[Freesurfer] T2 flair as additional scan in hippocampal subfields segmentation

External Email - Use Caution Hello I’d like to know if there is any advantage in having a T2 FLAIR as additional scan (in addition to our 1mm isotropic T1 scans) when using the hippocampal subfield segmentation tool. We do not have T2 nor PD available. Thanks for you help Anto

[Freesurfer] Reconall with no-MPRAGE T1w image?

External Email - Use Caution Hello, From the ReconAllTable (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see that the mri_normalize step (producing the T1.mgz file) has the -mprage option. I have two questions: 1. What is this option doing exactly? There

Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

d T1w sequences like FLASH. THe -mprage switch takes advantage of this to loosen the intensity gradient threshold in the region filling of the wm. 2. If you just leave out the -mprage switch it will revert to the default behavior cheers Bruce On Tue, 3 Sep 2019, Rovai Antonin wrote: Ex

Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

External Email - Use Caution (Continued) Of course I meant using the recon-all command! On 3 Sep 2019, at 15:48, Rovai Antonin mailto:antonin.ro...@erasme.ulb.ac.be>> wrote: External Email - Use Caution Hi Bruce, Thanks for your response. From what I read

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

ng how it looks? > freeview will use one of the images as the basis for it's display > coordinates, which can cause apparent slicing artifacts that are only display > issues for other volumes. > > cheers > Bruce > > On Tue, 3 Sep 2019, Rovai Antonin wrote: > &

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

:57, Bruce Fischl wrote: > > hmmm. Can you tar and gzip the whole subject dir and upload it to our ftp > site? > On Tue, 3 Sep 2019, Rovai Antonin wrote: > >> External Email - Use Caution >> >> Hey >> >> So opening only the conformed image in free

Re: [Freesurfer] Additional scans in hippocampal subfields segmentation

://www.erasme.ulb.ac.be/email-disclaimer > On 30 Aug 2019, at 11:00, Rovai Antonin > wrote: > > Hello > > I’d like to know if there is any advantage in having a T2 FLAIR as additional > scan (in addition to our 1mm isotropic T1 scans) when using the hippocampal > subfield segmentation too

Re: [Freesurfer] Additional scans in hippocampal subfields segmentation

> more accurate pial surfaces by avoiding dura. For the subfields I defer to > Eugenio > > cheers > Bruce > On Thu, 5 Sep 2019, Rovai Antonin wrote: > >> External Email - Use Caution >> >> I’m resending this request as I really would like to know wha

Re: [Freesurfer] aparcstats2table error

External Email - Use Caution Hi Devika, I ran into the same issue and in case you don’t want to change your PATH (like me), another option is to edit aparcstats2table script and simply replace the shebang from “#!/usr/bin/env python” to e.g. “#!/usr/bin/env python2” (please make

[Freesurfer] remark regarding tcsh with bad locale

External Email - Use Caution Hi, this is not really a question but rather a comment that, hopefully, will help those running into the issue I ran into today. I was using mri_glm-sim with --mczsim 2 option, and got an error saying that "2,0 must be 1.3, 2.0 ...". The issue is that

[Freesurfer] asegstats2table error with options --etiv and --no-vol-extras

External Email - Use Caution Hello, when using asegstats2table with the two flags --etiv and --no-vol- extras, I get the following error: ERROR: --etiv, cannot find EstimatedTotalIntraCranialVol in list It seems computing the ratio of volumes to etiv needs etiv to be included in

[Freesurfer] freeview Core Dumped Error after upgrade in ubuntu

External Email - Use Caution Dear experts, I use to have a perfectly working freesurfer installation on my Ubuntu 18.04 LTS machine, until that doomsday where I installed updates as recommended by ubuntu itself. Now, each time I run freeview, I get the following error: Aborted (

Re: [Freesurfer] freeview Core Dumped Error after upgrade in ubuntu

tribution name listed in /etc/apt/sources.list. > > Note that even if you are downgrading the kernel, as far as the apt > package manager is concerned you still have to run the various > “upgrade” commands to change the distribution to a different one even > if it is

[Freesurfer] color and sign of sig.mgh data

External Email - Use Caution Hello, I am creating sig.mgh overlays in a group analysis. On this map, I can see some blue and red vertices, corresponding to negative and positive values (respectively) on the map. On the other hand, I read in the documentation that sig.mgh is a map