[Freesurfer] Freesurfer Website Ports

External Email - Use Caution Hi, I am setting up an Access Control List for an isolated VLAN in which my center's neuroimaging computing workstations will be connected to our hospital's network for data back-up. We want to be able to connect to Freesurfer's website while

Re: [Freesurfer] Problem with freesurfer measures

External Email - Use Caution To obtain de stats from mri_anatomical stats i used *>>mris_anatomical_stats -a /usr/local/freesurfer/subjects/218/label/rh.myAAL.annot -f* */usr/local/freesurfer/subjects/218/stats/rh.myAAL.stats -b 218 rh* In another hand, the workflow to obatian the

[Freesurfer] "ERROR: crypt() returned null with 4-line file"

External Email - Use Caution Dear FreeSurfer developers, I have also encountered the error that Katja Zoner reported in

Re: [Freesurfer] quantification of volume of perivascular spaces

It might work, but I doubt it has been tested. On 3/31/2021 5:54 AM, Antonín Škoch wrote: External Email - Use Caution Dear experts, We would like to quantify volume of brain perivascular spaces. Ideally longitudinally - i.e. to study the dynamics of perivascular spaces in multiple

Re: [Freesurfer] Talairach Failed: Distorted T1

Correct. You can measure the volume of the brainstem and add it on. Eg, mri_segstats --ctab-default --seg aseg.mgz --id 16 --sum brainstem.dat On 3/30/2021 7:03 PM, Harkey, Thomas Jarrott wrote: External Email - Use Caution Douglas, Thank you for your help. Another question. The

Re: [Freesurfer] Subthalamic nucleus volume

If you want the volume in the native space, then why not just register your volume to mni space, then map the label back to the individual? You could probably do that all with FSL (or SPM). BTW, the "volume" you get is not at all likely to be accurate. It will just reflect the registration in

Re: [Freesurfer] ERROR: Cannot find stats file

Does that file exist? If not, have you run the amygdalar nuclei segmentation? On 3/30/2021 3:00 PM, atacan zeybek wrote: External Email - Use Caution External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to create a text file of amygdalar nuclei of given

Re: [Freesurfer] Problem with freesurfer measures

What are your command lines? On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote: External Email - Use Caution Thanks a lot, It works!, now I have obtained values to ctx and wm volumes for each area. However when I look at the gray matter volume values calculated by mri_anatomical

Re: [Freesurfer] functional to anatomical registration question

You can add --aparc+aseg (hit 'c' to toggle on and off), alternatively You can use tkregsiterfv (same command arguments) but add -aparc+aseg -seg-outline You will need to use the lta registration file (not the .dat) On 3/29/2021 6:13 PM, Nasiriavanaki, Zahra wrote: Dear Freesurferers, I have

Re: [Freesurfer] Running recon-all with FLAIR

Try this cd subject/mri mri_coreg --i orig/T2raw.mgz --targ orig.mgz --reg transforms/T2raw.lta You can run with multiple threads by adding --threads N where N is the number of threads On 3/29/2021 5:18 PM, Edina Szabó wrote: External Email - Use Caution Dear All, We are running

Re: [Freesurfer] make_average_subject error

It looks like you are still using the old make_average_subject as the time stamp is from Jan 19, 2017 (same for mri_aparc2aseg). Can you confirm that those are really the patches? On 3/29/2021 12:52 PM, Jordan Mullins wrote: External Email - Use Caution Hi Douglas, Just following

[Freesurfer] mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg

External Email - Use Caution Hello Freesurfer"s Developers, I am trying to follow *PetSurfer* (