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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1) What do you mean by an "open border"? 2) What kind of data?
doug
On 9/16/13 4:34 AM, Lijia Wang wrote:
Hi,
Two quick questions:
- How to draw an open border on activation surface map?
- How to set False Discovery Rate of one subject?
Thanks,
On Sun, Sep 15, 2013 at 12:00 AM, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to 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 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. Re: Resolved, crash during longitudinal process when it run mri_ca_register during CA reg. (Knut J Bjuland) 2. Re: Tracula and Qdec (Alan Francis) 3. Re: recon all question (Harms, Michael) 4. Re: Tracula and Qdec (Anastasia Yendiki) 5. Re: Tracula and Qdec (Alan Francis) 6. mapping extracted MNI152 ROIs to individual subjects (Paul Beach) 7. Getting around a design matrix with zero columns (ye tian) 8. Re: mapping extracted MNI152 ROIs to individual subjects (Thomas Yeo) 9. 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 <mailto: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 <mailto: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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and properly >> dispose of the e-mail. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Lijia Wang