Re: [Freesurfer] Flipping Thickness Matrices

2023-03-15 Thread Anam Anzak
External Email - Use Caution Dear Paul, Thank you for your reply! Just one thing we haven't really figured out... does mris_left_right_register take as input the thickness (mgh) files or the surfaces? I've been trying but can't really apply it to the thickness files. In theory,

Re: [Freesurfer] different results for gtmpvc with different tracers

2023-03-15 Thread Federica Di Antonio
External Email - Use Caution of course: I run the same line of command for both amyloid and tau pet images with a fwhm = 1 in order to see what have happened mri_gtmpvc --i taupet.nii --reg tau.reg.lta --psf 1 --seg gtmseg.mgz --auto-mask 1 .01 --mgx .01 --no-rescale --o tau.outp

Re: [Freesurfer] Freeview error

2023-03-15 Thread Huang, Yujing
Hi, Can you check if the path is correct? What does ‘ls -l /Users/results/sub-101/mri/T1.mgz’ show? If you do ‘mri_info /Users/results/sub-101/mri/T1.mgz’, does it report anything? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of tsengyuheng1...@gmail.com Sent: Tuesda

Re: [Freesurfer] Unable to Run Recon-all on T1 Image

2023-03-15 Thread Huang, Yujing
Hi Annie, It looks like ‘/packages/freesurfer-5.0.0/’ is your system Freesurfer install directory. It is a good idea to keep your SUBJECTS_DIR separate from Freesurfer install directory. Create your SUBJECTS_DIR where you have write permissions will solve the problem. Best, Yujing From: fre

Re: [Freesurfer] Freeview error

2023-03-15 Thread tsengyuheng1...@gmail.com
External Email - Use CautionHi Yujing, It shows “-rw-rw-r--  1 username staff  0 Mar 15 09:44 T1.mgz” and “error: mghRead(/Users/results/sub-101/mri/T1.mgz, -1): read error”. Best, Y. Z.  From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Date: Wednesday, March

Re: [Freesurfer] Freeview error

2023-03-15 Thread Huang, Yujing
Hi, It shows that T1.mgz is empty. How did you run recon-all? Can you do ‘ls -l /Users/results/sub-101/mri/’? Can you send recon-all.log in attachment? Does it work for your other subjects? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of tsengyuheng1...@gmail.com Sent

[Freesurfer] VM Password

2023-03-15 Thread Christian Owen
External Email - Use Caution Hi, Would you mind sending the password to unzip FS_7_2_0_ubuntu_18_04_06.ova. 7z? Christian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/frees

Re: [Freesurfer] VM Password

2023-03-15 Thread Juan Felipe Gaitan Nocua
External Email - Use Caution Yes, I need it please! On Wed, Mar 15, 2023, 8:48 AM Christian Owen wrote: > External Email - Use Caution > > Hi, > > Would you mind sending the password to unzip FS_7_2_0_ubuntu_18_04_06.ova. > 7z? > > Christian > ___

Re: [Freesurfer] WM edits, prevent surface from cutting sulcus

2023-03-15 Thread Fischl, Bruce R.,PHD
Hi Chris It sounds like a topological defect, but hard to say without seeing it. Can you post some images? Or follow Doug’s instructions about visualizing the defects and see if there is one in the sulcus you mention below? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf

[Freesurfer] mri_convert mosaic data

2023-03-15 Thread John Anderson
External Email - Use Caution Dear Freesurfer, I have ASL DICOM data from a Siemens scanner in mosaic format. For each subject, there are 64 DICOM files, which consist of both tags and controls. I would like to convert each individual DICOM into a separate NIfTI file or a single 4D

[Freesurfer] EasyReg usage

2023-03-15 Thread fidel vila
External Email - Use Caution Hi, I checked the archive for any pointers about specific use instructions for EasyReg and read the wiki page. I would like to register three T1w acquisitions on three planes (Axial, Cor, Sagittal). This was my first attempt: *mri_easyreg --ref [myimage

Re: [Freesurfer] EasyReg usage

2023-03-15 Thread Iglesias Gonzalez, Juan E.
Dear Fidel, This is really weird… that’s essentially the last step. I you eg didn’t have writing permissions, you’d get an error. Would it be possible to share the data, so I can try to reproduce the issue on my end? Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on

Re: [Freesurfer] mri_convert mosaic data

2023-03-15 Thread Huang, Yujing
Hi John, I’m assuming all 64 DICOM files are in the same directory. Which Freesurfer version are you using? If you are using 7.3.2, can you try mri_convert -dcm2niix to convert those DICOMs? It will use dcm2niix to convert. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf

Re: [Freesurfer] WM edits, prevent surface from cutting sulcus

2023-03-15 Thread Chris Adamson
External Email - Use Caution Hi Bruce, It was a topological defect. I found it after looking harder. My bad. Hi Chris It sounds like a topological defect, but hard to say without seeing it. Can you post some images? Or follow Doug's instructions about visualizing the defects

Re: [Freesurfer] WM edits, prevent surface from cutting sulcus

2023-03-15 Thread Fischl, Bruce R.,PHD
No worries. I’m glad it worked out Bruce On Mar 15, 2023, at 10:52 PM, Chris Adamson wrote:  External Email - Use Caution Hi Bruce, It was a topological defect. I found it after looking harder. My bad. Hi Chris It sounds like a topological defect, but hard to say without seeing it