[Freesurfer] autorecon1 crash (with nu_correct).

ubleshooting 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

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 e-mai

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

the dev version). 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,

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).

xt 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... >> >> >> >> >> >> On 01/11/2017 03:

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

u_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 subjects or just some of them?

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

an 12, 2017, at 1:55 AM, Jamie Hanson 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 > below: > > Subject Stamp: freesurfer-Linux-ce

[Freesurfer] Running qcache on old FS data

two other 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 Universit

Re: [Freesurfer] Running qcache on old FS data

> by copying 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 q

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

[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 requir

Re: [Freesurfer] Surface Viewer Issue.

wer Issue. > To: Freesurfer support list > Message-ID: <76a0cbb215b316.54354...@wiscmail.wisc.edu> > Content-Type: text/plain; CHARSET=US-ASCII > > i saw this problem on one redhat installation, not on any others, seems > something with the X library orientation > informat

[Freesurfer] Hippocampal subfield registration question.

ut? 2) 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 Researc

[Freesurfer] HandDrawn & Aseg amygdala comparisons.

Hi Freesurfer list- I was trying to compare hand-drawn amygdalae and amygdala volumes generated by mri_ca_label/aseg (similar to what Morey et al., 2009 did) and wanted some advice. My amygdalae are drawn by hand in pathological plane, with a quite labor intensive tracing routine. And I wondered t

[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 struc

Re: [Freesurfer] mri_ca_train parameters?

s, so if you have 30 subjects, and you > dont use a cluster, it will take much much much longer to complete. > > Nick > > > On Tue, 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

Re: [Freesurfer] mri_ca_train parameters?

 so on a single > machine, about 80 days. > > Nick > > > > > On Wed, 2009-04-08 at 16:32 -0500, Jamie Hanson wrote: >> > so that it just runs the command locally.  note that this script submits >> > multiple subjects to multiple nodes, so if you have 30 subject

[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.

should remove those 6 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. >> >&

[Freesurfer] recon-all w/ custom aseg atlas.

Hi Freesurfer folks- So I have been trying to create a custom aseg atlas (which I did, thanks much to Bruce and Nick!)... Now I want to run recon-all w/ that new custom aseg atlas (on additional subjects not included in .gca / atlas creation)... I checked the web and the listserv archive, but mig

[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 aseg.aut

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. Jun;1

[Freesurfer] cerebellum WM.

Hi Fellow Freesurfers- I am new to the world of FS and just had a quick question re: cerebellar white matter. After some skull-stripping issues (and adjusting the watershed algorithm numerous times), I just edited a bad skull-strip with manual aux vol value cloning. I ran autorecon2 again (and ag

[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?

> thalamus borders intentionlly, as we only use 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

[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 Hi

[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 the

Re: [Freesurfer] autorecon3 issue / cortical parcels error.

gt; cheers, > > Bruce > > > > > Just checked me results and still no luck / similar technicolor labels. > Any further thoughts? > > Best, > jamie. > > > > > > > > > On Sat, 5 Apr 2008, Jamie Hanson wrote: > > > > >

[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 Imag

[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 t

[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] Question re: hippocampal & amygdala subdivision files.

.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 Ce

[Freesurfer] Question re: Longitudinal processing stream transforms.

stions 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