[Freesurfer] How to convert surface-based atlas to annotation?

2023-01-05 Thread Andy Kim
External Email - Use Caution Dear FreeSurfer Developers, To analyze functional connectivity, I first got Shen 268 surface-based atlas from Neurovault. Now I want to extract average time series data from my subjects based on the atlas but I have no idea how to make annotation.

[Freesurfer] Thalamic segmentation tool: question about input files from recon

2023-01-05 Thread Verónica E
External Email - Use Caution Dear all, I am planning to run the thalamic segmentation (as implemented on FreeSurfer 7.1). The data has been already preprocessed with FreeSurfer 5.3, but I want to rerun the recon step on the newer FreeSurfer version. My question is, which recon

[Freesurfer] Passcode for the VM Ubuntu FS 7.2.0

2023-01-05 Thread Jonas Asgaard Bojsen
External Email - Use Caution Hi FreeSurfer team I have a Macbook Pro with M1 processor that I would like to run FreeSurfer for an upcoming project. From what I can tell, this can currently only be done using Virtualbox and the VM Ubuntu image. For this, your install guide says t

[Freesurfer] Requiring Password

2023-01-05 Thread Jaron Shelow
External Email - Use Caution I hope this email finds you well, I am contacting you in search of the password to the file FS_7_2_0_Ubuntu_18_04_06.ova.7z. Thank you for your cooperation and expedient response. Jaron Shelow ___ Free

Re: [Freesurfer] mri_segstats error:

2023-01-05 Thread Huang, Yujing
Hi Brooklyn, Can you check your recon-all command? Can you attach the recon-all.log? >From your message, it reads "recon-al1 -s cor 15". It should be recon-all. >There is also a space in your subject name. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Brooklyn Wrig

Re: [Freesurfer] How to convert surface-based atlas to annotation?

2023-01-05 Thread Huang, Yujing
Hi Andy, Based on my understanding from GIFTI specification, your .gii are functional files. I'm not sure if mris_convert supports it. I'm curious how you got the .gii files. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Andy Kim Sent: Thursday, January 5, 2023 3:05

Re: [Freesurfer] Aseg stats question

2023-01-05 Thread Douglas N. Greve
no, it is not On 1/4/2023 9:20 AM, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Dear Freesurfer team, I have found a warning about not using amygdala, hippocampus and brainstem volumes from asegstats file. I wonder if that is true. Best wishes, Rosie * *

Re: [Freesurfer] Additional question in "SynthSR and SynthSeg" FreeSurfer list - RE. 2022.12.15

2023-01-05 Thread Douglas N. Greve
On 1/4/2023 8:00 PM, Yoonho Hwang wrote: External Email - Use Caution Dear Douglas N. Greve, Thank you for quickly replying. Although I ask many questions, To reply to the mail kindly and quickly is very grateful for me. It became clear how to analyze it. Nevertheless, *_there is an

Re: [Freesurfer] Thalamic segmentation tool: question about input files from recon

2023-01-05 Thread Douglas N. Greve
I think it has to go through the whole recon as it uses wmparc.mgz and that is one of the last things created On 1/5/2023 4:16 AM, Verónica E wrote: External Email - Use Caution Dear all, I am planning to run the thalamic segmentation (as implemented on FreeSurfer 7.1). The data has

Re: [Freesurfer] Aseg stats question

2023-01-05 Thread Rosalia Dacosta Aguayo
External Email - Use Caution Thank you for the clarification, Douglas. Kind regards, Rosie On Thu, Jan 5, 2023 at 3:21 PM Douglas N. Greve wrote: > no, it is not > > On 1/4/2023 9:20 AM, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > Dear Freesurfe

Re: [Freesurfer] mri_glmfit with doss isn't working. v7.2

2023-01-05 Thread Douglas N. Greve
Oh, I see what you mean. Can you try putting the line "DOSS" (no quotes) into your FSGD file? On 1/3/2023 11:51 AM, miracle ozzoude wrote: External Email - Use Caution Hello Doug, Thanks for the quick response. I did see the error. However, I specified doss in the mri_glmfit command

Re: [Freesurfer] mri_glmfit with doss isn't working. v7.2

2023-01-05 Thread miracle ozzoude
External Email - Use Caution Hello Doug, Do you mean like this? GroupDescriptorFile 1 Title Rivermead cluster 2 DOSS Class PPCS_Male Class PPCS_Female Variables Age Sports Games Days_TBI RPQ_13 If yes, i did but still getting similar area Best, Paul On Tue, Jan 3, 2023

[Freesurfer] FreeSurfer VirtualBox 7z-archive code, Ubuntu login credentials, and license file

2023-01-05 Thread Jouhikainen, Pasi J
External Email - Use Caution Hello, I am an undergraduate neuroscience student at the University of Iowa. I have just started as a research assistant in a cognitive neuroscience laboratory on campus, and the principal investigator has asked me to start getting familiar with Fre

Re: [Freesurfer] How to convert surface-based atlas to annotation?

2023-01-05 Thread Andy Kim
External Email - Use Caution Hi Yujing, I got the surface-based shen 268 atlas GIFTI file from Neurovault: https://secure-web.cisco.com/1nc6gfn6VjjKigEYqWc-8kv59k1M4P4KJsOZNG-wzL9VI7sGz6VtoXvG_MRPd7n1hHecU3LLS5w43aE-t57NFuRIBnv_tzk-0nsXBcpiQ77ZmSTbj2GQVhLK-IB4_Wk3xKYdv4HdSgHx7rjD

[Freesurfer] recon-all terminates with error

2023-01-05 Thread MANSON ERIC NAAB
External Email - Use Caution Dear FreeSurfer experts, I am a first time FreeSurfer user trying to run a recon-all for a sT1_W image. However, recon-all terminates with an error "tag image orientation not found" I need help on how to resolve this. Kindly find the recon-all.log fil