[Freesurfer] World's leading AI Company for brain imaging is recruiting brain imaging scientists.

External Email - Use Caution Full/Part-time MR Imaging Analysis Scientist Overview World's leading AI Company for brain imaging is recruiting brain imaging scientists. With the team’s strong background in scientific research and medical industry, it focuses on the precise

[Freesurfer] lGI permutation and monte-carlo

External Email - Use Caution Hi experts, Upon reading your 2018 paper (cited below) and following threads on the archives, I am aware that I should use permutation testing for lGI analyses rather than monte carlo at p<0.05. However, I have a few questions below that I would

Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

External Email - Use Caution Hi Juan, If I want to seed T1 hippocampus.mgz to fill the ProbtrackX. How should I do that? Is it something like below: mris_convert lh.white lh.white.gii mri_convert lh.hippocampus.mgz lh.hippocampus.nii.gz and then label2surf -s lh.white.gii -o

Re: [Freesurfer] ver 7.1: recon-all executes out of order? {Disarmed}

External Email - Use Caution Dear Douglas, I compared recon-all scripts for versions 6 and 7. I see that -white for version 7 does something different than it was for version 6. The recon-all.makefile files in versions 6 and 7 are the same in this respect and consequently

[Freesurfer] Permutation --perm-resid unrecognized

External Email - Use Caution Hi experts, I am trying to run permutation test on my lGI data using the command line below but I get an error saying “ERROR: Flag --perm-resid unrecognized”. I've ran my mri_glmfit command line with flag --eres-save (see below) and have installed and

Re: [Freesurfer] mris_preproc label file not found

External Email - Use Caution I think all you need to do is copy (or symlink) fsaverage to your data directory, the label file is in there already. e.g.: cp -r $FREESURFER_HOME/subjects/fsaverage /home/neuroimagen/AnalisisLongitudinalLMM Best, Tim > On June 8, 2020 at 7:29

[Freesurfer] mris_preproc label file not found

External Email - Use Caution Dear experts, I am preparing my data for longitudinal statistical analysis following the steps in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics#LinearMixedEffectsModel. I try running the following comand : mris_preproc

Re: [Freesurfer] ver 7.1: recon-all executes out of order? {Disarmed}

External Email - Use Caution As far as I can tell, recon-all.cmd provides the list of the underlying commands executed by the recon-all script. It does not provide the list of switches to recon-all to use to invoke these commands. Even if it did, this would be the list of

Re: [Freesurfer] samseg with subfields {Disarmed}

External Email - Use Caution Ahh great, thank you! From: Douglas N. Greve Sent: Monday, June 8, 2020 11:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields

Re: [Freesurfer] samseg with subfields {Disarmed}

Actually, I don't think there is an example. You can run samseg without it running samseg2recon, but once you specify --s, it will run samseg2recon On 6/8/2020 11:22 AM, Sneha Pandya wrote: External Email - Use Caution Ahh perfect, thank you Doug  Can you share an example case when

Re: [Freesurfer] samseg with subfields {Disarmed}

External Email - Use Caution Ahh perfect, thank you Doug  Can you share an example case when we might have to run samseg2recon post running samseg? Thanks, Sneha From: Douglas N. Greve Sent: Monday, June 8, 2020 11:20 AM To:

Re: [Freesurfer] ver 7.1: recon-all executes out of order? {Disarmed}

Oh, that table is wrong. I don't even think it was right for version 6. If you look in recon-all.cmd, you will see just the commands (and their order) On 6/8/2020 10:38 AM, Roman Fleysher wrote: External Email - Use Caution Dear Douglas, I do not think -s and -sd is essential to

Re: [Freesurfer] samseg with subfields {Disarmed}

Oh, sorry, that way of running recon-all will run samseg2recon. Sorry, I lost track of what you are asking On 6/8/2020 10:45 AM, Sneha Pandya wrote: External Email - Use Caution Hi Doug, What do you mean it did not do anything different? What is your samseg command? * Our

Re: [Freesurfer] Fwd: Welcome to the "Freesurfer" mailing list

I think you just did  From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Paolo Zanotti Fregonara Sent: Monday, June 8, 2020 10:39 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fwd: Welcome to the "Freesurfer" mailing list External Email - Use Caution Hi Would

Re: [Freesurfer] samseg with subfields {Disarmed}

External Email - Use Caution Hi Doug, What do you mean it did not do anything different? What is your samseg command? * Our samseg command was as follow: samseg --t1w /home/ubuntu/T1.nii --sd /home/ubuntu --s subjID --refmode t1w --threads 4 –parallel * Once this

Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

Get a new version of mri_seghead from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_seghead and copy it into $FREESURFER_HOME/bin let me know if it works On 6/5/2020 5:09 PM, Boris Rauchmann wrote: External Email - Use Caution thanks, the subj I sent you the logfile has a

Re: [Freesurfer] ver 7.1: recon-all executes out of order? {Disarmed}

External Email - Use Caution Dear Douglas, I do not think -s and -sd is essential to the issue. I just wanted to draw attention to this not standard call in my set up. There are reasons for it and it worked for version 6. Yes, all prior steps of recon-all were executed,

Re: [Freesurfer] How can I create a grey matter volume in Matlab?

External Email - Use Caution Yes, I do only need cortex gray matter. Great, then I'll use the ribbon.mgz in order to create a gray matter mesh. Thank you for your answer! Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Douglas N.

Re: [Freesurfer] How can I create a grey matter volume in Matlab?

When you say "gray matter" do you mean all gray matter or just cortex? If just cortex, then you need to take all the voxels between white and pial surfaces. This is already done in the ribbon.mgz file On 6/8/2020 10:05 AM, Franziska Klein wrote: External Email - Use Caution Hello

[Freesurfer] MRInormFindControlPoints

External Email - Use Caution Dear all, When running the long step for a subject with 7 timepoints with FS version 7.1.0 recon-all -long SUBJECT1.1 SUBJECT1.base -all -hires I get the following error in the mri_normalize step: # mri_normalize -g 1 -seed

Re: [Freesurfer] QDEC correlation analysis

In the qdec  output, there should be a file called Xg.dat and one called contrast/C.dat (where contrast is the name of the contrast of interest) X = load('Xg.dat'); C = load('contrast/C.dat'); y = MRIread('input-to-qdec.mgz'); % Not sure what this is called ymat = fast_vol2mat(y); yvertex =

Re: [Freesurfer] ver 7.1: recon-all executes out of order?

I'm not sure what you are trying to communicate here abut -s and -sd. It is hard to debug without the log file. Had you run the earlier steps in the recon before running this command? On 6/8/2020 1:25 AM, Roman Fleysher wrote: External Email - Use Caution Dear FreeSurfer Develovers,

Re: [Freesurfer] Mixing freesurfer versions

We have not idea what was in the dev versions, but in general we recommend against mixing versions. Those versions are all about a year apart, so I suspect that there were some substantial changes. On 6/8/2020 12:42 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: Hi FS developers,

Re: [Freesurfer] tkregisterfv -ss

The version 7 tkregiserfv should work. If you don't have that, try this one https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv On 6/6/2020 11:30 AM, Boris Rauchmann wrote: External Email - Use Caution Dear all, is there a way to use  freeviews -ss command to obtain

Re: [Freesurfer] samseg with subfields {Disarmed}

On 6/5/2020 4:47 PM, Sneha Pandya wrote: External Email - Use Caution Thank you Doug. it is not run by default * When I ran “samseg2recon –s subject” after running samseg, it did not do anything different, am I missing anything? What do you mean it did not do anything

Re: [Freesurfer] How can I create a grey matter volume in Matlab?

External Email - Use Caution Hello again, unfortunately, nobody is responding. . Until now I am able to create meshes from the freesurfer output files with the isosurface() and read_surf() functions from a MATLAB based toolbox . However, I still do not know with which

Re: [Freesurfer] mz3 for freesurfer brain render

I still don't understand. Was Tim's summary of what you want correct? You want to create a surface around subcortical structures, eg, hippocampus and then display values on that surface? On 6/5/2020 3:18 PM, Kate Marvel wrote: External Email - Use Caution Hi Douglas, I would like

Re: [Freesurfer] statement on recent events

Thanks Tim Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Tim Schäfer Sent: Monday, June 8, 2020 3:20 AM To: Freesurfer support list Subject: Re: [Freesurfer] statement on recent events External Email - Use Caution Thanks for

Re: [Freesurfer] statement on recent events

External Email - Use Caution Thank you very much, Bruce. Rosalia Do not bother just to be better than your contemporaries or predecessors. Try to be better than yourself. --Faulkner On Mon, Jun 8, 2020 at 9:21 AM Tim Schäfer wrote: > External Email - Use Caution >

[Freesurfer] QDEC correlation analysis

External Email - Use Caution Hello FreeSurfer Developers, I have a few questions about the p value in QDEC. I want to use matlab to calculate the p value in a vertex in the QDEC result. 1. In my design, there is a continuous variable A and two Nuisance factors B and C. How to

Re: [Freesurfer] statement on recent events

External Email - Use Caution Thanks for speaking up! We all have plenty of room to improve, and that's of course not limited to the US. -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy