Hi,
Two quick questions: 1) How to draw an open border on activation surface map? 2) How to set False Discovery Rate of one subject?
Thanks,
On Sun, Sep 15, 2013 at 12:00 AM, freesurfer-request@nmr.mgh.harvard.eduwrote:
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Today's Topics:
- Re: Resolved, crash during longitudinal process when it run mri_ca_register during CA reg. (Knut J Bjuland)
- Re: Tracula and Qdec (Alan Francis)
- Re: recon all question (Harms, Michael)
- Re: Tracula and Qdec (Anastasia Yendiki)
- Re: Tracula and Qdec (Alan Francis)
- mapping extracted MNI152 ROIs to individual subjects (Paul Beach)
- Getting around a design matrix with zero columns (ye tian)
- Re: mapping extracted MNI152 ROIs to individual subjects (Thomas Yeo)
- Re: Interpretation of interaction effect in qdec (ye tian)
Message: 1 Date: Fri, 13 Sep 2013 19:11:28 +0200 From: Knut J Bjuland knutjorgen@outlook.com Subject: Re: [Freesurfer] Resolved, crash during longitudinal process when it run mri_ca_register during CA reg. To: freesurfer@nmr.mgh.harvard.edu Message-ID: BLU0-SMTP155871B1490571BAB6BB181C33B0@phx.gbl Content-Type: text/plain; charset="iso-8859-1"
Closed, not bug in Freesurfer.
On 09/12/2013 10:31 PM, Knut J Bjuland wrote:
When I run recon-all -base 1_template -tp 1_first -tp 1_secon -all -debug. It crash during CA Reg Thu Sep 12 19:59:01 CEST 2013. I can send the rest of the log. Knut J
#-------------------------------------- #@# CA Reg Thu Sep 12 19:59:01 CEST 2013 /cluster/home/kjbjuland/freesurfer/long/NTNU_PRE_023_template/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_a ll_2008-03-26.gca transforms/talairach.m3z
not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log
======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA
'/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'...
label assignment complete, 0 changed (0.00%) det(m_affine) = 1.55 (predicted orig area = 5.2) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.932, neg=0, invalid=96777
On 09/12/2013 10:14 AM, Knut J Bjuland wrote:
Hi, I have run recon-al longitudinal process on abel cluster with this command recon-all -base @filename@_template -tp @filename@ -tp @filename@v2 -all -debug. However, it crashed or is killed when it ran mri_ca_register. I have looked through the log, and I have not found a reason for it being killed even tough I added -debug. The cluster is running sbatch and CentOS release 6.4. Are there any debug options I can add or are there any debugversion of mri_ca_register I can download? This happen every time I run the program. I have asked for 8g ram when ran the program.
Best regards Knut J?rgen Bjuland
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