Re: [Freesurfer] recon-all for 0.85 isotropic images error (bump)

External Email - Use Caution Dear Kristine, I haven't had any issues processing high resolution data with version 6 or 7 using either the -cm or -hires flag. However, I never used the -cw 256 flag as my FoV was never greater than 256. Could you post the size of the created

[Freesurfer] T1 and DTI nifti data stored after running recon-all and trac-all

External Email - Use Caution Hi, I run both recon-all and trac-all for each subject. Where are the original T1 and DTI data stored in the output files? Thank you so much! Best, Qi ___ Freesurfer mailing list

[Freesurfer] problem about PVC of PETSurfer {Disarmed}

External Email - Use Caution Hello Freesurfer, We know that the freesurfer7 has given a new module to separate hippocampal subfields in MRI image, but we encoumter problems in registering the PET image with MRI image. We find that the resolution radio of PET image is not enough,

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

External Email - Use Caution I got the sum area and average area of the label, there is no significant difference between the mTBI group and health control, either.However, the label was significant different in the fsaverage between mTBI group and health control after multiple

[Freesurfer] qdec replacement

External Email - Use Caution Hello I was just wondering if there were any updates on a FSv7 replacement for QDEC for vertex-wise cortical thickness analyses? Or if there were any recommendations for analyses in other programs? Thanks! David -- David Pagliaccio, Ph.D.

Re: [Freesurfer] distance between two vertices in Freeview

Hi Mona, The 3D scale bar in freeview is not for measurement. It is simply a scale bar for the field of view. I don’t think you can use that to measure the distance between two points. Best, Ruopeng On Nov 17, 2020, at 11:45 AM, Nasiriavanaki, Zahra mailto:znasiriavan...@mgh.harvard.edu>>

[Freesurfer] Postdoctoral Fellowship in Cognitive Neuroscience - Braga Lab @ Northwestern University {Disarmed}

External Email - Use Caution We are seeking a postdoctoral fellow to join the Braga Lab (

[Freesurfer] distance between two vertices in Freeview

Dear Freesurfer experts Hi I was trying to measure the dimensions of a surface ROI in a flatten map on Freeview. I used the 3D scale bar to measure the longest diameter of the ROI. My question is how the scale bar is calculating the distance between the two points? Is it the euclidean distance

[Freesurfer] smoothing on ?h.w-g.pct.mgh files

External Email - Use Caution Dear Freesurfer experts, I computed the gray to white matter signal intensity ratio using the pctsurfcon command and extracted the ?h.w-g.pct.mgh files. How can I conduct a smoothing procedure on these surface files? Thanks for your help, -- Enrico

Re: [Freesurfer] Cortical thickness volume ROI to surface {Disarmed}

External Email - Use Caution Thank you for your response! Here the commands: #register image to MNIspace flirt -in mydata_T1.nii.gz -ref fsl/data/standard/MNI152_T1_1mm -out mydata_T1_MNI.nii.gz -omat mydata_T1_MNI.mat #Create a registration from the ROI-anatomical volume to a

[Freesurfer] question about PVC of PETSurfer

External Email - Use Caution Hello Freesurfer, We know that the freesurfer7 has given a new module to separate hippocampal subfields in MRI image, but we encoumter problems in registering the PET image with MRI image. We find that the resolution radio of PET image is not

[Freesurfer] Error in longitudinal pipeline {Disarmed}

External Email - Use Caution Hi FreeSurfer experts Recently I started working on the longitudinal data. I followed the pipeline described in the below link. Also, I attached my longitudinal table along with freesurfer data.