Re: [Freesurfer] aseg.mgz not created

Hi Sarah, It doesn't look like your recon-all is done processing yet from the attached recon-all.log. You should also have these two files: recon-all-status.log recon-all.done What did they report? Thanks. Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of O'Dor, Sarah,PhD Se

Re: [Freesurfer] aseg.mgz not created

Hi Sarah I think you didn't give it any flags other than the subject and input. You need to specify -all if you want it to run all the steps it knows how to Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of O'Dor, Sarah,PhD Sent: Tuesday, November 15, 2022 9:31 AM To: fre

[Freesurfer] Freesurfer Passcode

External Email - Use Caution Hi! I am trying to 3D print my child's recent brain MRI. Can I please have the passcode to unzip the Virtualbox image for Freesurfer? Thanks in advance! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.e

[Freesurfer] Recon-all in post stroke aphasic patients.

External Email - Use Caution Dear FreeSurfer experts, I would like to run the recon-all command in MRI images of post-stroke aphasic patients. Should I use a particular flag in the recon-all command to avoid important errors during cortical reconstruction?. We are only interested

Re: [Freesurfer] Fwd: Longitudinal FS pipeline consistently interrupts at -Sphere for all participants

External Email - Use Caution Hi, I just wanted to check in with my questions below? Thanks! Julie On Thu, 10 Nov 2022 at 17:03, Julie Ottoy wrote: > Hi, > > Yes you are right! Taking out the -parallel solved the issue! Does this > mean v7 longitudinal recon-all does not support

Re: [Freesurfer] Recon-all in post stroke aphasic patients.

Hi Steve, You can use ‘-hemi ’ to select which hemisphere to process. If you are interested in right hemisphere only, pass ‘-hemi rh’ to recon-all along with other flags. I don’t have answers to your first question. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ste

[Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1

Hi, If I do: $ freeview -v myfile.nii.gz If I'm pointed at my 6.0.1 freesurfer, this works fine. In 7.2, the freeview window pops up, the loading bar gets to 99%, then then nothing else happens. I'm not sure what to do to debug this further. -- Daniel M. Drucker, Ph.D. Director of IT McLean

Re: [Freesurfer] Pial surfaces include cerebellum - unable to fix with manual edits

Hi Tommi If you point us at the location of the data (and we have access) we will take a look Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Raij, Tommi A. Sent: Monday, November 14, 2022 11:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Pial surfaces i

Re: [Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1

External Email - Use Caution This happens to me when I control-C in the terminal to quit freeview, instead of clicking the X in the upper right corner. Doing this works for me: rm -rf ~/.config/Massachusetts?General?Hospital But this would blow away settings for other apps yo

Re: [Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1

You can run this command to clear the settings of freeview only: rm ~/.config/Massachusetts\ General\ Hospital/freeview.conf Ruopeng On Nov 15, 2022, at 5:05 PM, Dierker, Donna mailto:do...@wustl.edu>> wrote: External Email - Use Caution This happens to me when I control-C in the ter

[Freesurfer] about using -norandomness flag with recon-all

External Email - Use Caution Hello Freesurfer Team: Because of ensuring that results are exactly the same from run to run, norandomness flag is used with recon-all. To better understand the randomness, we have a few questions listed below. 1. Which algorithms inside the recon-al

[Freesurfer] Original image and the mask file dimension mismatch

External Email - Use Caution Hello Team, I have a nifti file of dimension (256, 256, 156) but once I run the freesurfer recon-all the subregions mask "*aparc.DKTatlas+aseg.mgz*" has a dimension of (256,256,256) due to this I am unable to view the segmentation overlaid on the origin

Re: [Freesurfer] aparcstats2table segmentation fault error

External Email - Use Caution Difficult to enlarge your screenshots and read the text, but it looks like even though the output from the setup script displays the path to FREESSURFER_HOME, the script wrapper for the shell cannot verify that path actually exists.   And it looks li

[Freesurfer] Unsupported Datatype

External Email - Use Caution Hello, I’m getting the following error, not sure how to resolve! developer@developer-VirtualBox:~$ mri_convert dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii dicom-series-005-t2_swi_tra_p2_3mm_Mag.mgz mri_convert dicom-series-005-t2_swi_tra_p2_3mm_Mag.ni