Re: [Freesurfer] dcmunpack: Issues with the -run argument

External Email - Use Caution You are right, I see 'Found 2 unique series: 9 11' and it works with both of the numbers. I assume I have to do this with every single series in the data, am I correct? Is there a way to do this automatically avoiding specifying the series in each

Re: [Freesurfer] dcmunpack: Issues with the -run argument

External Email - Use Caution You are right, I see 'Found 2 unique series: 9 11' and it works with both of the numbers. I assume I have to do this with every single series in the data, am I correct? Is there a way to do this automatically avoiding specifying the series in each

[Freesurfer] unsubscribing from mailing list

External Email - Use Caution Hi Freesurfer Team Please unsubscribe my email from the list Email: ghamarir...@gmail.com Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] mri_segstats dimension mistach

External Email - Use Caution Hello, I'm trying to run the mri_segstats on different input volume. The input volume has the same dimensions as the original volume used to perform recon-all. However, when trying to use the following command: "mri_segstats --seg

Re: [Freesurfer] dcmunpack: Issues with the -run argument

External Email - Use Caution dcmunpack -src-targ -fsfast -run 1. specify full path to your dicom directory for ‘-src ’ 2. specify full path for ‘-targ ’, or it will be created under the directory where you ran dcmunpack 3. I think you should see ‘Found 18 unique

Re: [Freesurfer] Asymmetry analysis

External Email - Use Caution Thank you. I guess I am still confused on how to actually get results to visualize. I would like to assess left-right hemispheric cortical asymmetry . Ideally, i would like the analysis to be paired (ie. L vs R for each subject, rather than the average

Re: [Freesurfer] Error Help

External Email - Use Caution Yup, That solved it! Thank you for your help! I totally missed that. Misque > On Jul 3, 2023, at 9:36 AM, Huang, Yujing wrote: > > External Email - Use Caution > > > lta_convert looks fine in /Applications/freesurfer/7.4.1/. >

Re: [Freesurfer] Error Help

External Email - Use Caution lta_convert looks fine in /Applications/freesurfer/7.4.1/. Your ‘export FREESURFER_HOME=Applications/freesurfer/7.4.1’ doesn’t have the leading ‘/’. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Misque Boswell Sent: Monday, July 3,

Re: [Freesurfer] Error Help

External Email - Use Caution Thank you, Yujing. Here it is: Misques-MBP-3 / % /Applications/freesurfer/7.4.1/bin/lta_convert -all-info 7.4.1 ProgramName: lta_convert ProgramArguments: /Applications/freesurfer/7.4.1/bin/lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp:

Re: [Freesurfer] re-running recon-all after aseg.presurf.mgz edits

External Email - Use Caution With '-autorecon2-noaseg -autorecon3', I believe aseg.mgz is re-created. So, aseg.stats should reflect the changes. I'm not sure cortex.label is re-created with these two options. So, not sure about ?h.aparc.stats. Best, Yujing From:

Re: [Freesurfer] Error Help

External Email - Use Caution Can you run the following at prompt? 'Applications/freesurfer/7.4.1/bin/lta_convert -all-info' I'm not a Mac user. Do you need '/' in front of 'Application'? Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Misque Boswell Sent:

Re: [Freesurfer] Error Help

External Email - Use Caution Hello Yujing, Thank you for your response. I followed the directions for setup and sourced SetUpFreeSurfer.sh as you stated. All goes as planned up to this point. Misques-MBP-3 / % export FREESURFER_HOME=Applications/freesurfer/7.4.1 Misques-MBP-3

Re: [Freesurfer] Hippo subfields long

External Email - Use Caution Dear Andrei, The script requires that you’ve run the main FreeSurfer longitudinal pipeline (see Longitudinal Processing in the wiki). Don’t worry about the files, they have different names and can coexist without issues  Cheers, /E -- Juan Eugenio

Re: [Freesurfer] Error Help

External Email - Use Caution Hi Misque, I see the error in your recon-all.log “ 7.4.1 (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460) ERROR: Executable 'lta_convert -all-info failed! Is it missing from the distribution?' “ Here is some information on how to set up