[Freesurfer] Question re: Longitudinal processing stream transforms.

uggestions are deeply appreciated. Thanks much, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org ___ Freesurfer mailing list

[Freesurfer] Question re: hippocampal & amygdala subdivision files.

lSpace.mgz), but what was the file without any suffix (e.g., lh.hippoAmygLabels-T1.long.v21.mgz)? Or is that the file I'm looking for? Any information is deeply appreciated! Thanks much, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center

[Freesurfer] Freesurfer versions & Amygdala Subnuclei.

project?) Thanks much, and all the best, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org ___ Freesurfer mailing list Freesurfer

[Freesurfer] Hippocampal subfield registration question.

) If so, are there relevant documents regarding checking the outputs to flag potential poor registration/segmentation? Any information or thoughts are greatly appreciated! Thanks much! All the best, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research

Re: [Freesurfer] Running qcache on old FS data

suggestions to try? Thanks much! On Thu, Jun 14, 2018 at 12:47 PM Jamie Hanson wrote: > > I tried that, but no luck. FS ran into issues with ?h.white.H and then > ?h.w-g.pct.mgh (maybe more errors). Is there a way to use qcache in 4.5? > Could I simply download and install v.4

Re: [Freesurfer] Running qcache on old FS data

or soft linking lh.curv to lh.white.K. You can probably get > it to at least finish. > > > On 06/06/2018 03:41 PM, Jamie Hanson wrote: > > > > External Email - Use Caution > > > > > > Hello all, > > > > I was trying to run qcache on s

[Freesurfer] Running qcache on old FS data

folks had run into this issues; I, however, didn't see a final solution to things. Any thoughts or suggestions are greatly appreciated! Thanks much! Best, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh

Re: [Freesurfer] autorecon1 crash (with nu_correct).

tion are you > on? > > On Jan 12, 2017, at 1:55 AM, Jamie Hanson <jlhans...@wisc.edu> wrote: > > Hello Zeke, > > I included the terminal output error for the stable version of Freesurfer, > but get the same error with the dev version. Here's an example, pasted &g

Re: [Freesurfer] autorecon1 crash (with nu_correct).

e we get nu_correct). Unforutnately, the person who would > > handle this (Zeke) is away until next Wed. Can it wait until then? > > > > > > > >> On 01/11/2017 04:58 PM, Jamie Hanson wrote: > >> > >>Is it happening on all subjec

Re: [Freesurfer] autorecon1 crash (with nu_correct).

ndle this (Zeke) is away until next Wed. Can it wait until then? > > > > > On 01/11/2017 04:58 PM, Jamie Hanson wrote: > >> >> Is it happening on all subjects or just some of them? >> >> >> all of them... >> >> >> >> >>

Re: [Freesurfer] autorecon1 crash (with nu_correct).

> Is it happening on all subjects or just some of them? all of them... > > > On 01/11/2017 03:45 PM, Jamie Hanson wrote: > >> Apologies my email must have clipped it out. >> I pasted it below. >> >> >> >> === >> >> He

Re: [Freesurfer] autorecon1 crash (with nu_correct).

). Anyone else run into this issue or have thoughts about troubleshooting it? Thanks much! Best, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org On Wed, Jan 11, 2017

Re: [Freesurfer] autorecon1 crash (with nu_correct).

I'm seeing it for multiple subjects, same issue. I can't get passed the autorecon1 steps. Any thoughts? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

[Freesurfer] autorecon1 crash (with nu_correct).

it? Thanks much! Best, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] Surface Viewer Issue.

saw this problem on one redhat installation, not on any others, seems something with the X library orientation information and openGL greg On 10/08/14, Jamie Hanson wrote: Hi Freesurfer List, I had a (hopefully quick) question about surface viewers and data orientation in tksurfer v

[Freesurfer] Reducing Used Disk Space?

Hi Freesurfer List, Do folks have any recommendations on reducing the amount of space used by each subject? I looked a bit in the list archives but didn't see any recent tips. I had a large potential sample size (n=~750) and didn't know if I would have the estimated 375GBs processing would

Re: [Freesurfer] Brain cortical structures segmentation - comparison of hippocampal volumes

also of note, there are three recent papers comparing manual hippocampal tracing to freesurfer automated segments... Shen L, Firpi HA, Saykin AJ, West JD. (2009). Parametric surface modeling and registration for comparison of manual and automated segmentation of the hippocampus. Hippocampus.

[Freesurfer] mri_cc / aseg issue.

Hi Freesurfer folks- I created a custom aseg atlas and now, I am running into some issues w/ recon-all. Here is part of my terminal output... --- cp aseg.auto.mgz aseg.mgz #-- #...@# CC Seg Wed May 6 20:40:19 CDT 2009 mri_cc -aseg aseg.auto.mgz -o

[Freesurfer] Custom Aseg Atlas Question.

Hi Freesurfer folks- I am in the midst of creating a custom aseg atlas and had a quick question regarding when to use v. discard subjects. I just ran the second iterations of mri_ca_train (when you use all the subjects in subjects.csh and are training from segmented subjects using M3D_ONE) and I

Re: [Freesurfer] Custom Aseg Atlas Question.

subjects? best, jamie. Bruce On Tue, 28 Apr 2009, Jamie Hanson wrote: Hi Freesurfer folks- I am in the midst of creating a custom aseg atlas and had a quick question regarding when to use v. discard subjects. I just ran the second iterations of mri_ca_train (when you use all the subjects

Re: [Freesurfer] mri_ca_train parameters?

, 2009-04-07 at 12:16 -0500, Jamie Hanson wrote: Hi Freesufer folks- I was just about to start constructing a custom aseg atlas and I wondered if there were any recommendations for any of the optional flags? Any parameters yield better results (especially for specific brain regions)?  I

[Freesurfer] mri_ca_train parameters?

Hi Freesufer folks- I was just about to start constructing a custom aseg atlas and I wondered if there were any recommendations for any of the optional flags? Any parameters yield better results (especially for specific brain regions)? I was focused on improving amygdala segmentation for my

[Freesurfer] applying a transform to volumes + surfaces?

Hi Freesurfers- Apologies for my recent multitude of questions (and big thanks for Bruce and colleagues for all their fabulous troubleshooting!). But I was wondering about applying transforms to my freesurfer data. I know this was asked on the listserv re: transformation on other dataset, but I

[Freesurfer] problematic pial

Hi Freesurfers- I was trying to run freesurfer on a study template and was having major problems with pial surface generation. Orig and Main surfaces seem to be ok, but there are major missing chinks in pial surface. Just to give some background, the template was being using for Diffeomorphic

[Freesurfer] after recon-all.

Hey Folks- So I just finished autorecon-all on a few subjects and wanted to do some prelim analyses. On the tutorial pages, there is some talk of using QDEC or FSGD... I couldn't really find a good page contrasting the two... or is there not a difference? Is FSGD just a dated version? And per

[Freesurfer] ReconAllDevTable Q.

Which version of Freesurfer is the ReconAllDevTable on the wiki for? Is it for v.3.0x or v.4.0? ... has anything changed in that regard for v.4.0? jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500

[Freesurfer] preprocessing, eh?

Hello Freesurfers- I wondered what the word was on preprocessing before you get into the land of freesurfer and recon-all. I have some Inversion Recovery-T1s, where bias / field inhomogeneity is a slight issue. The standard N3ing that is done autorecon1 really wasn't cutting it (it was fine, but

Re: [Freesurfer] preprocessing, eh?

it for cortical surface models. cheers, Bruce On Mon, 27 Aug 2007, Jamie Hanson wrote: Hello Freesurfers- I wondered what the word was on preprocessing before you get into the land of freesurfer and recon-all. I have some Inversion Recovery-T1s, where bias / field inhomogeneity