Re: [Freesurfer] [External] Re: Mapping the labels onto the aparc atlas

External Email - Use Caution Hi, I'm assuming the .annot is wrong because it doesn't map the entire gray matter ribbon, whereas when the .annot is mapped unto the gray matter ribbon using mri_aparc2aseg, its grabbing the surround gray matter. I am attaching a picture as

Re: [Freesurfer] volumes/surfaces FS6.0 vs FS7.2/3.2

Hello Jim, All subjects should be processed with the same version of freesurfer, especially for longitudinal studies. Either v6.x or 7.x should work for your purposes. If you decide to go with v7.x, you can make a copy of the subjects run in v6.0, then run v7.x using the outputs of v6.0, and

Re: [Freesurfer] Calculating Distortion in mris_flatten()

Hi Sarah It is something like: 100 * (mean(abs(distance error)) / mean(original_distances)) Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Sarah Lavelle Sent: Tuesday, November 8, 2022 12:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Calculating

[Freesurfer] Fwd: average lobar cortical thickness

External Email - Use Caution Dear Freesurfer experts, I would like to know if this procedure is correct. I have cortical thickness data from aparc+aseg for every ROI in DTK atlas (i.e. output of recon-all). I need average cortical thickness in frontal, parietal, temporal,

[Freesurfer] Calculating Distortion in mris_flatten()

External Email - Use Caution Hi freesurfers, Does anyone know how to measure the distortion of your inflated surface -> flatmap transformation (using mris_flatten)? When being run, the function outputs "final distance error ...%" in the terminal. What exactly does this mean? and

Re: [Freesurfer] Convert image in native coordinate space

External Email - Use Caution Hello Yujing, Thank you so much for your reply! I understand. It helps me a lot. Thank you! Best regards Haiyun On Mon, Nov 7, 2022 at 3:39 PM Huang, Yujing wrote: > Hi Haiyun, > > > > You can convert lh.pial.native to GIFTI using mris_convert -

Re: [Freesurfer] acompcor in fsfast

Just as a quick verification and follow up using 1. Specifying the number of components eg. if I want 5 -nuisreg the various components I want to regress out “-comp 6 – comp 7 comp 8 comp 9 2. Also just a follow up, how do I go ahead and run an ICA instead of the regular connectivity

Re: [Freesurfer] Mapping the labels onto the aparc atlas

I'm not sure what you are saying. Are you saying that the annot/surf looks right but the seg in the volume looks wrong or that they both look wrong? On 10/31/2022 2:58 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution Hi Freesurfer devs, We have

Re: [Freesurfer] design is ill-conditioned

can you send the mkanalysis-sess command? On 10/31/2022 12:17 PM, Loeffler, Martin wrote: External Email - Use Caution Dear experts, I’m running into an error when running selxavg3. It says the design is ill-conditioned. I’m a bit stuck, because the same pipeline works in most

Re: [Freesurfer] Segmentation of hippocampus(left), grey and white matter regions.

Try running recon-all on the unskull stripped data. Alternatively, if  you just want hippo you can run mri_synthseg or samseg On 10/31/2022 5:32 AM, PRASAD D wrote: External Email - Use Caution Hello everyone. I’m new to FREESURFER I would like to segment the sMRI images. I have

Re: [Freesurfer] Cutting an occipital patch

can you send the terminal output from selxavg3-sess? On 10/31/2022 4:38 AM, Noam Khayat wrote: External Email - Use Caution Hi again Douglas, Do you know the answer to my last mail? Do I need to compress all functional nii files to one single file? Thanks! Noam ‫בתאריך יום ב׳, 24

Re: [Freesurfer] Question about color look up table

are you looking at a surface or a volume? for volume, there is an opacity slider in freeview On 10/28/2022 11:06 PM, Yoshito Saito wrote: External Email - Use Caution Hello. I would like to ask a question about the color look-up table. I want to change the opacity of color on a

Re: [Freesurfer] intensity statistics in aseg.stats

the intensity is the T1-weight instensity of the norm.mgz image (after intensity normalization, white matter mean ~= 110). It may or may not be useful. In some cases, the intensity changes, so you could test that On 10/28/2022 1:55 AM, Zeng, Qi wrote: External Email - Use Caution Hi

Re: [Freesurfer] dcmunpack

just install FS On 10/27/2022 4:56 PM, Jang, Woo Ju Albert W.,PhD wrote: Hi, I need to unpack dcm files to my local workstation via /dcmunpack/ command. Is it possible to install this command on my local workstation? Best, Albert ___ Freesurfer

Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error

is it in $FREESURFER/bin ? If so, is that folder in your path? On 10/27/2022 12:49 PM, Gillian Grennan wrote: External Email - Use Caution Realized I sent this to the support list not back to you! But it says "command not found" when I run 3dvolreg and 3dvolreg.afni On Wed, Oct 26,

Re: [Freesurfer] change in mask size

Also see https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 10/27/2022 12:00 PM, Wighton, Paul wrote: Hi Padma, You can use the --like flag of mri_convert to convert the output of the skull stripping back to the dimensions of the original file

Re: [Freesurfer] Question regarding General Linear Model analysis with Freesurfer

On 10/26/2022 10:05 PM, Lyna Mariam El Haffaf wrote: External Email - Use Caution Hi! I hope you are doing well! I am working on a paper where we used Freesurfer for whole brain analysis in intergroup comparison (g2v1). The objective of the analysis is to see if there is an

Re: [Freesurfer] acompcor in fsfast

When you run fcseed-sess, specify -pca instead of -mean. When you run mkanaysis-sess, specify the number of components you want when specify -nuisreg On 10/26/2022 6:29 PM, Addison, Reuben wrote: Hi, I am running resting State functional connectivity and I want to run everything in

[Freesurfer] Help: Vertex Properties

External Email - Use Caution Hi, I’m wondering if there’s a way to get the properties of individual vertices such as: 1)Coordinates 2)Surface area 3)angles 4) Side lengths 5) distance matrix from other vertices And can you get these properties for individual surfaces/