Re: [Freesurfer] help with labels

External Email - Use Caution I found the vertex for the holes but how can i modify them or how can I solve them? El mié, 27 ene 2021 a las 16:36, Douglas N. Greve () escribió: > Look at the surface superimposed on the volume along with the AAL > segmentation to make sure that it

[Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all a subject, but i got the following error. Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /home/shujirominami/freesurfer/subjects/todai_test/mri/orig/001.

[Freesurfer] Regarding the developer password.

External Email - Use Caution Hello! I have followed the Freesurfer installation guide with VB and Ubuntu but I have not been able to log in. It asks for a developers password and I was hoping maybe it would be possible for you to send it to me? I noticed many people were writing

[Freesurfer] SAMSEG longitudinal processing questions

External Email - Use Caution Hi FreeSurfers, Thank you for sharing the new SAMSEG tool, which I consider a major breakthrough in image processing! I have a few questions about using SAMSEG vs SAMSEG_Long: 1. What volumetric differences should I expect between running SAMSEG on

Re: [Freesurfer] Parallel computing for recon-all

On 1/27/2021 2:02 PM, Wei Shao wrote: External Email - Use Caution Hi, Douglas Thanks for your kind reply. 1 I run the same subject on a server with openmp 8 flags cost 7 hours, without openmp 8 flag would be 7h10minutes. Can you send the two recon-all.log files? 3 Could you be

Re: [Freesurfer] recon all

No head motion correction because  there is only one image On 1/27/2021 6:59 PM, 郑凤莲 wrote: External Email - Use Caution Hi experts, We have segmented hippocampus using Freesurfer 6.0. I have a question that is there "head motion correct" in this step? If yes, how does it examined?

Re: [Freesurfer] help with labels

You can manully edit the annotation or you can manually edit the AAL segmentation to fill in the holes On 1/28/2021 6:09 AM, Alberto Del Cerro Leon wrote: External Email - Use Caution I found the vertex for the holes but how can i modify them or how can I solve them? El mié, 27 ene

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

Run mri_concat input.mgz --rms --o 001.mgz then pass 001.mgz to recon-all On 1/28/2021 3:13 AM, 南修司郎 wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all a subject, but i got the following error. Checking for (invalid) multi-frame inputs... ERRO

Re: [Freesurfer] question on data quality - examples in appendix

On 1/27/2021 1:34 PM, Nils B. wrote: External Email - Use Caution Hello and thank you for you answer, to the first point: Freesurfer is recognizing this area as Gray Matter. Can I just delete this part manually and see if the WM/GM pials are correct or would this lead to other prob

[Freesurfer] FW: FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

External Email - Use Caution Hi Andrew, This is the output: -bash-4.2$ touch /tmp/mytempfile && rm -f /tmp/mytempfile touch: cannot touch ‘/tmp/mytempfile’: Permission denied Yes, I am running it through the High Performance Computing (HPC) cluster. Is there a way to work aro

Re: [Freesurfer] Parallel computing for recon-all

External Email - Use Caution > 1 According to documents, freesurfer is OpenMP code , I use -openmp 8 > flag like: recon-all -alli -i input.file  -s output.file -openmp 8  > to tun the recon command on a server, but it doesn't work for me (the > running time is very similar for the

Re: [Freesurfer] Parallel computing for recon-all

No, use of -threads or -openmp will always trigger the openmp code. The -parallel may introduce other parallel. I did not write this part of the code so I'm not sure, and I think I might have broken the -parallel implementation when I did the last recon-all rewrite On 1/28/2021 11:23 AM, Michae

Re: [Freesurfer] Regarding the developer password.

External Email - Use Caution Hello Anete, Sending the info to your email shortly. -R.On Jan 28, 2021, at 08:05, Anete Sneidere wrote:External Email - Use Caution Hello!I have followed the Freesurfer installation guide with VB and Ubuntu

Re: [Freesurfer] LME Univariate Analysis

External Email - Use Caution Just following up on my email below to see if anyone is able to help? Thanks! Nárlon Cássio Nárlon Cássio Boa Sorte Silva, PhD CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain

[Freesurfer] data sharing of freesurfer processed data

External Email - Use Caution Does the freesurfer group have any recommendations or procedures for public sharing data that has been processed with freesurfer? In particular, procedures to automatically swap out participant IDs to anonymize the data? Stacey M. Schaefer, Ph.D. Ce

Re: [Freesurfer] Parallel computing for recon-all

External Email - Use Caution On 1/28/21 6:00 PM, Douglas N. Greve wrote: > No, use of -threads or -openmp will always trigger the openmp code. The > -parallel may introduce other parallel. I did not write this part of the > code so I'm not sure, and I think I might have broken th

[Freesurfer] Fwd: SAMSEG longitudinal processing questions

Forwarding Stefano's answers... Forwarded Message Subject:Re: [Freesurfer] SAMSEG longitudinal processing questions Date: Thu, 28 Jan 2021 16:45:39 + From: Stefano Cerri To: Douglas N. Greve CC: Koen Van Leemput External Email - Use Caution

Re: [Freesurfer] Using mri_surf2surf to split files

Sorry, can you include the previous correspondence so that I have context. Also, please remember to post to the list On 1/28/2021 12:07 PM, Karan Desai wrote: External Email - Use Caution My bad, I meant to say surfaces. Right now the files are downsampled on fsaverage4 space and I ne

[Freesurfer] Voxel-wise volumes vs APARC volumes

External Email - Use Caution Dear Freesurfer experts, I'm stuck on something which I think has to do with how Freesurfer calculates volumes, but can't quite wrap my head around it, hopefully you can enlighten me. I have already produced robust results for our data using region-b

Re: [Freesurfer] Using mri_surf2surf to split files

External Email - Use Caution Yes, I have attached a link to the previous correspondence from the Freesurfer mailing archives here: https://secure-web.cisco.com/1iDGELrOBJ3D4x9wlujRbDDOmlAxaN5wTKfgu2a-gPCrN-lTjoEg1uHDuP06Ys4S-8OSaulNrVFHnmL1VkLq2xGSlKwDQzHnzi0SP8xvQN-UF2q5msZVt7i-n