[Freesurfer] The specific steps of the mri_surf2surf command

External Email - Use Caution Hello, Fs I am not familiar with the exact steps of sampling a pre-segment file into the FSAVERAGE5 space. In other words, I am not very familiar with the exact steps of the mri_surf2surf command.___ Freesur

[Freesurfer] which file is freesurfer autoseg result?

External Email - Use Caution hello, FSI do the brain region parcellation, I have label(ground truth) for each subject. I want to use my own neural network segmentation results and Freesurfer automatic segmentation results comparison, to get a qualitative and quantitative results

[Freesurfer] can the white matter surface is from the individual sMRI?

External Email - Use Caution Hello, Fs can I get the white matter surface from individual smri??___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] the white matter surface is from the individual sMRI?

External Email - Use Caution Hello, Fs can I get the white matter surface from individual smri??___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] In Freesurfer, the sulc value of the gyrus is NOT positive, on the contrary, they are negative?

External Email - Use Caution Hello, Fs  In Freesurfer, the sulc value of the gyrus is NOT positive, on the contrary, they are negative?? by the way, how the mean curvature reflects the degree of fold? Since the mean curvature is a local measurement, does the mean curvature map re

[Freesurfer] Can FS use the recon all command to automatically divide it into DKT32 areas?

External Email - Use Caution Hello, Fs I saw an article that gave the Dice coefficient and ACC of Freesurfer's automatic segmentation, so I am curious, can Fs automatically divide it into 32 regions?___ Freesurfer mailing list Freesurfe

[Freesurfer] freesurfer install error

External Email - Use Caution Hello, Fs After installing FreeSurfer, use tkregister2, tkmedit, tkurfer, and recon all -- help to verify whether the installation is successful.  The first and fourth commands are OK, but the second and third commands display the same error: glut: fa

[Freesurfer] mri_surf2surf command error

External Email - Use Caution Hello, Fs I want to template some subject to fsaverage5, but now I meet some problems FreeSurfer version: Fs6 Download the files: HLN-12-2.tar.gz    OASIS-TRT-20-1.tar.gz   Twins-2-1.tar.gz  Twins-2-2.tar.gz(https://secure-web.cisco.com/1yywjdkihIUyeuY

[Freesurfer] Principle of registration to fsaverage5 space

External Email - Use Caution Hello, everyone I have downloaded a folder, there's manual.annot file, but no lh.area file.  So, I created a bert from this subject use recon -all command, but there's no manual.annot file.  Can I use the manual.annot file in download folder template

[Freesurfer] Failed to load surface

External Email - Use Caution Hello, Fs I can visualize the lh.white lh.sphere lh.pial and so on. But when I visulized the lh.sulc lh.thickness and  other feature files, the error will be displayed as follows: Failed to load surface. Do you know how to visualize these feature file

[Freesurfer] convert .vtk to .annot

External Email - Use Caution Hello, everyone I have lh.labels.DKT31.manual.vtk file, but I want to convert it to lh.labels.DKT31.manual.annot. Now, I use fs6 version, if you know please tell me! I also heard that convetr .vtk to .label then convert .label to .annot, just use mri

[Freesurfer] recon labels.DKT31.manual.nii.gz appears ERROR: Talairach failed

External Email - Use Caution Hello, everyone I have download the labels.DKT31.manual.nii.gz in mindboggle datsets, I want to use recon-all command to get lh.labels.DKT31.manual.annot. But, when I run: recon-all -i labels.DKT31.manual.nii.gz -s bert5 -all, appears ERROR: Talairac

[Freesurfer] how to use recon-all command

External Email - Use Caution Hello, everyone my freesurfer enviroment: Last login: Mon Dec 21 16:45:53 2020 from 10.16.10.109 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /home/

[Freesurfer] Can't find Mindboggle datasets

External Email - Use Caution Hello, everyone In mindboggle website, the data is freesurfer-output, But I just want to download the 101 source data, use recon -all command preprocess them by myself. I don't know where to download the source datasets, If you know, please give me a

[Freesurfer] mri_surf2surf lh.area does not match surface (148208, 146833)

External Email - Use Caution Hello, Fs When I run the following command: mri_surf2surf --srcsubject HLN-12-2 --sval area --src_type curv --trgsubject fsaverage5 --trgsurfval /home/tj/application/freesurfer/subjects/min_template/HLN-12-2-target/area --trg_type curv --hemi lh

[Freesurfer] how to convert .vtk file to .annot file?

External Email - Use Caution Hello, Fs Do you know how to convert the .vtk to .annot file? I want to visualization with. Annot file by freeview. Looking forward to your reply!___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu h

[Freesurfer] mri_surf2surf Cannot allocate memory

External Email - Use Caution Hello,Fs When I used mri_surf2surf command to template the lh.thickness to fsaverage5 space, the error appeared: Command: mri_surf2surf --srcsubject OASIS-TRT-20-1 --sval thickness --src_type curv --trgsubject fsaverage5 --trgsurfval /home/tj/applica

[Freesurfer] what command can be used to template .vtk file to fsaverage5 space?

External Email - Use Caution Hello, what command can map VTK file to fsaverage5 space? I want its vertex number to be 10242. If you know, please give me an example. Looking forward to your reply___ Freesurfer mailing list Freesurfer@nmr.

[Freesurfer] There is no view-label option after loading the .annot file

External Email - Use Caution Hello, Fs my freesurfer version is 6,  I see others have the view button after load .annot file, But my version does not have this option.  Do I need to update the version? And I have installed fs6, can I install fs 7.1 on the same machine? What's mor

[Freesurfer] The non-existent field'numEntries' is referenced.(write_annotation.m)

External Email - Use Caution hello, fs when i use the write_annotation.m, the error message occurs: `The non-existent field'numEntries' is referenced. Error write_annotation (line 62) count = fwrite(fp, int32(ct.numEntries),'int'); Error test_1 (line 13) write_annotation('rh.apa

[Freesurfer] why can't I receive a reply from others in my mailbox?

External Email - Use Caution Hello,  After i asked a question, why can't I receive a reply from others in my mailbox?___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] replace the vertex_label_index in .annot file

External Email - Use Caution hello, Previously, rh.white and rh.aparc.2009s.annot were used to generate vertex_id and vertex_label,  ' from freesurfer_surface import Surface from freesurfer_surface import Label from freesurfer_surface import Annotation surface = Surface.read_tri

[Freesurfer] Open the .annotation file with Notepad is garbled

External Email - Use Caution Hello, FreeSurfer Why is it garbled when I open the .annotation file with Notepad? Is there any solution?  Looking forward to your reply___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail

[Freesurfer] The usage about annotation view

External Email - Use Caution hello, FreeSurfer  I have loaded rh.pial and rh.aparc.2009s.annot, why my version does not have the label view option that can see the annotation? Is it a version issue? My FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

[Freesurfer] Put the updated vertex_label into .annotation

External Email - Use Caution hello, After I updated the vertex_label of rh.aparc.a2009s.annot with an algorithm, now I want to replace the vertex_label in the .annot with the updated vertex_label, mainly to see the effect of the segmentation, do you know what to do ? if you know

[Freesurfer] mri_surf2surf template rh.white to fsaverage5

External Email - Use Caution hello,Fs Because I want to build an N*N matrix based on the fixed-point number N of rh.white, but the original rh.white has too many fixed-point numbers, a memory error occurs. I saw a paper, which can be registered to the fsaverage5 space, and t