Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation

Hi Katie, The core.py file has been updated now. Please try downloading it again and applying the same fix as before. Best, Avnish From:

[Freesurfer] MGH35 template

Hi Mark, Sorry for the late reply. The population template was built using the FA images only, so there is no corresponding T1 template image. You can use the transforms stored in dmri/xfms in your TRACULA directory to map the subject’s anatomical images to this template space, or you can set

Re: [Freesurfer] mri_easyreg tool

Sorry for the late response, I went on vacation the very same day you posted your question. The floating image is the one you want to deform, and the reference image is the one you use as target for the registration /deformation. In other words: the deformed floating image should overlap with

Re: [Freesurfer] different clusters in mri_surfcluster output versus viewing in Freeview

External Email - Use Caution Hi Yujing, Thank you for explaining that. I believe that mri_surfcluster is the correct output, in that it is carrying out a one-sided test of significance at 2 (Sig = -log(pvalue), i.e., p < 0.01). For the Configure options, is there a similar

Re: [Freesurfer] Correlating and/or linear regressing surface overlays

It looks like you are doing the right thing. You indicated not to use a contrast matrix. If you want to test a contrast, I think the matrix would be [0 1] (I think it adds an offset regressor) On 2/10/2023 4:50 PM, Finn, Quentin wrote: External Email - Use Caution Freesurfer

Re: [Freesurfer] Hole in the insula

That looks like a GM lesion (maybe some kind of stroke). I don't think we have a way to fix it. On 2/7/2023 10:34 AM, Aaron Tanenbaum wrote: External Email - Use Caution  I have this subject that has holes in the insula. Please see attached. I was wondering what should freesurfer

[Freesurfer] Please unsubscribe me

External Email - Use Caution Hi, Please, unsubscribe me from your mailing list. Thank you, Manuela ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

Re: [Freesurfer] Nuisance regressors

you would add them as task regressors and set up first level contrasts as you describe. I'm not sure of your last question (ie, second-level comparison of their effect). Do you want to compare, eg, respiration vs motion? I'm not sure how you would do that. On 2/6/2023 5:18 AM, Marilena

Re: [Freesurfer] Extracting brain volume seperately

We do not generate a scalp segmentation (but you can use samseg which generates skull and something like skin). If you want to create a binary volume with a chosen seg or tissue type = 1 and everything else = 0, you can use something like mri_binarize --i aseg.mgz --match 4 5 14 15 43 44 --o

Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS

External Email - Use Caution Dear All, Thank you very much for your interest. I contacted my system administrator and he fixed it. fsbuild , 22 Şub 2023 Çar, 18:04 tarihinde şunu yazdı: > > The best solution (which I think was previously emailed to you) is to have > an admin/IT

Re: [Freesurfer] different clusters in mri_surfcluster output versus viewing in Freeview

Hi Christine, Sig = -log(pvalue) In freeview, the overlay thresholds can be adjusted by clicking 'Configure' button (under the Overlay dropdown menu). For mri_surfcluster (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster), I think you can try to adjust these options to match

[Freesurfer] Failing to execute QDEC

External Email - Use Caution Hi Freesurfer experts, I am trying to run Qdec on schizophrenia pre and post intervention scans. I created .dat and .levels files within the qdec folders and loaded the .dat file into qdec gui. It is suddenly crashing when I select my design and hit

[Freesurfer] Visualizing transparent surface with non transparent annotations

External Email - Use Caution Dear Experts, I would like to use Freeview to achieve the following. I would like to visualize a transparent brain surface, with only some annotations visible. In other words, I would like the surface to be transparent, but the annotations I choose

[Freesurfer] SEEKING A DYNAMIC POSTDOC TO INVESTIGATE BRAIN GUT MICROBIOME INTERACTIONS

External Email - Use Caution > Dear Freesurfer Community, > > We are looking for a postdoc for this exciting position (2-3 years)- details > below > >

Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS

External Email - Use Caution The best solution (which I think was previously emailed to you) is to have an admin/IT person update your system by doing the following: 1) Copy the link for the freesurfer release install package matching your Ubuntu system, e.g., 7.3.2

Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS

Thanks for the interest in our software! Could you please try running this command from the terminal? sudo apt-get install libncurses5 Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on behalf of behçet ayyıldız Reply-To: Freesurfer support list Date: Wednesday,

Re: [Freesurfer] [FreeSurfer] recon-all exited with error

Hi Krystal, Can you try running recon-all without '-parallel' flag? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Krystal Xiwing Yau Sent: Saturday, February 18, 2023 7:45 PM To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with

Re: [Freesurfer] How to calculate the mean FA value in the hippocampus

Please ignore my second question. It looks correct in your original email. I must mess up when doing cut and paste. From: Huang, Yujing Sent: Wednesday, February 22, 2023 9:55 AM To: Freesurfer support list Subject: RE: [Freesurfer] How to calculate the mean FA value in the hippocampus Hi Lin,

Re: [Freesurfer] How to calculate the mean FA value in the hippocampus

Hi Lin, I’m not sure why the results are different. The input/output volumes for mri_binarize can be either mgz or nii.gz. With your first method, can you try to convert aparc+aseg_diffspace.nii.gz to left_hippocampus.nii.gz directly? Also your second to last command ‘mri_convert

[Freesurfer] Sulcal depth and Gyrus height

External Email - Use Caution Hi, I want to obtain the gyral height and the sulcal depth for every region of the aparc atlas. I know that in the file lh.sulc the positive values are the depth of the sulcus and the negative one are the height of the gyrus. How can I obtain

Re: [Freesurfer] Freeview displaying images in the wrong orientation

Can you send us a screenshot or even better, a sample image file? Ruopeng > On Feb 22, 2023, at 7:34 AM, Nathan Kindred (PGR) > wrote: > >External Email - Use Caution > > Hi, > > When I am displaying certain images in freeview the orientation does not > match what is

[Freesurfer] Freeview displaying images in the wrong orientation

External Email - Use Caution Hi, When I am displaying certain images in freeview the orientation does not match what is displayed in both orient_mri and SPM. The coronal and horizontal views seems to be okay but the midsagittal view is often wrong with the front of the brain

[Freesurfer] (no subject)

External Email - Use Caution Hi, I want to obtain the gyral height and the sulcal depth for every region of the aparc atlas. I know that in the file lh.sulc the positive values are the depth of the sulcus and the negative one are the height of the gyrus. How can I obtain