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

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

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

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] mri_convert mosaic data

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

Re: [Freesurfer] EasyReg usage

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

[Freesurfer] EasyReg usage

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

[Freesurfer] mri_convert mosaic data

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

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

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

Re: [Freesurfer] VM Password

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 >

[Freesurfer] VM Password

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

Re: [Freesurfer] Freeview error

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

Re: [Freesurfer] Freeview error

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,

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

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:

Re: [Freesurfer] Freeview error

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:

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

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

Re: [Freesurfer] Flipping Thickness Matrices

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

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

External Email - Use Caution Hi there, I am trying to run recon-all using the Agave Supercomputer at ASU. When I try to run recon-all, these error messages pop up prohibiting me from running recon-all on my T1 image. Here is the error message I received: