[Freesurfer] How to do permutation for multiple comparison correction?

External Email - Use Caution Dear FS experts, Instead of using mri_glmfit-sim, I am trying to implement a customized multiple comparison correction algorithm using permutation. Before I implement my own, I want to make sure my permutation idea is correct. So I was looking at how m

Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

External Email - Use Caution wb_command -file-information on the .dlabel.nii file should do the trick. Matt. From: on behalf of Alina Rojas Reply-To: Freesurfer support list Date: Monday, July 20, 2020 at 6:13 AM To: Freesurfer support list Subject: Re: [Freesurfer] HCP-MMP1

[Freesurfer] FsAverage4 vertex coordinates

Hi FreeSurfer developers, I'm looking for the xyz coordinate table for the vertices of the FsAverage4 atlas. I have fMRI data that has been sampled to the FsAverage4 space and it would be helpful if I could understand where a given vertex is located in the brain in terms of coordinates. Does an

Re: [Freesurfer] Error for version 7.1.0 when run the recon-all

Hi Molly, You might have accidentally passed a non-unicode character to the command line (maybe somewhere in the path to the input volume). Sometimes this happens if code is copy-pasted from elsewhere. Can you try running it again but manually typing out the recon-all command? Otherwise, I’m no

Re: [Freesurfer] T2 or FLAIR data to improve pial surfaces

External Email - Use Caution Equal to that of the T1 From: on behalf of "Glasser, Matthew" Reply-To: Freesurfer support list Date: Monday, July 20, 2020 at 11:42 AM To: Freesurfer support list Subject: Re: [Freesurfer] T2 or FLAIR data to improve pial surfaces *EXTERNAL EMAI

Re: [Freesurfer] T2 or FLAIR data to improve pial surfaces

External Email - Use Caution What is the resolution of these images? Matt. From: on behalf of "Batra, Vinita R." Reply-To: Freesurfer support list Date: Monday, July 20, 2020 at 11:13 AM To: Freesurfer support list Subject: [Freesurfer] T2 or FLAIR data to improve pial surfa

Re: [Freesurfer] [EXT] Re: PetSurfer Crashing {Disarmed}

External Email - Use Caution My mistake, I think that fixed it. Thank you! Anna From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve Sent: Monday, July 20, 2020 11:45 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXT] Re

[Freesurfer] T2 or FLAIR data to improve pial surfaces

External Email - Use Caution Dear FreeSurfer experts, I have both T2 and FLAIR images for the majority of the subjects in my study, and I want to use them to improve pial surface reconstruction during recon-all as explained in [1]. My questions are: 1) In general, should I prefe

Re: [Freesurfer] PetSurfer Crashing

Did you really mean to pass subject/mri/gtmseg.lta ? The registration is supposed to be the registration of the input (PET.template.nii.gz) to the anatomical. subject/mri/gtmseg.lta is the registration of gtmseg.mgz to the anatomical. On 7/20/20 11:21 AM, Crawford, Anna wrote: Extern

Re: [Freesurfer] Fwd: One hemisphere recon-all ERROR

sorry, I thought I answered this a while back. Try using -hemi lh instead of -lh On 7/18/20 1:22 PM, Alina Rojas wrote: External Email - Use Caution Hello Freesurfer community, I was wondering if you could look at the e-mail below. Thank you! Alina Anfang der weitergeleiteten Nach

Re: [Freesurfer] Right and left on MRI scan and on images

This information is extracted out of the dicom header, so as long as you are converting directly from dicom, the information will be correct. You can run mri_info orig.mgz and it will print out a lot of information, including the orientation string. Eg, RAS means that the fastest (column) dimen

[Freesurfer] PetSurfer Crashing

External Email - Use Caution Hello, I am trying to run the PetSurfer process for the first time. I was able to run gtmseg and mri_coreg which seemed to go okay. When I tried running mri_gtmpvc, it is crashing, but I am not sure why. The command I am using and output are below.

[Freesurfer] Flag(s) for parallel processing

Hi Douglas, You asked a good question which prompted me to do an experiment with just "-threads 8 -itkthreads 8". The run time has been quite slower (~8 hours) compared to ~5 hours it took with "-parallel -openmp 8". I agree with you about the underestimation of run time with the latter flags

[Freesurfer] Error for version 7.1.0 when run the recon-all

External Email - Use Caution Hi list, I tried to run the latest version Freesurfer (7.1.0) on the Ubantu 18.04 system. I downloaded the “freesurfer-linux-centos7_x86_64-7.1.0.tar.gz” and successfully installed. I tried to run "recon-all -s bert -autorecon1" and the terminal replie

Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

External Email - Use Caution Thank you for the quick answer! For the archive and my understanding…the pscalar gives out a column with 360 values, these values are the average thickness of my one subject and finally, the data I was searching for: cortical thickness values from my

Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

External Email - Use Caution I would use https://balsa.wustl.edu/file/show/3VLx which is the CIFTI label file. The pscalar is not a label file, but rather the average thicknesses in each cortical area. You can view the average thicknesses in Connectome Workbench or print out t

Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

External Email - Use Caution Thank you, the ciftify was run successfully! But now I have questions to the wb-command -cifti-parcellate: wb_command -cifti-parcellate - the cifti file to parcellate - a cifti label file to use for the parcellation - which mapping