[Freesurfer] overlay properties tksurfer window incomplete...

Hi: I have an ubuntu based computer with Freesurfer 5, and it seems that because the font size or the screen resolution, the lowest part of the "Overlay Properties" window in tksurfer didn't appears (Ok and Cancel buttons, for example, etc)... Any solution ?... Sincer

[Freesurfer] remote access to freesurfer installation...

External Email - Use Caution Hi: Is there a freesurfer facility where an MRI study can be processed remotely? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] T1 gadolinium

External Email - Use Caution Hi: SynthSeg is useful for T1-GD volumetric images? Another algorithm, software? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785

[Freesurfer] infantFS computer requierements

? VRAM? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] trac-all error

r for model-based eddy-current distortion correction, ERROR: must specify PE direction" Why? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

[Freesurfer] installation of two versions of freesurfer on same computer...

External Email - Use Caution Hi: How can I install two different versions of freesurfer on the same computer? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] CT conversion from DICOM to MGZ

0 and rerun." Where can I find the FS_RESCALE_DICOM option ? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail i

[Freesurfer] SynthSeg with CT images.

External Email - Use Caution Hi: I tried SynthSeg using CT images, but I got very bad results... CT images must have some specific characteristics? I tried with axial acquisition and volumetric one Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las

Re: [Freesurfer] SynthSeg with CT images.

External Email - Use Caution Hi Benjamin: I tested with the clipping, and it works ok with a CT image. Sincerely Gonzalo Rojas Costa El mié, 8 de mar de 2023, 14:39, Benjamin Billot escribió: > Yes, agreed. > > Gonzalo: Also, if SynthSeg still gives you a bad res

Re: [Freesurfer] SynthSeg with CT images.

External Email - Use Caution Ok... Thanks you very much... Gonzalo Rojas Costa On Wed, Mar 8, 2023 at 5:38 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > I added a flag (--ct) to mri_synthsr in FreeSurfer so people don’t need to > c

[Freesurfer] CT and mri_synthsr

/home/developer/Documents/OAS31367/sub-OAS31367_sess-d0142_run-01_CT_0_80.nii.gz --o /home/developer/Documents/OAS31367 --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread predicting 1/1 Killed What does "Killed" mean? Any log file? Sincerely, Gonzalo R

[Freesurfer] mri_synthsr with CT images

/home/developer/Documents/OAS31367/sub-OAS31367_sess-d0142_run-01_CT_0_80.nii.gz --o /home/developer/Documents/OAS31367 --cpu SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread predicting 1/1 Killed What does "Killed" mean? Any log file? Sincerely, Gonzalo R

[Freesurfer] mri_synthseg error...

self._metric_methods[self._label_length].create(*args) tensorflow.python.framework.errors_impl.AlreadyExistsError: Another metric with the same name already exists." Which could be the problem ? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 44

[Freesurfer] multiple axial slice screenshots

External Email - Use Caution Hi: I need to take screenshots to all axial slices of a volumetric image that I am viewing using freeview (flair with a segmentation). Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list

[Freesurfer] automatic screenshots to all axial slices

External Email - Use Caution Hi: I need to take screenshots of all axial slices of a volumetric image that I am viewing using freeview (flair with a segmentation). How can I do it automatically? Sincerely, Gonzalo Rojas Costa

[Freesurfer] mri_synthseg problem with CT... freesurver v 7.3.2

from 0-80 hounsfield units... Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] fsl fmri thresh_zstat1.nii file showing in fsaverage pial surface

External Email - Use Caution Hi: I processed an fMRI task using FSL. I got the standard image coregistered result... How can I show the thresh_zstat1.nii file in fsaverage pial surface? Sincerely, Gonzalo Rojas Costa

[Freesurfer] Longitudinal SAMSEG with multi-contrast data

utput outputDir/" ? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addres

[Freesurfer] online freesurfer

External Email - Use Caution Hi: Is there a freesurfer-based system that allows processing online an mprage image? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] freeview error....

lling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb." How can I correct it? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list

[Freesurfer] windows-based software to read freesurfer images...

External Email - Use Caution Hi: Is there any software for microsoft windows (and/or ubuntu) that allows you to read mgz file format images, and transformations in lta format? Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae Universi

[Freesurfer] freeview runtime error...

External Email - Use Caution Hi: I got the following error running freeview in Ubuntu: "freeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb

[Freesurfer] Freesurfer remotely processing

External Email - Use Caution Hi: Is there any free implementation that allows me to process images with freesurfer remotely? Sincerely Gonzalo Rojas Costa Medicine School Finis Terrae University ___ Freesurfer mailing list

[Freesurfer] freeview runtime error...

External Email - Use Caution Hi: I tried to run freeview, but I got the following error: "This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, min

Re: [Freesurfer] freeview runtime error...

External Email - Use Caution Hi: I tested all the commands that you told me, but, I still have the error that I had specified to you: "gonzalorojascosta@gonzalobrain:~$ freeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling th

Re: [Freesurfer] freeview runtime error...

External Email - Use Caution Hi: it is freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460, under Ubuntu 18.04.4 LTS. In a real physical ubuntu. Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

[Freesurfer] dt_recon and corregistration (2)...

External Email - Use Caution Hi: The error is in a misalignment between the FA and CC_Anterior section. Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University ___ Freesurfer mailin

[Freesurfer] dt_recon, CC_Anterior (T1) and FA corregistration.

External Email - Use Caution Hi: I used the following commands: dt_recon --i sub-OAS30003_ses-d1631_run-01_dwi.nii.gz --b sub-OAS30003_ses-d1631_run-01_dwi.bval sub-OAS30003_ses-d1631_run-01_dwi.bvec --s OAS30003_MR_d1631 --o dt_recon_result cd dt_recon_result mri_vol2vol --mo

[Freesurfer] hounsfield units for some aseg.mgz labels

External Email - Use Caution Hi: I completed the co-registration of CT to a freesurfer processed MRI image using the command: mri_coreg --mov sub-OAS30001_sess-d3132_CT.nii.gz --reg reg.lta --s OAS30001_MR_d0757 How can I get the mean and SD hounsfield units of some aseg.mgz

[Freesurfer] hounsfield units based in some aseg.mgz labels

External Email - Use Caution Hi: I completed the co-registration of CT images to a freesurfer processed MRI image using the command: mri_coreg --mov sub-OAS30001_sess-d3132_CT.nii.gz --reg reg.lta --s OAS30001_MR_d0757 How can I get the mean and SD Hounsfield units (from co

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