What are the contents of the run list file?
On 04/19/2017 09:32 AM, Taylor, Johnmark wrote:
Here's the contents of analysis.info http://analysis.info:
# FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07 greve Exp $ # MKACMD /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/mkanalysis-sess -analysis glm_single_all_ps_0 -fsd bold -runlistfile runlist_single.txt -native -nuisreg mcprextreg 3 -fwhm 0 -event-related -nconditions 8 -paradigm spiralpara.par -spmhrf 0 -per-session -refeventdur 12 -TR 1.5 -polyfit 2 -force -nskip 8 # DATE Sat Apr 1 18:30:53 EDT 2017
analysis glm_single_all_ps_0 mcstem fmc fsd bold runlistfile runlist_single.txt TR 1.5 RegDOF 6 PerSession 1 RawSpace volume native mask brain RawFWHM 0 RawSTC none UseB0DC 0 ApplySubCortMask 1 inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 8 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 nconditions 8 parname spiralpara.par RefEventDur 12 timewindow 40.000000 prestim 0 TER 0.050000 spmhrf 0 stimulusdelay -.75000000000000000000 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 Condition 6 Condition06 Condition 7 Condition07 Condition 8 Condition08 nuisreg mcprextreg 3
On Tue, Apr 18, 2017 at 9:49 PM, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions toAl freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu <mailto:freesurfer-owner@nmr.mgh.harvard.edu> When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Fwd: fix topology problem (miracle ozzoude) 2. mri_glmfit error with aparc table flag (miracle ozzoude) 3. Re: Any advices for hires surface reconstruction? (Douglas Greve) 4. Re: Inconsistency in SI axis coordinate between FreeSurfer recon-all seg image and BrainVoyager (Douglas Greve) 5. Re: Selxavg3-sess Looking for (and can't find) "fmc.sm0" (Douglas Greve) ---------------------------------------------------------------------- Message: 1 Date: Tue, 18 Apr 2017 21:06:00 -0400 From: miracle ozzoude <miracooloz@gmail.com <mailto:miracooloz@gmail.com>> Subject: [Freesurfer] Fwd: fix topology problem To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <CANfOk0hQPdgzKMGQRRfFCvUZ8X+tmP=mL9r-mtQDMpWQVH4MyA@mail.gmail.com <mailto:mL9r-mtQDMpWQVH4MyA@mail.gmail.com>> Content-Type: text/plain; charset="utf-8" ---------- Forwarded message ---------- From: miracle ozzoude <miracooloz@gmail.com <mailto:miracooloz@gmail.com>> Date: Mon, Apr 17, 2017 at 8:40 AM Subject: fix topology problem To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Hello freesurfer, I am running recon-all on a scan and for the past 4 days, it hasn't finished the fix topology step of recon-all. I have attached the recon.log in the email. Thanks Best, Paul