[Freesurfer] Monte Carlo simulation - vertex wise threshold question

External Email - Use Caution Hi FreeSurfer experts, I am trying to understand the Monte Carlo Z simulation in FreeSufer (mri_glmfit-sim) and have a question about the vertex wise /cluster forming threshold. In the simulation, a vertex wise threshold (ex. -cache 3 abs) is set

Re: [Freesurfer] Putting results from probabilistic tractography on the surface

I think it is short for "delta" - how far about the samples are On Mon, 9 Jul 2018, Sims, Sara A wrote: External Email - Use Caution Bruce, What does "del" mean in the --projdist-avg flag? Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology

Re: [Freesurfer] Putting results from probabilistic tractography on the surface

External Email - Use Caution Bruce, What does "del" mean in the --projdist-avg flag? Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 sno...@uab.edu On 6/26/18, 2:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behal

[Freesurfer] Longitudinal Processing question

External Email - Use Caution Hello FreeSurfer experts, I have a few questions on the longitudinal processing stream. I am interested in studying longitudinal morphometry changes in a pediatric population. The age range of this population is between 4-20 years with age deltas bet

Re: [Freesurfer] Infant atlas/pipeline

Hi Kelli, Our beta version is ready and I can set you up with it. Please, send me a note directly and I can help you with that. Lilla On Sun, 8 Jul 2018, Dominick, Kelli wrote: External Email - Use Caution Hello Freesurfer Experts,  I am hoping to use Freesurfer in infa

[Freesurfer] Matched analysis with 2 controls 1 case weighting

Hello Freesurfer Experts, I'm writing with a quick question about matched analysis. We have a cohort of MRI data collected such that there are two controls for each case, and these 2 controls are each matched to a specific case using a propensity score algorithm (~400 subjects total). For our

Re: [Freesurfer] questions regarding bias correction prior to Freesurfer processing

Hi Stacey we recommend processing all of your subjects the same way. Do you understand why some would have a big bias field and some would not? It was always the same coil, wasn't it? cheers Bruce On Mon, 9 Jul 2018, STACEY M SCHAEFER wrote: External Email - Use Caution

Re: [Freesurfer] niiWrite(): error opening file tmp.nii

External Email - Use Caution Hi Bruce, This is my full command line! I just started using this and I am not really sure what you mean by recon-all.log. Skolarikis-MacBook-Pro:~ kskol$ export FREESURFER_HOME=/Applications/freesurfer Skolarikis-MacBook-Pro:~ kskol$ source $FREESUR

Re: [Freesurfer] niiWrite(): error opening file tmp.nii

Hi Konstantina, you have to set SUBJECTS_DIR equal to an actual directory path in your filesystem, the “” is just a placeholder. Best, Andrew From: on behalf of Konstantina Skolariki Reply-To: FS Help Date: Monday, July 9, 2018 at 10:30 AM To: FS Help Subject: Re: [Freesurfer] niiWrite(): er

[Freesurfer] questions regarding bias correction prior to Freesurfer processing

External Email - Use Caution Hello Freesurfer experts, Our current 3T T1s exhibit structural hyperintensities due to the inhomogeneity of the receiver coil, but not all scans have hyperintensity issues. The local MRI physicist suggests running N4BiasFieldCorrection through mul

Re: [Freesurfer] niiWrite(): error opening file tmp.nii

Hi Konstantina can you include the full command line, screen output and recon-all.log in the type of email? Otherwise it will be difficult for us to help thanks Bruce On Mon, 9 Jul 2018, Konstantina Skolariki wrote: External Email - Use Caution Hi Bruce, I managed to ove

Re: [Freesurfer] niiWrite(): error opening file tmp.nii

External Email - Use Caution Hi Bruce, I managed to overcome said error but now during example 2 another error pops up. Skol-MacBook-Pro:~ kskol$ export SUBJECTS_DIR= -bash: syntax error near unexpected token `newline' Thanks, Konstantina F

Re: [Freesurfer] changing label outlines in tksurfer

Hi Martin, There is no option to change the thickness of the label outlines right now. I’ll explore the possibilities to add an option for that. Best, Ruopeng > On Jul 9, 2018, at 7:21 AM, Loeffler, Martin > wrote: > >External Email - Use Caution > > Dear Bruce, > > thanks

Re: [Freesurfer] Run the recon-all -all pipeline on structural T1w images in pediatric sample

Hi Laurel and Johannes Satra Ghosh published a paper a few years ago using FS on pretty young subject's and found that at least the registration component was not biased by age: https://www.ncbi.nlm.nih.gov/pubmed/20621657 Have you tried running your datasets to see how things work? I think

Re: [Freesurfer] niiWrite(): error opening file tmp.nii

Hi Konstantina do you have write access to the partition you are putting the subjects_dir on? And can you please send us the full command line, screen output and recon-all.log? cheers Bruce On Mon, 9 Jul 2018, Konstantina Skolariki wrote: External Email - Use Caution H

[Freesurfer] Extract Value from pcc.nii.gz

Hi FS Experts, I am doing the FAST analysis. After I finished the isxconcat-sess and got PCC.nii.gz, how can I extract the value from PCC.nii.gz file? Meanwhile, if I want to make group comparisons by using mri_glmfit, how to extract the values? Looking forward to your response Thank you. Zhu

[Freesurfer] Missingness and recent developments in longitudinal pipeline for pediatric samples

External Email - Use Caution Dear FS Experts and Community, we are working on a longitudinal dataset of structural T1w images in a pediatric sample assessed at 2 waves, 2 years apart (aged 6/7 and 8/9). As far as we know, it is yet unresolved whether the Freesurfer longitudina

[Freesurfer] Run the recon-all -all pipeline on structural T1w images in pediatric sample

External Email - Use Caution Dear FS Experts and Community, we would like to run the recon-all -all pipeline on structural T1w images in a pediatric sample ages 6-9. We intend to assess cortical thickness, surface area, and subcortical volume in both ROIs and for whole brain a

[Freesurfer] niiWrite(): error opening file tmp.nii

External Email - Use Caution Hi FreeSurfer Developers, I have downloaded freesurfer on my mac and after "setup & configuration” I tried to perform example 1 from "test your FreeSurfer Installation”. However when I type the command, this error message shows up: $Id: mri_convert.

Re: [Freesurfer] changing label outlines in tksurfer

External Email - Use Caution Dear Bruce, thanks for your quick response! I managed to do most of what I wanted in freeview. My last question: Is there any possibility to increase the thickness of the label outlines? Here the new code: freeview -f ${case_dir}/surf/rh.inflated:cu

[Freesurfer] Learning which data derivatives matter most

External Email - Use Caution Dear all, To learn which neuroimaging data derivatives (intermediate or final analysis outputs) matter most to people conducting analyses and reusing data we have put together a survey: https://goo.gl/forms/5ghpVbiiPHd8BN153 Please take a moment and f