[Freesurfer] Manual Segmentation Adjustments

External Email - Use Caution Hi everyone, I hope you're all doing well! I'm running into a bit of trouble with some manual adjustments to our segmentation results and was wondering if anyone has encountered something similar. After running recon-all, I noticed that the white an

Re: [Freesurfer] manual segmentation

On 1/21/2022 7:49 AM, 刘卫 wrote: External Email - Use Caution Hello FreeSurfer Developers, Hello, I would like to ask if there are other correction methods besides  multiple comparison correction when surface based group analysis. You can use FDR (mri_fdr) Can I use the 6.0 versio

[Freesurfer] manual segmentation

External Email - Use Caution Hello FreeSurfer Developers, Hello, I would like to ask if there are other correction methods besides multiple comparison correction when surface based group analysis. Can I use the 6.0 version of free to analyze the results of the 7.2 version prepr

Re: [Freesurfer] manual segmentation

not sure what you mean by "manual segmentation" or why you would do that again. We do recommend at least inspecting the data visually On 10/27/2021 11:35 AM, 刘卫 wrote: External Email - Use Caution Hello FreeSurfer Developers, I would like to ask, on free surfer, can I directly analyz

[Freesurfer] manual segmentation

External Email - Use Caution Hello FreeSurfer Developers, I would like to ask, on free surfer, can I directly analyze the data that I run automatically? Do I need to perform manual segmentation again? Thanks! ___ Freesurfer mail

Re: [Freesurfer] Manual segmentation to volume

Use $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz as the target when you are using the 1mm (there is a mri2.mm folder for 2mm) On 12/19/2019 11:34 AM, Benjamin Ineichen wrote: External Email - Use Caution Many thanks for your quick reply! I tried your suggestion. I got the error fst

Re: [Freesurfer] Manual segmentation to volume

External Email - Use Caution Many thanks for your quick reply! I tried your suggestion. I got the error fstal unknown. So I tried talres 1 instead of fstal 1: mri_vol2vol --talres 1 --interp nearest --mov example.mgz --s 001.mgz --regheader --o example.mni305.mgz but got the err

Re: [Freesurfer] Manual segmentation to volume

in this case, I might try mri_vol2vol, something like mri_vol2vol --fstal 1 --interp nearest --mov example.mgz --s subject --regheader --o example.mni305.mgz That is a linear transform. If you want a non-linear, I can walk you through that too On 12/18/19 10:13 AM, Benjamin Ineichen wrote: > >

[Freesurfer] Manual segmentation to volume

External Email - Use Caution Dear Freesurfer experts, I have a manual segmentation of a certain brain feature done in Freeview. I want to pool these segmentations from different subjects to create some kind of a heat map/probability map. In order to do this, I assume I need to co

Re: [Freesurfer] Manual segmentation issues

PS: For instance you can notice that the added voxels in the axial slice, coordinates * -39.69, 10.78, 11.54*were not included in the surface. By the way, the subject is 13 months old. On Tue, May 10, 2016 at 5:06 PM, Saturne Fox wrote: > Bruce, > > I just uploaded the directory through the

Re: [Freesurfer] Manual segmentation issues

Bruce, I just uploaded the directory through the FTP server, the name of the archive is 00M034.tar.gz . Concerning our issue we tried to identify the problem in the light of your advices and we observed that the *orig *file contains most of the manual modifications, which are then lost

Re: [Freesurfer] Manual segmentation issues

Hi Antoine we need the entire subject directory tarred and gzipped if you want us to look. And please upload it to our ftp site thanks Bruce On Mon, 9 May 2016, Saturne Fox wrote: ​[icon_10_generic_list.png]   sanlm_IRC04H_00M034_P_1_WIP_T1W_3D_IRCstandard3...[x_8px.png] ​Dear Bruce,   

Re: [Freesurfer] Manual segmentation issues

​ sanlm_IRC04H_00M034_P_1_WIP_T1W_3D_IRCstandard3... ​Dear Bruce, Most of the time the added voxels are included in the orig file but are lost in the ?h.white one. Here is the subject file. Thanks a

Re: [Freesurfer] Manual segmentation issues

Hi Antoine if you upload the entire subject dir we will take a look. It sounds like it might be a topological defect. You can check this by seeing if the orig.nofix contains the voxels that you added, but the orig does not. cheers Bruce On Mon, 9 May 2016, Saturne Fox wrote: Dear freesurf

Re: [Freesurfer] Manual segmentation issues

Hi Saturne you need to give us more information if you want us to help you. cheers Bruce On Mon, 9 May 2016, Saturne Fox wrote: Dear freesurfer users community,     I need your help concerning manual segmentation issues. ___ Freesurfer mail

Re: [Freesurfer] Manual segmentation issues

Dear freesurfer users, I need your help concerning manual segmentation issues. In fact I used the editing tool with an intensity of 250 to add some missing part on the wm.mgz file but some of the added areas were not considered for the creation of the surface. Some of th

[Freesurfer] Manual segmentation issues

Dear freesurfer users community, I need your help concerning manual segmentation issues. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is i

Re: [Freesurfer] Manual segmentation

Hi, Douglas     I´m making changes in aseg.mgz and I need to know how is the comand to save the changes in the new segmentation (in tkmedit: File - New segmentation, or File - Save segmentation or if there is another comand in the menu to save the changes).   

Re: [Freesurfer] Manual segmentation

can you be more specific? What are you using to create the manual segmentations? Kelly Silva wrote: Hello, I´d like to know what´s the comand to save the new manual segmentations of the subcortical structures. Thanks, Kelly --

[Freesurfer] Manual segmentation

Hello,    I´d like to know what´s the comand to save the new manual segmentations of the subcortical structures.   Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___

Re: [Freesurfer] manual segmentation of subcortical structures

Hi Jose, not sure I understand. Do you mean to edit the aseg.mgz to improve hippocampus and thalamus? We don't have any protocols for this, although you could certainly do it in tkmedit or freeview. Changing these shouldn't have much affect on cortical thickness. cheers, Bruce On Mon, 16

[Freesurfer] manual segmentation of subcortical structures

Hi there, we have a bunch of MRI scans already segmented by using the typical FS recons protocol. Now we would like to improve the hippocampus and thalamus delimitation by manual segmentation, but several basic questions arose: 1. Are there radiological protocols (commonly used) to segment thes