[Freesurfer] help with labels

External Email - Use Caution Hello Freesurfer team, I did an AAL atlas on the surface using mri_vol2surf, however when I look at this overlay there are many holes in the labels with vertices that don't belong to any label. Could u help me with this problem?

Re: [Freesurfer] mri_convert error: GetSDCMFileInfo(): dcmGetDWIParams() 7

External Email - Use Caution Yes, it runs to completion with --no-dwi. And for now, we don't need the bvals and bvects. Thanks a lot for your help! On 26.01.2021 16:16, Douglas N. Greve wrote: > It throws an error when trying to extract the bvals or bvects. Can you try it >

Re: [Freesurfer] Saving more than one figure using freeview

That’s great! Thanks Ruopeng! Should I also add the -noquit flag in each line: freeview foo.mgz -viewport x -ss pic1.jpg -noquit -viewport y -ss pic2.jpg -noquit -viewport z -ss pic3.jpg -noquit Thanks! Noam From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Wang, Ruopeng Sent: Tuesday,

Re: [Freesurfer] help with labels

Look at the surface superimposed on the volume along with the AAL segmentation to make sure that it intersects the segmentation at all vertices. You can find the vertex numbers for the holes, and then go specifically to that vertex On 1/27/2021 6:27 AM, Alberto Del Cerro Leon wrote:

Re: [Freesurfer] Using mri_surf2surf to split files

not sure what you mean. volumes? surfaces? which volumes? On 1/27/2021 1:18 AM, Karan Desai wrote: External Email - Use Caution Hi FreeSurfer developers, I have preprocessed files in single niftis and would like to split the data for each file into left and right hemispheres to run

Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

It needs to be there. Sorry, I rewrote parts of the stream for v7 and did not consider the impact on NHP streams (since they are not part of our package). You might have to use older versions of FS to make this work. On 1/26/2021 11:10 PM, Koch, Erin M. wrote: External Email - Use Cau

Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

External Email - Use Caution Hi Dr. Greve, Thanks for your reply. However, it shows me the command line error when I try to run it after having the file replaced. Please kindly see below. Is there any other settings I should run before that? Even the - -help can't be passed. Th

Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

Try making it executable with chmod a+x $FREESURFER/bin/mri_glmfit-sim On 1/27/2021 10:41 AM, Na, Xiaoxu wrote: External Email - Use Caution Hi Dr. Greve, Thanks for your reply. However, it shows me the command line error when I try to run it after having the file replaced. Please k

Re: [Freesurfer] Saving more than one figure using freeview

For command file you don’t need to add -noquit. On Jan 27, 2021, at 10:28 AM, Peled, Noam mailto:npe...@mgh.harvard.edu>> wrote: That’s great! Thanks Ruopeng! Should I also add the -noquit flag in each line: freeview foo.mgz -viewport x -ss pic1.jpg -noquit -viewport y -ss pic2.jpg -noquit -vie

Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

External Email - Use Caution Dr. Steve, I gave it all the permissions, but still not working. By the way, is there an excutable file coming with this, like mri_glmfit? $ls -l /home/xiaoxu/freesurfer/bin/mri_glmfit-sim -rwxrwxrwx 1 root 1590 39574 Jan 27 09:19 /home/xiaoxu/freesu

Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

External Email - Use Caution Hi Dr. Steve, I figured this out by using dos2unix, since I found this file has "with CRLF line terminators" while checking with command line "file". In case, anyone may need this as well. I got exactly what I need for further analysis in the cache.

[Freesurfer] Java / Matlab Runtime error

External Email - Use Caution Hello, I’m helping a user run freesurfer/7.1.0 on CentOS 8.1. They initially encountered an error due to the missing Matlab Compiler Runtime (MCR). I downloaded the package and installed it in the location suggested by the error message : LINUX:

Re: [Freesurfer] 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] Java / Matlab Runtime error

Hi Ali, Can you please remove the MCR directory and install it using the instructions found at https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime? I think this will fix the issue. Best, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Snedden, Ali Date: Wednesday, Janu

Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

External Email - Use Caution Thanks for the info. Is it possible to put in a "fake" aseg.presurf.mgz file? Do you think this is a possible work around, or is the inflation for flat map generation somehow reliant on this file now? Erin From: fr

Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

It should not need it for the inflation. You can try adding -no-cortex-label and see how far you get On 1/27/2021 12:39 PM, Koch, Erin M. wrote: External Email - Use Caution Thanks for the info.  Is it possible to put in a "fake" aseg.presurf.mgz file?  Do you think this is a possibl

Re: [Freesurfer] Java / Matlab Runtime error

External Email - Use Caution Thank you. That seemed to work. Best, == Ali Snedden, Ph.D. HPC Scientific Programmer The High Performance Computing Facility Abigail Wexner Research Institute at Nationwide Children’s Hospital From: on behalf o

Re: [Freesurfer] Parallel computing for recon-all

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. 3 Could you be more specific about run them by hand? is this mean I run different tasks like sk

[Freesurfer] recon all

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? I am looking forward to your reply. Thanks very much. Sincerely, Zheng | | 郑凤莲 | | 邮箱

Re: [Freesurfer] cerebellar parcellation using the Buckner2011_17Networks atlas

External Email - Use Caution Hi Anna, Just to clarify, you are saying the approach discussed in the email thread ( https://secure-web.cisco.com/11YmIxUdyE6MP2qZsI_1Q5e2j-7ZwBZsBSwwjucLd02V-n0kkFOu05sw1h_m1IQYUlCinucxr87MoZ03O3vT3Iu9krKnzliYaHWYB_mVe0eEi6sEYINc0S2Ya1Mb8sr46AH1I2JQ8

Re: [Freesurfer] Using mri_surf2surf to split files

External Email - Use Caution My bad, I meant to say surfaces. Right now the files are downsampled on fsaverage4 space and I need to now split it into the respective left/right hemispheres. For context, these are .nii.gz files currently. Is there a way to easily do this in Freesu

Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

External Email - Use Caution It completed! Thank you the help. Get Outlook for iOS