that I should run the rest of recon-all stage from autorecon2. Best, Paul On Fri, May 19, 2017 at 11:32 AM, Bruce Fischl wrote: > yes, or try rerunning watershed with different parameters. YOu don't have > to remove the entire skull that was left - j

Re: [Freesurfer] fix topology issue

yes, or try rerunning watershed with different parameters. YOu don't have to remove the entire skull that was left - just the connection between it and wm On Fri, 19 May 2017, miracle ozzoude wrote: Hello Bruce, Yes, the skull is still attached. Should I remove the skull for all the slices and

Re: [Freesurfer] fix topology issue

Hello Bruce, Yes, the skull is still attached. Should I remove the skull for all the slices and re-run it again? Best, Paul On Fri, May 19, 2017 at 10:28 AM, Bruce Fischl wrote: > Hi Paul > > you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically > something big is wrong like sku

Re: [Freesurfer] Hippocampal subfield segmentation problem

Dear Artyom, You’re probably running out of RAM memory in those few cases. How much RAM do you have? Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 19 May 2017, at

[Freesurfer] Longitudinal study concept question

In writing a paper of longitudinal changes in a large heterogeneous population with no group comparisons, what would be considered "more important" to include: absolute ROI volumes, or volumes corrected for ICV? Using ICV corrected volumes makes sense when comparing groups, but when just describin

[Freesurfer] Hippocampal subfield segmentation problem

Dear experts, I am running running hippocampal subfield segmentation using the most recent version of the FSv6.0 on LinuxMint 17.3 Rosa. For some (~ 25%, but not all) participants I did not get the subfields. I have later realized that although segmentation finished with out errors, I got the

Re: [Freesurfer] fix topology issue

Hi Paul you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically something big is wrong like skull attached to brain or something cheers Bruce On Fri, 19 May 2017, miracle ozzoude wrote: Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline go

Re: [Freesurfer] Manuel edits (message 5)

no, it's best to visually determine it since things change over space (for both biological and technical reasons) On Fri, 19 May 2017, Caroline Beelen wrote: Dear Bruce, Thank you for answering my question. However, I'm still in a bit confused... Therefore, I have one more question: Would

Re: [Freesurfer] Cuda 8, Centos 7, FreeSurfer 6

The Cuda code shipped with freesurfer6 has not been updated in awhile and can more-or-less be considered deprecated. It will however build against the Cuda5 libraries on Centos6 and Centos7. And Ive seen reports on the list of it being built against newer Cuda libs. However, it might require si

Re: [Freesurfer] Corrupted file (Matlab runtime 2012b Linux) on server?

I just did a test and it finished to completion for me. Is it possible there is some restriction of the network you are currently on? On 05/19/2017 03:28 AM, Marco Bucci wrote: > Hi all, > > I tried on a Linux server with Debian (also as sudo) > > |curl > "http://surfer.nmr.mgh.harvard.edu/fswiki

[Freesurfer] lgi vertex coordinate problem

Hi there, I am trying to use local gyrification index values for the purpose of adaptive smoothing. I use recon -all and calculate lgi values for vertices on the surface. To show related voxels on the MR volume I changed vertex coordinates to voxel coordinates with the help of freesurfer_surf2voxe

Re: [Freesurfer] Improving the brainmask.mgz using aseg.mgz for getting rid of dura

Hi Karteek, as for higher resolution (>0.7mm) the brainmask often includes lots of residual, I changed my pre-processing slightly. Currently I do bias field correct my 7T data with SPM and create a mask of the WM, GM and CSF segmentation you get along with it. Then I recon-all -autorecon1 the

Re: [Freesurfer] Manuel edits (message 5)

Dear Bruce, Thank you for answering my question. However, I'm still in a bit confused... Therefore, I have one more question: Would it then be best to choose a particular WM intensity value to rely upon for adding control points or to rely upon sight? Thank you very much! Kind regards, Caroli

[Freesurfer] Corrupted file (Matlab runtime 2012b Linux) on server?

Hi all, I tried on a Linux server with Debian (also as sudo) curl "http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bLinux.tar.gz"; -o "runtime2012b.tar.gz" The transfer stops at about two minutes from the end. I tried to download the file manua

[Freesurfer] Contrast matrix regressing out effect of diagnosis and age

Dear Freesurfer experts, I am running a GLM-model in which I have 6 classes (diagnosis) and two covariates age and variable X). I want to look at mean correlation of variable X. My contrast matrix is as follows: 0 0 0 0 0 0 0 0 0 0 0 0 0.17 0.17 0.17 0.17 0.17 0.17 0.17 (approx. 1/6) Did I get