Re: [Freesurfer] repost aseg.mgz error

Hi Douglas, Thanks for the reply, this was my thought too. The files have been uploaded. Thanks! Jasmin On Fri, Aug 12, 2016 at 12:59 PM, Douglas N Greve wrote: > I'm guessing that the registration failed on it. Can you tar up the > subject and upload to our file

Re: [Freesurfer] FW: TRACULA re-init error

Hi - Does this directory exist? ERROR: fio_pushd: /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni I'd have to see the entire trac-all.log file to tell you for sure. The first error may show up earlier than the one that causes the crash. Thanks, a.y On Mon, 8 Aug

Re: [Freesurfer] TRACULA tract endpoints on cortical surface

Hi Barbara - This can be done with mri_vol2surf. The projection that's described in that passage can be done with --projdist-max -6 6 1, and the surface smoothing with --surf-fwhm 6. There are other options in mri_vol2surf, I'd recommend playing with the settings to see what works better for

Re: [Freesurfer] repost aseg.mgz error

I'm guessing that the registration failed on it. Can you tar up the subject and upload to our file drop (URL) below? On 08/12/2016 12:00 PM, Jasmin Alves wrote: > Dear Freesurfer > > I encountered an error on the aseg mask for a participant, both > hemispheres for the aseg appear on one

Re: [Freesurfer] Recon-all

Yes, but if you have edited your data in any way, FS will notice this and keep your edits. On 08/12/2016 11:43 AM, Heidi Foo wrote: > Hi Allison, > > Thanks for the reply. Does that mean I can't use the preprocessed > images from 5.3 and run it with 6.0 but I'll have to use the raw T1 >

[Freesurfer] repost aseg.mgz error

Dear Freesurfer I encountered an error on the aseg mask for a participant, both hemispheres for the aseg appear on one hemisphere of the brain mask. I ran it a few times and I also used different T1s but it consistently showed this error. Is there a way I can correct this? Thanks, Jasmin --

[Freesurfer] Postdoctoral Position in pediatric imaging: Boston Children's Hospital/Harvard Medical School

Postdoctoral Position at Boston/Children's Hospital & Harvard Medical School The GaabLab (gaablab.com) at the Laboratories of Cognitive Neuroscience in collaboration with the Fetal-Neonatal Neuroimaging and Developmental Science

Re: [Freesurfer] Recon-all

Hi Allison, Thanks for the reply. Does that mean I can't use the preprocessed images from 5.3 and run it with 6.0 but I'll have to use the raw T1 images? Thanks. Regards, Heidi On Friday, 12 August 2016, Allison Moreau wrote: > Hi Heidi, > > Once 6.0 is released

Re: [Freesurfer] REPOST: problem with Qdecrc file

Hi Clara, Try to start qdec in the same directory. If that fails create a qdec sub directory underneath the subjects _dir and put the files there. Best Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] REPOST: problem with Qdecrc file

Dear FreeSurfer experts, I'm trying to run a 2stage Model in QDEC but I have troubles with incorporating the .Qdecrc file. Sadly the option of spc etc doesn't show up the Design tab when I want to chose a measure. the file is in the same directory the table.dat file is in. What might be the

Re: [Freesurfer] Recon-all

Hi Heidi, Once 6.0 is released and you have installed it, you can simply source that version of FreeSurfer and rerun your subjects the same way you did for 5.3. Best, Allison On 08/12/2016 06:02 AM, Heidi Foo wrote: Hi FreeSurfer Team, I have done recon-all using FS 5.3 and I would like

[Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

Dear experts, I am in trouble with two ways of computing mean intensity with mri_segstats. First I have used on .annot files with three different labels inside (SegId 1 to 3) : *mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum* which

[Freesurfer] Recon-all

Hi FreeSurfer Team, I have done recon-all using FS 5.3 and I would like to run the recon-ed images from 5.3 in FS 6.0. May I know how I should go about doing that? Thank you. Regards, Heidi Foo ___ Freesurfer mailing list

Re: [Freesurfer] Freesurfer Digest, Vol 150, Issue 14

The error is: "Mapping unhit to unknown. Found 137851 unhit vertices". The file is made, but when trying to select it from the annotation tab in Freeview, Freeview crashes too. Regards, Caroline -Oorspronkelijk bericht- Van: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] qdec error

Hi Kaja. This is not an answer from the official group, but I am used to linux so i ve seen this error before. This particular error is printed out when the GL installation doesn't include the GLX extensions in an X window environment (GLX not found. Aborting.). Check to see if there are any

[Freesurfer] Inter-rater and intra-rater reliability

Dear FreeSurfer experts, I have a question regarding manual interventions during the recon-all script of FreeSurfer 5.3.0 (i.e. setting control points, performing white matter edits). How can we check for inter- and intra-rater reliability? In an earlier post you mentioned an intra- and