[Freesurfer] How to only include frontal and temporal lobes in surface based group analyses and multiple comparison correction

External Email - Use CautionDear FreeSurfer Developers,   I'm looking to use a mask/label to only include the frontal and temporal lobes when using mri_glmfit for surface based group analyses and mri_glmfit-sim --perm for multiple comparison correction.   I noticed that

Re: [Freesurfer] [External] Re: Error using segmentHA_T1.sh

Please try: segmentHA_T1.sh subject1_preOp_T1MRI_axial-anon /Users/lou.blanpain/Desktop/freesurfer_output/ Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Blanpain, Lou" Reply-To: Freesurfer

Re: [Freesurfer] missing one tract but differently for a few subjects

Hi Qi - Are those two images in the same space, or in different spaces (the aparc+aseg_mask in T1 space and the FA map in diffusion space)? If the latter is true, there is no reason to expect them to have the same orientation. Checking the registration between T1 and diffusion space is a

Re: [Freesurfer] [External] Re: Error using segmentHA_T1.sh

External Email - Use Caution Sure thing: segmentHA_T1.sh '' /Users/lou.blanpain/Desktop/freesurfer_output/subject1_preOp_T1MRI_axial-anon Note: the folder “subject1_preOp_T1MRI_axial-anon” contains the recon-all output, i.e. folders label, mri, scripts etc. Thank you for the

Re: [Freesurfer] Error using segmentHA_T1.sh

Hi Lou, Can you please send us your exact command line? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Blanpain, Lou" Reply-To: Freesurfer support list Date: Wednesday, August 26, 2020 at

[Freesurfer] Error using segmentHA_T1.sh

External Email - Use Caution Hello, I attempted using segmentHA_T1.sh after running recon-all on a subject, but got the following error: “ Error using segmentSubjectT1_autoEstimateAlveusML (line 72) Side must be 'left' or 'right' “ I am using the following specs: _ platform:

Re: [Freesurfer] Run recon-all in MATLAB

External Email - Use Caution Hi Tim, Thanks a lot for the quick response. I used system and it is working now  Have a nice day, Aldo From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tim Schäfer Sent: Wednesday, August 26, 2020 1:58

Re: [Freesurfer] HBT segmentation missing voxels

Dear Liz, Other than killing the fissure, the rest should be the same. Could you please send us un example? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On 8/26/20, 11:30,

Re: [Freesurfer] Run recon-all in MATLAB

External Email - Use Caution Hi Aldo, What do you mean by 'still is not working'? What command did you run where (Matlab or Shell), and what was the error message? I've had a quick look at that website, and from what I can tell it does not try to tell you how to run recon-all

[Freesurfer] Run recon-all in MATLAB

External Email - Use Caution Hi Freesurfer community, Does someone know how to run recon-all on MATLAB ? I tried the settings suggest on https://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/FreeSurfer, but still is not working; Thanks a lot in advance and have a great

Re: [Freesurfer] Visualizing significant clusters, monte-carlo and permutation

External Email - Use Caution I mentioned in # 3 in my previous post what happens (and also attached images for you to see). Will you please tell me if its okay that the shades of these colours look different from my QDEC outputs? On Mon, Aug 24, 2020 at 10:22 AM Douglas N. Greve

[Freesurfer] HBT segmentation missing voxels

External Email - Use Caution Hello there, I am using Freesurfer v7.1.0 software, and I am interested in the longitudinal segmentation of the hippocampus (HBT). I am currently inspecting my output hippocampal segmentations, and couldn’t help but noticing missing voxels in the

Re: [Freesurfer] Global surface area and global thickness values {Disarmed} {Disarmed}

Yes! On 8/26/20 9:30 AM, Palin, Tara wrote: External Email - Use Caution Again, thank you for your explanation of how these variables are calculated. However, the the main question still left is, are these values the most representative of the whole cerebral surface area and the

Re: [Freesurfer] Global surface area and global thickness values {Disarmed} {Disarmed}

External Email - Use Caution Again, thank you for your explanation of how these variables are calculated. However, the the main question still left is, are these values the most representative of the whole cerebral surface area and the whole cerebral thickness for both the left

Re: [Freesurfer] Error message when using mri_glmfit-sim "ERROR: could not open .csd"

And one more thing, I noticed that you were using a cluster forming threshold of 1.3 (p<.05). This low a threshold is not recommended when using mc-z (you can use it with permutation, which is more generally recommended) On 8/25/2020 12:18 PM, Diógenes Diego wrote: External Email -

Re: [Freesurfer] Error message when using mri_glmfit-sim "ERROR: could not open .csd"

oh, wait, I do see the error in there now, but it did not appear to cause the program to fail. I tracked down and fixed the problem. It should not actually create any issues for your output, so you can just ignore the error. On 8/25/2020 12:18 PM, Diógenes Diego wrote: External

Re: [Freesurfer] Error message when using mri_glmfit-sim "ERROR: could not open .csd"

That file was apparently not created when running mri_glmfit-sim, but the log files did not show an error On 8/25/2020 12:18 PM, Diógenes Diego wrote: External Email - Use Caution What is the reason for this message? ERROR: could not open

Re: [Freesurfer] WM & GM mean thickness

Look in the ?h.aparc.stats file for mean cortical thickness; I'm not sure what you mean by the thickness of white matter. On 8/26/2020 8:25 AM, vittal korann wrote: External Email - Use Caution Dear FreeSurfer experts I'm trying to get global mean thicknesses of white matter and

[Freesurfer] WM & GM mean thickness

External Email - Use Caution Dear FreeSurfer experts I'm trying to get global mean thicknesses of white matter and gray matter separately. But *stats* folder in the *subjects *list does not mention explicitly. Is there a way to get these two thicknesses? Any assistance would be

Re: [Freesurfer] use of ANTs Denoising in FS 7.1

External Email - Use Caution Dear Jim, I had been looking at the effect of denoising the data to improve processing speed in case of noisy data in an ISMRM abstract couple of years ago. However, I haven't had the time to follow up on this. Glad to see something similar now