[Freesurfer] SAMSEG and statistics

External Email - Use Caution Hi FreeSurfer community, I recently discovered the SAMSEG application in the FreeSurfer 7.2.0 release and started to give a try on few subjects were FreeSurfer was having a hard time to segment brain structures (due to poor contrast). So I have few q

[Freesurfer] Postdoctoral fellow in multimodal neuroimaging

External Email - Use Caution We are seeking a full-time postdoctoral fellow with a strong background in resting state fMRI data analysis to join our team. We aim to better understand the neural correlates of visual perceptual dysfunctions observed in survivors of brain injury. We a

[Freesurfer] Get the password by sending an email request to the freesurfer help list. - Freesurfer VirtualBox Image

External Email - Use Caution Hi, My name is Cristina and I'm a PhD Student from Clinical Neurosciences Group in IRB LLEIDA. I downloaded " Freesurfer VirtualBox Image" and I need the paswword to login as the user "developer" in the login menu. I'm waiting for your answer, Best

Re: [Freesurfer] [External] Re: [External] Re: white matter measurements for labels/annotations

for the annot, it should get the color table from the annot itself. for the output, there is not an option to change the colortable, but you can just mri_convert -ctab your.ctab file.mgz file.mgz On 2/14/2022 3:49 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

If you want to do an ROI analysis using FS-based ROIs, you should do that at the individual level. Resample the PET to the anatoimical space, then run mri_segstats passing the PET with --i and using --seg to spec the segmentation. If you really want to do it in MNI305 space, then it is the same

Re: [Freesurfer] PetSurfer: CORTICAL volume-based analysis

I just sent info on how to do this, but see step 5 in the wiki On 2/14/2022 6:27 PM, Jennifer Bramen wrote: External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I am following the steps from the PetSurfer wiki. I see instructions

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

Did it create the output folder and some output files? I noticed that there is a "error: No such file or directory" error On 2/14/2022 8:46 PM, 정현우 wrote: External Email - Use Caution Hi Dr. Greve, Thank you for your reply. I attached the fsgd file, mtx file and the Xg.dat file

Re: [Freesurfer] Longitudinal Stream Error

Does that file exist? ps. Please remember to post to the list. Thanks! On 2/15/2022 5:06 PM, Willett, Andrew Sunday wrote: Dr. Greve, I hope this email finds you well. Thank you for your response to my listed question on Freesurfer’s mailing list on Sunday! I wanted to reach out to followup

Re: [Freesurfer] SAMSEG and statistics

On 2/16/2022 4:12 AM, k3...@free.fr wrote: > External Email - Use Caution > > Hi FreeSurfer community, > > I recently discovered the SAMSEG application in the FreeSurfer 7.2.0 release > and started to give a try on few subjects were FreeSurfer was having a hard > time to segment brain

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hi Dr. Greve, Yes, it seems like the output folder and some output files were created. After running the mri_glmfit, 'three_group_comparison.area.lh.glmdir' folder was created. In the glmdir folder, 'three_group_comparison.area' folder was created, an

[Freesurfer] Mass-univariate LME - contrast for one group

External Email - Use Caution Dear FreeSurfer experts, I am trying to use the spatiotemporal mass-univariate LME approach for my data but am struggling with choosing the right contrast. I have one group with 14 subjects, two timepoints for each subject and age. My goal is to test

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

It looks like it is failing when computing the partial correlation coef. Try  running it with --no-pcc On 2/16/2022 10:53 AM, 정현우 wrote: External Email - Use Caution Hi Dr. Greve, Yes, it seems like the output folder and some output files were created. After running the mri_glmfit,

Re: [Freesurfer] How to measure correlation using FreeSurfer

External Email - Use Caution Hello Douglas, I am afraid I am getting error while running "mris_preproc --fsgd steplengthSD_vol.fsgd" ERROR: no subjects specified I believe I am missing very basic and doing wrong while exporting specific paths and subject names. Could you please

[Freesurfer] vertex indices in EPI space - mri_surf2vol registration issues

Dear FS users, I’m trying to get surface indices from surfaces generated with recon-all into a volume in native functional/EPI space. I’m using mri_surf2vol for that, though if there is a better alternative solution, I’m happy to take it. My issue is that the output index volume (vtxvol) I get

[Freesurfer] SAMSEG mesh format and content

External Email - Use Caution Hi all, previous question from Florent triggered my interest in SAMSEG and I am running now couple of cases to see what it gives. I would like to ask - SAMSEG can also output a mesh. How is the mesh stored in file? - how can it be visualized (Pa

Re: [Freesurfer] Longitudinal Stream Error

Dr. Greve, I don't believe that file exists--fsaverage folder was empty. We re-ran these files through v7.2.1 while seeking solutions. Is it going to produce tenable findings if we run Freesurfer v7.2.1 cross-sectional data through Freesurfer's v6.0's longitudinal stream? Best, Andrew

Re: [Freesurfer] Virtualbox: developer's password

External Email - Use Caution Hello Pål Please let us know how much memory your machine has and what OS is running.  I would also check you have 20-30G of free disk space on your boot drive, e.g., the C: drive on Windows. - R. On Feb 16, 2022, at 12:47, Pål Gunnar Larsson

Re: [Freesurfer] Get the password by sending an email request to the freesurfer help list. - Freesurfer VirtualBox Image

External Email - Use Caution Sending the info to your email shortly. - R. On Feb 16, 2022, at 10:02, Cristina Pereira Priego wrote:External Email - Use CautionHi,My name is Cristina and I'm a PhD Student from Clinical Neuroscien

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hi Dr. Greve, Thank you for your suggestion. Unfortunately, the same problem occurred when I ran the command with --no-pcc. Folders and files with the same names were created. and the following error message (identical to the previous one) appeared. e