[Freesurfer] Maximum level of verbosity

Hallo, I must run FreeSurfer 6.0.0 with a maximum level of verbosity. I require as much log output as possible for monitoring purposes. Someone gave me the hint to run recon-all with DIAG=0x04040. Is this the highest possible log level for running FreeSurfer. Thank you very much. Regards, Jens

Re: [Freesurfer] cuda-gpu problem

Dear Richard, This command recon-all -all -i grp237_t1.nii -s grp237 -sd grp237 -use-gpu -itkthreat 4 took 5.18 hrs and recon-all -all -i grp237_t1.nii -s grp237 -sd grp237 -use-gpu -openmp 4 took 4.69 hrs without any error. Thank you very much for your suggestions. Ramesh On Tue, May 23, 2017

Re: [Freesurfer] Maximum level of verbosity

nope, I guess set it to 0x and setenv DIAG_VERBOSE 1. It will write out lots of things though On Wed, 24 May 2017, Jens Offenbach wrote: > Hallo, > I must run FreeSurfer 6.0.0 with a maximum level of verbosity. I require as > much log output as possible for monitoring purposes. Some

Re: [Freesurfer] Question - multiple comparisons in FS versus SPSS

I think you're first statement is accurate. On 5/24/17 1:45 AM, Noordermeer, S.D.S. wrote: > Thank you for your answer! I already thought so, but it is good to hear it > from the expert. > > Would it be correct to state (as the reviewer persistently asks for it) that > it may be somewhat inform

[Freesurfer] Entorhinal cortex extraction

Dear Freesurfer Developers, I want to extract the entorhinal cortex from the original T1 image of my subect's MRI scans. Is there a way to do it; I used the the commands below to extract the CA1 subfield of the hippocampus. Is there a similar way to do the same for the entorhinal cortex? mri_

Re: [Freesurfer] Entorhinal cortex extraction

you can mri_binarize --match 1006 --i aparc+aseg.mgz --o left.entorhinal.mgz (use 2006 for right). These values you can get from $FREESURFER_HOME/FreeSurferColorLUT.txt On 5/24/17 9:57 AM, Stephanos Leandrou wrote: Dear Freesurfer Developers, I want to extract the entorhinal cortex from the

Re: [Freesurfer] Question - multiple comparisons in FS versus SPSS

Thanks again!! I will write it down like that and will use the uncorrected maps as possible supplementary material. Best, Siri -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: woensdag 24 mei

[Freesurfer] Contrast matrix format

Hi all, I’m trying to perform a group analysis according to the tutorial on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis For my own analysis, I have 4 total groups, and I’m trying to do a contr

Re: [Freesurfer] Contrast matrix format

yes, that is correct On 5/24/17 10:38 AM, Taylor Hilton wrote: Hi all, I’m trying to perform a group analysis according to the tutorial on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis For my own analysis, I have 4 total groups, and I’m trying to do a contr

[Freesurfer] Cortical thickness repeated measures

Hi all, I have a repeated measures design with two groups (drug and placebo) and two time points (baseline and follow-up). The groups are not very well matched so I'd like to control for age and gender. The data was also acquired across three sites which I'll need to control for. I do not have

[Freesurfer] mri_watershed help

Dear Freesurfer community, I am using the mri_watershed command to create BEM surfaces and have run into an issue with a large posterior chunk of skull being treated as brain. [cid:image002.jpg@01D2D47E.75797E70] I have attempted the following to correct the issue: 1.Removed the -atla

Re: [Freesurfer] Maximum level of verbosity

Thanks a lot. I will give it a try. Regards, Jens Gesendet: Mittwoch, 24. Mai 2017 um 15:06 Uhr Von: "Bruce Fischl" An: "Freesurfer support list" Betreff: Re: [Freesurfer] Maximum level of verbosity nope, I guess set it to 0x and setenv DIAG_VERBOSE 1. It will write out lots of things t

Re: [Freesurfer] cuda-gpu problem

Hi Ramesh, I do not know if you have considered this at all but I at least wanted to bring it to your attention. If you have please disregard. I've been doing I.T. for over 20 years and the Nvidia card you have listed is the Geforce 610 concerns me that all of the effort you're going through wo

[Freesurfer] error in long_mris_slopes

Dear Freesurfer experts, I'm running into some problems when running the long_mris_slopes command (longitudinal 2 stage model) to get the rate of change for thickness and area for each hemisphere. This is the command I ran: for i in thickness area ; do for j in rh ; do lon

[Freesurfer] Cortical thickness extraction from analysis

Hello, I am performing a group analysis to compare the cortical thickness between controls and patients (in fsaverage space with a smooth of 15) and I obtain two clusters. I want to extract the average cortical thickness in these clusters for each participant of the analysis. And I have a coup

[Freesurfer] Question regarding errors with TRACULA pre-processing

Hi, I keep trying to run TRACULA and getting the following errors: ERROR: run list is longer than subject list and : Command not found. : Command not found. : Command not found. Badly placed (. **My configuration file is below: *** # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmen

[Freesurfer] Question - how to smooth and transform into a template

-- Original Message -- Date: Wednesday, May 24, 2017 01:48:33 PM From: "Gwang-Won Kim" To: Subject: Question: how to smooth and transform into a template Hello FreeSurfer Developers,I read a sentence in a paper associated with Free Surfer as following: Before statistical evaluation, cor

Re: [Freesurfer] Question - how to smooth and transform into a template

mri_surf2surf should do both of those things for you (assuming you have run recon-all) cheers Bruce On Thu, 25 May 2017, Gwang-Won Kim wrote: -- Original Message -- Date: Wednesday, May 24, 2017 01:48:33 PM From: "Gwang-Won Kim" To: Subject: Question:

[Freesurfer] Download link not responding

Hi there,  I am trying to download the latest version of Freesurfer but the download link is not responding. Is this a known problem or am I the only one who is facing this? Sabir___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.

Re: [Freesurfer] Download link not responding

I just tested it and it worked for me. The freesurfer download is rather large ( > 4Gigs). Occasionally people write to the list having troubles downloading the file and its usually because of restrictions on their network. On 05/24/2017 04:52 PM, Sabir Saluja wrote: > Hi there, > > I am try

[Freesurfer] smoothing kernal

Hi there I labelled sulci in 40 T1 volumes and have created surface overlays using mri_vol2surf and then registered these to fsaverage using mri_surf2surf. I want to generate a statistical probability map using mri_concat and then mris_fwhm for each sulcus. What is an acceptable FWHM to use? It is

Re: [Freesurfer] smoothing kernal

not sure what you are trying to do or why you would want to smooth the prob map On 05/24/2017 05:03 PM, Trisanna Sprung-Much wrote: > Hi there > > I labelled sulci in 40 T1 volumes and have created surface overlays > using mri_vol2surf and then registered these to fsaverage using > mri_surf2su

Re: [Freesurfer] smoothing kernal

Hi Doug I'm doing just that - creating a statistical probability map to look at the overlap across the 40 subjects for a given sulcus. When we do this volumetrically it is traditional to smooth using FWHM of 3mm (about the width of a sulcus). *I was told for surface data it needs to be more than t

Re: [Freesurfer] smoothing kernal

hmmm, I agree with Doug. Why would you want to smooth? The probability maps will have their own smoothness, which will reflect how well they register across subjects cheers Bruce On Wed, 24 May 2017, Trisanna Sprung-Much wrote: > Hi Doug > I'm doing just that - creating a statistical probabilit

Re: [Freesurfer] smoothing kernal

I guess I can't really advise you since I don't understand the application. what will you do with this smoothed map? There is no fixed smoothing kernel applicable for volume or surface-based analysis. Usually it depends on the spatial extent of the effect you are looking for. On 05/24/2017 05:

Re: [Freesurfer] Installing and enabling cuda

On 24 May 2017 at 00:36, Ramesh Babu wrote: > Now I am getting confusion, really which version of cuda I have?. Because > when I give these command "cudadetect" nvcc -V, and cat > /usr/local/cuda/version.txt I am getting different answers. > > rb@rameshbabu:~$ cudadetect > Detecting CUDA... Ther

Re: [Freesurfer] Installing and enabling cuda

Dear Richard, There is some response for cudadetect command which I have pated in earlier mail. But no ./cudadetect file. rb@rameshbabu:~$ ./cudadetect bash: ./cudadetect: No such file or directory I have nvcc file in /usr/local/cuda/bin but still not located. rb@rameshbabu:~$ which nvcc (no r

Re: [Freesurfer] cuda-gpu problem

Dear Peter, Thank you very much for your suggestion. You mean to say, 4.6 hrs duration for recon-all process is because of cpu not gpu? If I run this process without gpu card then I should get the same speed. Right? Ok I will remove my graphic card and run directly from mother board connection whi