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

External Email - Use Caution Dear Falk, Thank you for your input! I have just tried without the T2 image as well, but it still output the same error. My original image size was 224*320*320 (voxel size 0.85*0.85*0.85), and the produced orig.mgz was 320*320*320 (voxel size 0.85*0.8

Re: [Freesurfer] About mri_vol2surf {Disarmed}

External Email - Use Caution How can I load the AAL onto the mni152 subject with the surface? El lun., 16 nov. 2020 a las 17:10, Douglas N. Greve () escribió: > Which MNI space? If mni152, then run recon-all on the mni152 template, > then run mri_vol2surf with --regheader mni152

Re: [Freesurfer] Striatum Mask for Choi et al 2012 {Disarmed}

External Email - Use Caution Hi Dr. Yeo: Thank you! That is very helpful! Best, Renxi On Nov 16, 2020, at 6:58 PM, Thomas Yeo mailto:ytho...@csail.mit.edu>> wrote: External Email - Use Caution Hi Renxi, Because there is typically a bit of error when you do the MNI15

[Freesurfer] mri_segstats question

External Email - Use Caution Hi Freesurfer experts: I am trying to extract the mean-time series from the functional image using mri_segstats. However, the cerebral white matter signals were cropped out in my functional images, and the regions that I am trying to extract signal f

Re: [Freesurfer] About mri_vol2surf {Disarmed}

External Email - Use Caution I tried to run mri_vol2surf with the following command: mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img, however i obtain an error ANALYZE FORMAT ERROR:

[Freesurfer] calculating hemisphere total grey matter volume

External Email - Use Caution Hello Freesurfer, Once I had run reconall, I tried to calculating left hemisphere total grey matter volume and right hemisphere total grey matter volume by doing the sum of: TGM_left=lhcortexvol + Left-Cerebellum-Cortex + (Left-Thalamus-Proper + Left

[Freesurfer] Single Hemisphere Option Availability for Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal)

External Email - Use Caution Dear Freesurfer team, Thank you so much for your support for this software thus far. As we were considering using the module for segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal), we came across an i

[Freesurfer] RHEL 7 and tkmedit {Disarmed}

External Email - Use Caution Dear Freesurfer Gurus We just upgraded our server to RHEL 7. However, we want to do some white/pial edits on some brains using Freesurfer 5.1.0. We know this is an old version, but we are combining some new data with a lot of old data that had been pr

[Freesurfer] Mean thickness estimation

External Email - Use Caution Hi, I want to estimate the mean cortical thickness. For this I have summed the thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, I also have the average mean thickness of left and right hemispheres (direct output variables o

Re: [Freesurfer] Mean thickness estimation

Hi Stephanie By using the average/std within region, then averaging those, you are weighting small regions more. I would just use the average/std across cortex. Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Stephanie K Sent: Wednesday, November 18, 2020 12:24 PM To: f

Re: [Freesurfer] tkregister issue with reg-feat2anat

External Email - Use Caution Hi again, I did try to amend the VERSION line to what is listed in the original 7.1.0 file, yet I still received the "Command not found" error. I have attached output with and without --debug flag when executing the original 7.1.0 reg-feat2anat vs.

[Freesurfer] -openmp vs -threads, -parallel options in recon-all

External Email - Use Caution Hello, What is the difference between the -openmp and -threads option for recon-all? Do they reflect the same thing: Number of threads used concurrently? If we want to use 10 threads for the recon-all command, which option should we use? -openmp or

Re: [Freesurfer] -openmp vs -threads, -parallel options in recon-all

They are exactly the same. The two flags go to the same code. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of d m Sent: Wednesday, November 18, 2020 5:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] -openmp vs -threads, -parallel options

[Freesurfer] Group Analysis

External Email - Use Caution Hi Freesurfer experts, I was looking to run the three steps of group analysis-mris preproc, mri surf2surf using the measure volume and unsure of how to go about it since the wiki page talks about thickness only. I would appreciate any help. Best, Sara

Re: [Freesurfer] Error in longitudinal pipeline {Disarmed}

External Email - Use Caution Dear FreeSurfer experts This is just a gentle reminder for my query! Looking forward to your assistance to resolve the issue. With regards Korann On Tue, Nov 17, 2020 at 1:16 PM vittal korann wrote: > Hi FreeSurfer experts > > Recently I started w

Re: [Freesurfer] Mean thickness estimation

External Email - Use Caution Hi Bruce, Thanks for the prompt reply. It is my understanding that l_thickness, r_thickness and estimated intracranial volume are accurately measured. Would I still need to identify and remove outliers if visual inspection of the images has not been do

[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 enough,