Re: [Freesurfer] mri_glmfit-sim error

[Douglas Greve]

hi Glen, no cluster will show up if the p-value for all clusters is 
above .05. You can change this with --cwpvalthresh to something like 
.99. That should give you all the clusters. Also, you don't have to run 
the full simulation again; you can use the --no-sim option and it will 
use the simulation that you already did.

doug


On 6/3/13 9:45 PM, Glen Lee wrote:

Indeed, I initially tried 10,000 iterations and got nothing.
What else then could have gone wrong?

FYI, I use v5.1.0.


On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


You will need more like 1 iterations instead of 100.
doug

On 06/03/2013 04:49 PM, Glen Lee wrote:
> Hello Freesurfer experts--
>
> I ran mri_glmfit-sim to validate the group level GLM result
(which was
> already done using mri_glmfit), but I was not able to get any result
> out of it.
>
>  Even with a quite liberal threshold (2), no vertices came out
(below
> is what I typed in for the random permutation).
>
>  mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2  --sim-sign
> abs --overwrite
>
> What is strange is that I was clearly see a number of clusters
when I
> overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster
> shows up in  perm.abs.2.sig.cluster.mgh.
> I should be able to see the identical map between those right?
>
> FYI, I also pasted the content in perm.abs.2.sig.cluster.summary
below.
> As can be seen, nothing is listed in the stats table.
>
> Any of your help would be greatly appreciated.
> -Glen
>
>
>
>
>
>
> # Cluster Growing Summary (mri_surfcluster)
> # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
> # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
> # CreationTime 2013/06/03-20:19:31-GMT
> # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
> GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
> GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig
> GLM/osgm/perm.abs.2.sig.voxel.mgh --sum
> GLM/osgm/perm.abs.2.sig.cluster.summary --ocn
> GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot
> GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf
> GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
> GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
> # cwd /glen/2D/results/LH
> # sysname  Linux
> # hostname sumo.uphs.upenn.edu 

> # machine  x86_64
> # FixVertexAreaFlag 1
> # FixSurfClusterArea 1
> #
> # Input  GLM/osgm/sig.mgh
> # Frame Number  0
> # srcsubj fsaverage_sym
> # hemi lh
> # surface white
> # annot aparc
> # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
> # SearchSpace_mm2 59961.4
> # SearchSpace_vtx 82070
> # Bonferroni 0
> # Minimum Threshold 2
> # Maximum Threshold infinity
> # Threshold Signabs
> # AdjustThreshWhenOneTail 1
> # CW PValue Threshold: 0.05
> # Area Threshold0 mm^2
> # CSD thresh  2.00
> # CSD nreps100
> # CSD simtype  perm
> # CSD contrast osgm
> # CSD confint  90.00
> # Overall max 3.495 at vertex 61659
> # Overall min -4.18843 at vertex 73402
> # NClusters  0
> # Total Cortical Surface Area 59961.4 (mm^2)
> # FixMNI = 0
> #
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ  CWP
>  CWPLowCWPHi   NVtxs   Annot
>
>
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--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] error in 5.3

[Welsh, Robert]

Hi,

We were re-processing a subject to test the fix for 5.2 to 5.3. The initial 
recon-all and subsequent autrecon2 and autorecon3 were run a few days ago under 
5.2. Yesterday I installed 5.3 and we ran the following:

export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer
recon-all -s s_ALS51 -white -smooth2 -inflate2 –autorecon3

It ran for about 4.5 hours and then gave this error:

---
[rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log
SUBJECTS_DIR/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer
FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4
Loading source label.
Invalid argument
ERROR reading 
/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh.label
Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 
EDT 2008 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s s_ALS51 exited with ERRORS at Mon Jun  3 18:32:01 EDT 2013

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
---

Some help would be appreciated. There is a file lh.BA1.label but not 
lh.BA1.thresh.label, indeed there are no files with "thresh" in their name 
under that subject.

Thanks!

-Robert

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Re: [Freesurfer] mri_glmfit-sim error

[Glen Lee]

Indeed, I initially tried 10,000 iterations and got nothing.
What else then could have gone wrong?

FYI, I use v5.1.0.


On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve
wrote:

> You will need more like 1 iterations instead of 100.
> doug
>
> On 06/03/2013 04:49 PM, Glen Lee wrote:
> > Hello Freesurfer experts--
> >
> > I ran mri_glmfit-sim to validate the group level GLM result (which was
> > already done using mri_glmfit), but I was not able to get any result
> > out of it.
> >
> >  Even with a quite liberal threshold (2), no vertices came out (below
> > is what I typed in for the random permutation).
> >
> >  mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2  --sim-sign
> > abs --overwrite
> >
> > What is strange is that I was clearly see a number of clusters when I
> > overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster
> > shows up in  perm.abs.2.sig.cluster.mgh.
> > I should be able to see the identical map between those right?
> >
> > FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below.
> > As can be seen, nothing is listed in the stats table.
> >
> > Any of your help would be greatly appreciated.
> > -Glen
> >
> >
> >
> >
> >
> >
> > # Cluster Growing Summary (mri_surfcluster)
> > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
> > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
> > # CreationTime 2013/06/03-20:19:31-GMT
> > # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
> > GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
> > GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig
> > GLM/osgm/perm.abs.2.sig.voxel.mgh --sum
> > GLM/osgm/perm.abs.2.sig.cluster.summary --ocn
> > GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot
> > GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf
> > GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
> > GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
> > # cwd /glen/2D/results/LH
> > # sysname  Linux
> > # hostname sumo.uphs.upenn.edu 
> > # machine  x86_64
> > # FixVertexAreaFlag 1
> > # FixSurfClusterArea 1
> > #
> > # Input  GLM/osgm/sig.mgh
> > # Frame Number  0
> > # srcsubj fsaverage_sym
> > # hemi lh
> > # surface white
> > # annot aparc
> > # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
> > # SearchSpace_mm2 59961.4
> > # SearchSpace_vtx 82070
> > # Bonferroni 0
> > # Minimum Threshold 2
> > # Maximum Threshold infinity
> > # Threshold Signabs
> > # AdjustThreshWhenOneTail 1
> > # CW PValue Threshold: 0.05
> > # Area Threshold0 mm^2
> > # CSD thresh  2.00
> > # CSD nreps100
> > # CSD simtype  perm
> > # CSD contrast osgm
> > # CSD confint  90.00
> > # Overall max 3.495 at vertex 61659
> > # Overall min -4.18843 at vertex 73402
> > # NClusters  0
> > # Total Cortical Surface Area 59961.4 (mm^2)
> > # FixMNI = 0
> > #
> > # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ  CWP
> >  CWPLowCWPHi   NVtxs   Annot
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
> 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
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Re: [Freesurfer] SORRY POSTED THE WRONG ERROR..This is the the right one

[Douglas N Greve]

Do you have read permission to it?
doug

On 06/03/2013 06:26 PM, Manish Dalwani wrote:
> I need help with this error...I do see the a LICENSE file in the 
> freesurfer directory.
>
> --
> ERROR: FreeSurfer license file /Applications/freesurfer/license.txt 
> not found.
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
> -- 
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 
> /Applications/freesurfer/subjects/anat_5214/MR100021.dcm...
> Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue 
> Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64
>
> recon-all -s 5214 exited with ERRORS at Mon Jun  3 16:24:01 MDT 2013
>
> For more details, see the log file 
> /Applications/freesurfer/subjects/5214/scripts/recon-all.log
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] help with this error

[Douglas N Greve]

It looks like you don't have permissions to that file. Try changing the 
permission with chmod (need to change them for all your dicom files)
doug
On 06/03/2013 06:17 PM, Manish Dalwani wrote:
> Dear Freesurfer's
>
> I have been using (a slightly older version) Freesurfer on linux and 
> it works fine. I just recently installed freesurfer on the mac 
> workstation OS X 10.8.1. I get the following error:
>
>
> server:subjects manishdalwani$ cd anat_5214
> server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s 5214
> ERROR: MR100021.dcm exists but is not readable
> Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue 
> Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64
>
> recon-all -s  exited with ERRORS at Mon Jun  3 15:57:24 MDT 2013
>
> For more details, see the log file
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> Kindly help!
> Regards,
> Manish
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] SORRY POSTED THE WRONG ERROR..This is the the right one

[Manish Dalwani]

I need help with this error...I do see the a LICENSE file in the freesurfer 
directory.

--
ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found.
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
-- 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Applications/freesurfer/subjects/anat_5214/MR100021.dcm...
Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 
13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64

recon-all -s 5214 exited with ERRORS at Mon Jun  3 16:24:01 MDT 2013

For more details, see the log file 
/Applications/freesurfer/subjects/5214/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] help with this error

[Manish Dalwani]

Dear Freesurfer's

I have been using (a slightly older version) Freesurfer on linux and it works 
fine. I just recently installed freesurfer on the mac workstation OS X 10.8.1. 
I get the following error:


server:subjects manishdalwani$ cd anat_5214
server:anat_5214 manishdalwani$ recon-all -i MR100021.dcm -s 5214
ERROR: MR100021.dcm exists but is not readable
Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 
13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64

recon-all -s  exited with ERRORS at Mon Jun  3 15:57:24 MDT 2013

For more details, see the log file 
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Kindly help!
Regards,
Manish___
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Re: [Freesurfer] BrainSegNotVent

[Douglas N Greve]

If you have 5.3 installed, you can just run

mri_segstats --seg mri/aseg.mgz --sum stats/aseg.v53.stats --pv 
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab 
/usr/local/freesurfer/stable5/ASegStatsLUT.txt --subject subjectname

this will only create a new stats file (aseg.v53.stats). If you just 
want to replace the one that is there, then spec aseg.stats instead of 
aseg.v53.stats

doug


On 06/03/2013 05:54 PM, Derek James Dean wrote:
> Hello,
>
> I am a novice, working with aseg.stats data that were processed using 
> Freesurfer 5.1. A colleague requested a measure of total brain volume 
> that does not include CSF for each subject.  My understanding is that 
> Freesurfer 5.2 and new versions provide BrainSegNotVent, which seems 
> like the best measure for what my colleague requested.  Is there a way 
> to compute the BrainSegNotVent value with the Freesurfer 5.1 processed 
> data? Do I need to re-run recon all with Freesurfer 5.3?  Is there 
> another way to get a total brain matter volume measure not including CSF?
>
> Thank you in advance for your help with this question.
>
> Best,
>
> Derek Dean
> University of Colorado at Boulder
> Dept. of Psychology and Neuroscience
>
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] image with Cerebellum

[Bruce Fischl]

Hi Siddharth

yes, the brain.finalsurfs.mgz will be a skull stripped image (as will 
brianmask.mgz)


cheers
Bruce
On Mon, 3 Jun 2013, Ray, Siddharth wrote:



Hi,

 

I am new to freesurfer and just want to know can I just have skull-stripped
image (with cerebellum) anywhere between stages in Freesurfer 5.3??

 

Please let me know.

 

Thanks,

Siddharth


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[Freesurfer] image with Cerebellum

[Ray, Siddharth]

Hi,

I am new to freesurfer and just want to know can I just have skull-stripped 
image (with cerebellum) anywhere between stages in Freesurfer 5.3??

Please let me know.

Thanks,
Siddharth
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Re: [Freesurfer] mri_glmfit-sim error

[Douglas N Greve]

You will need more like 1 iterations instead of 100.
doug

On 06/03/2013 04:49 PM, Glen Lee wrote:
> Hello Freesurfer experts--
>
> I ran mri_glmfit-sim to validate the group level GLM result (which was 
> already done using mri_glmfit), but I was not able to get any result 
> out of it.
>
>  Even with a quite liberal threshold (2), no vertices came out (below 
> is what I typed in for the random permutation).
>
>  mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2  --sim-sign 
> abs --overwrite
>
> What is strange is that I was clearly see a number of clusters when I 
> overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster 
> shows up in  perm.abs.2.sig.cluster.mgh.
> I should be able to see the identical map between those right?
>
> FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below.
> As can be seen, nothing is listed in the stats table.
>
> Any of your help would be greatly appreciated.
> -Glen
>
>
>
>
>
>
> # Cluster Growing Summary (mri_surfcluster)
> # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
> # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
> # CreationTime 2013/06/03-20:19:31-GMT
> # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd 
> GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig 
> GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig 
> GLM/osgm/perm.abs.2.sig.voxel.mgh --sum 
> GLM/osgm/perm.abs.2.sig.cluster.summary --ocn 
> GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot 
> GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf 
> GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o 
> GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
> # cwd /glen/2D/results/LH
> # sysname  Linux
> # hostname sumo.uphs.upenn.edu 
> # machine  x86_64
> # FixVertexAreaFlag 1
> # FixSurfClusterArea 1
> #
> # Input  GLM/osgm/sig.mgh
> # Frame Number  0
> # srcsubj fsaverage_sym
> # hemi lh
> # surface white
> # annot aparc
> # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
> # SearchSpace_mm2 59961.4
> # SearchSpace_vtx 82070
> # Bonferroni 0
> # Minimum Threshold 2
> # Maximum Threshold infinity
> # Threshold Signabs
> # AdjustThreshWhenOneTail 1
> # CW PValue Threshold: 0.05
> # Area Threshold0 mm^2
> # CSD thresh  2.00
> # CSD nreps100
> # CSD simtype  perm
> # CSD contrast osgm
> # CSD confint  90.00
> # Overall max 3.495 at vertex 61659
> # Overall min -4.18843 at vertex 73402
> # NClusters  0
> # Total Cortical Surface Area 59961.4 (mm^2)
> # FixMNI = 0
> #
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ  CWP   
>  CWPLowCWPHi   NVtxs   Annot
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] possible to display data obtained through mri_segment as heatmap?

[Douglas N Greve]

if you are working with the aseg, then you could

aseg = MRIread('aseg.mgz');
overlay = aseg;
overlay.vol = zeros(size(overlay.vol));
ind = find(aseg.vol == 17); % Find left hippocampal voxels
overlay.vol(ind) = value from you table corresponding to left hippo

you would then replicate with each ROI. The "17" comes from 
$FREESURFER_HOME/FreeSurferColorLUT.txt

doug


On 06/03/2013 03:58 PM, Salil Soman wrote:
> Thank you Doug. Any pointers you can provide on how to try out this 
> process in Matlab would be great.
>
> Best wishes,
>
> Sal
>
>
> On Mon, Jun 3, 2013 at 11:19 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> we don't have a way to do this. With a little programming you
> could do this in matlab. let me know if you need pointers
> doug
>
>
> On 06/01/2013 04:43 PM, Salil Soman wrote:
>
> Dear Doug,
>
> Thank you for your response. I am not sure I understand what I
> would be overlaying.
>
> I would like to display the T1 volume for the subject, but for
> each voxel color value, I would like that to reflect the mean
> intensity value that I calculated using mri_segstats. I do not
> see a way to do this in freeview. Any pointers to further
> details would be greatly appreciated.
>
> Best wishes,
>
> Sal
>
>
> On Fri, May 31, 2013 at 12:46 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
> you can just specify an overlay on the freeview command line
>
>
> On 05/31/2013 03:26 PM, Salil Soman wrote:
>
> I have been able to generate the table. I was asking
> about an
> actual image (that could be visualized in freeview or
> something else).
>
> Thank you.
>
> -S
>
>
> On Fri, May 31, 2013 at 12:25 PM, Douglas N Greve
>  
>  >
>  
>
>  
> Do you mean table data or data that you have on a map?
>
> On 05/31/2013 03:20 PM, Salil Soman wrote:
>
> Dear Doug,
>
> Thank you for your recent advise with using
> freesurfer to
> extract mean values from non structural image
> data. Is
> there a
> way to generate an image (e.g. heat map)
> displaying those
> values in free view?
>
> Best wishes,
>
> Sal
>
>
> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
>  >
>  
>
>  >>
> Phone Number: 617-724-2358 
> >
>   >>
> Fax: 617-726-7422 
> >  
>
> >>
>
> Bugs:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> 
>
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
> 
>
> 
>
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
> 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
>

[Freesurfer] mris_preproc --qdec-long problem

[Martin Reuter]

Hi Chris,

this is a good question for the list (cc'ed), others may or will have 
the same problem.

The problem is with your table file, specifically the new line 
character. DOS uses \r\n , Mac \r and Linux \n.
Your text file uses \r, so it probably was created on a mac.

The problem is that the "cat" command (at least in linux) does not work 
on your file:
cat long.qdec.table.dat is empty

You can convert the \r to \n (linux format):
  tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat

and then should be able to run the preproc command.

People with DOS formats should not run the above "tr' command as they 
will end up with 2 newlines instead of 1. Maybe DOS txt files work with 
'cat' directly (so there is no need)? If anyone on the list knows a good 
way of cat and awk a file independently of the new line (and working on 
all OS), let me know. This is the command I use:

cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#") 
printf("%s.long.%s\n", $1, $2)}'

to generate the subjects id's from the table's first two columns.

Best, Martin



On 06/03/2013 03:45 PM, Christopher McCarthy wrote:
> Dr. Reuter,
>
> We corresponded in the past about QDEC, and you gave me great help. 
>  The lab I work for is now moving towards using the Longitudinal Mixed 
> Effects Model.  When I go to run the command:
>
> mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target 
> study_average --hemi lh --meas thickness --out lh.thickness.mgh
>
> I get the error: 'ERROR: no subjects specified.'  I am attaching my 
> long.qdec.table.dat, which works fine when loaded by QDEC.  Do you 
> have any idea of why I am getting this error?
>
> Thanks,
>
> Chris McCarthy

-- 
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web  : http://reuter.mit.edu

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Re: [Freesurfer] freeview v5.3 reposition surface

[Bruce Fischl]

Hi Adam
you don't need to rerun mris_make_surfaces I don't think, but you will 
want to rerun mris_thickness to recompute the thickness after saving the 
new (repositioned) surfaces


cheers
Bruce
On Mon, 3 Jun 2013, Adam Martersteck wrote:



Hi Freesurfer experts,

I noticed that Freeview has gotten an upgrade from v5.1 to v5.3 and the
reposition tool now has a GUI and it works!

Dr. Fischl said in response to Dr. Pietro De Rossi on October 24th, 2012
that the pipeline for the reposition surface tool was not yet implemented
and you still needed to rerun “mris_make_surface (including mris_thickness
to regenerate the thickness 
map)”.[https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2012-October/02620
9.html
I noticed that the freeview virtual representation of the surfaces are
immediately regenerated.

Should I be running the mris_make_surface command after saving the new
surface(s)?

Thanks,

Adam Martersteck

Cognitive Neurology and Alzheimer's Disease Center
Northwestern University Feinberg School of Medicine
320 E. Superior Street, Searle 11
Chicago, IL 60611


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[Freesurfer] mri_glmfit-sim error

[Glen Lee]

Hello Freesurfer experts--

I ran mri_glmfit-sim to validate the group level GLM result (which was
already done using mri_glmfit), but I was not able to get any result out of
it.

 Even with a quite liberal threshold (2), no vertices came out (below is
what I typed in for the random permutation).

 mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2  --sim-sign abs
--overwrite

What is strange is that I was clearly see a number of clusters when I
overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster shows
up in  perm.abs.2.sig.cluster.mgh.
I should be able to see the identical map between those right?

FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below.
As can be seen, nothing is listed in the stats table.

Any of your help would be greatly appreciated.
-Glen






# Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
# $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
# CreationTime 2013/06/03-20:19:31-GMT
# cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd
GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig
GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig
GLM/osgm/perm.abs.2.sig.voxel.mgh --sum
GLM/osgm/perm.abs.2.sig.cluster.summary --ocn
GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot
--annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o
GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white
# cwd /glen/2D/results/LH
# sysname  Linux
# hostname sumo.uphs.upenn.edu
# machine  x86_64
# FixVertexAreaFlag 1
# FixSurfClusterArea 1
#
# Input  GLM/osgm/sig.mgh
# Frame Number  0
# srcsubj fsaverage_sym
# hemi lh
# surface white
# annot aparc
# SUBJECTS_DIR /usr/local/freesurfer5-1/subjects
# SearchSpace_mm2 59961.4
# SearchSpace_vtx 82070
# Bonferroni 0
# Minimum Threshold 2
# Maximum Threshold infinity
# Threshold Signabs
# AdjustThreshWhenOneTail 1
# CW PValue Threshold: 0.05
# Area Threshold0 mm^2
# CSD thresh  2.00
# CSD nreps100
# CSD simtype  perm
# CSD contrast osgm
# CSD confint  90.00
# Overall max 3.495 at vertex 61659
# Overall min -4.18843 at vertex 73402
# NClusters  0
# Total Cortical Surface Area 59961.4 (mm^2)
# FixMNI = 0
#
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
   CWPHi   NVtxs   Annot
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[Freesurfer] freeview v5.3 reposition surface

[Adam Martersteck]

Hi Freesurfer experts,

I noticed that Freeview has gotten an upgrade from v5.1 to v5.3 and the
reposition tool now has a GUI and it works!

Dr. Fischl said in response to Dr. Pietro De Rossi on October 24th, 2012
that the pipeline for the reposition surface tool was not yet implemented
and you still needed to rerun “mris_make_surface (including mris_thickness
to regenerate the thickness map)”. [
https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2012-October/026209.html
I noticed that the freeview virtual representation of the surfaces are
immediately regenerated.

Should I be running the mris_make_surface command after saving the new
surface(s)?

Thanks,

Adam Martersteck

Cognitive Neurology and Alzheimer's Disease Center
Northwestern University Feinberg School of Medicine
320 E. Superior Street, Searle 11
Chicago, IL 60611
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[Freesurfer] correlation between resting state fmri and brain perfusion

[Chen, Yasheng]

Hi all,

Sorry to post a question not related to the brain surface analysis.

I wonder why there are not many studies looking into the correlation between 
perfusion and resting state fmri.  Perfusion should play an important role in 
modulating resting bold signal.  Does any one have some experience using either 
ASL or perfusion measurement from PET to look into how these things are 
correlated?  Is this an area worth pursuing?  

Thank you very much!

Yasheng

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Re: [Freesurfer] possible to display data obtained through mri_segment as heatmap?

[Salil Soman]

Thank you Doug. Any pointers you can provide on how to try out this process
in Matlab would be great.

Best wishes,

Sal


On Mon, Jun 3, 2013 at 11:19 AM, Douglas N Greve
wrote:

> we don't have a way to do this. With a little programming you could do
> this in matlab. let me know if you need pointers
> doug
>
>
> On 06/01/2013 04:43 PM, Salil Soman wrote:
>
>> Dear Doug,
>>
>> Thank you for your response. I am not sure I understand what I would be
>> overlaying.
>>
>> I would like to display the T1 volume for the subject, but for each voxel
>> color value, I would like that to reflect the mean intensity value that I
>> calculated using mri_segstats. I do not see a way to do this in freeview.
>> Any pointers to further details would be greatly appreciated.
>>
>> Best wishes,
>>
>> Sal
>>
>>
>> On Fri, May 31, 2013 at 12:46 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>> you can just specify an overlay on the freeview command line
>>
>>
>> On 05/31/2013 03:26 PM, Salil Soman wrote:
>>
>> I have been able to generate the table. I was asking about an
>> actual image (that could be visualized in freeview or
>> something else).
>>
>> Thank you.
>>
>> -S
>>
>>
>> On Fri, May 31, 2013 at 12:25 PM, Douglas N Greve
>> > > >
>> >
>> >>
>> wrote:
>>
>> Do you mean table data or data that you have on a map?
>>
>> On 05/31/2013 03:20 PM, Salil Soman wrote:
>>
>> Dear Doug,
>>
>> Thank you for your recent advise with using freesurfer to
>> extract mean values from non structural image data. Is
>> there a
>> way to generate an image (e.g. heat map) displaying those
>> values in free view?
>>
>> Best wishes,
>>
>> Sal
>>
>>
>> -- Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> > >
>> >
>> >
>> Phone Number: 617-724-2358 
>> >
>> Fax: 617-726-7422  >
>> >
>>
>> Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>> 
>> 
>> >
>> 
>> 
>> >
>> FileDrop: 
>> https://gate.nmr.mgh.harvard.**edu/filedrop2
>> 
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>> 
>> 
>> >
>> > html >
>>
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
>> greve/ 
>>
>>
>>
>> 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.
>>
>>
>>
>> -- Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> > >
>> Phone Number: 617-724-2358 
>> Fax: 617-726-7422 
>>
>> Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>> 
>> 
>> >
>> FileDrop: 
>> https://gate.nmr.mgh.harvard.**edu/filedrop2
>> 
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>> 
>> 

Re: [Freesurfer] Fwd: Fwd: mir_convert produces a darkened file

[Erin Browning]

I only have one input. The last posting's orig.jpg was 001.mgz, and
motioncor.jpg is orig.mgz. We usually run motioncor because it produces the
orig.mgz which has been conformed.


On Mon, Jun 3, 2013 at 2:41 PM, Bruce Fischl wrote:

> what does the 001.mgz look like? Do you have more than one input
> (otherwise you wouldn't need motion correction)? If so, you'll need to do
> this for each one
>
> On Mon, 3 Jun 2013, Erin Browning wrote:
>
>  The orig.mgz is hyerintense (there's a screenshot of it in another post
>> now). The AFNI file is in float.
>> I ran:
>>
>> mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz -odt float
>> --out-scale 1.5 -ns 1
>>
>> and then I ran motioncor:
>>
>> recon-all -subjid freesurfer -motioncor
>>
>> Attached is what the scan looks like after each step; it's still coming
>> out
>> hyperintense like before. I'm concerned it will segment poorly again.
>>
>>
>>
>>
>>
>> On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl 
>> wrote:
>>   Hi Erin
>>
>>   that can happen if you lose too much dynamic range when
>>   "conforming". What does the orig.mgz look like? What voxel
>>   format is the afni file in (uchar? float?) mri_convert has a -ns
>>   1 flag to turn off intensity scaling ("no scale"). If the brik
>>   was in float you could use something like (from the mri dir)
>>
>>   mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz
>>   --out-scale  -ns
>>
>>
>>   this will turn off auto scaling (-ns) then use the scale factor
>>   you supply isntead (), which you should estimate to bring
>>   white matter intensities to around 110.
>>
>>   cheers
>>   Bruce
>>
>>
>>
>>   On Mon, 3 Jun 2013, Erin Browning wrote:
>>
>>
>> It seems like it getting darker messes up the
>> normalization later on; could
>> this be the case? Here's what it looks like in AFNI
>> (1029-afni.jpg), and
>> here's what it looks like after we run motioncor
>> (1029-orig.jpg).
>>
>>
>> On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve
>> 
>> wrote:
>>
>>   that will not change the intensities at all.
>> It is probably just
>>   a display issue. Try changing the
>> brightness/contrast. The
>>   artifact might cause problems later on, but
>> this  is not an
>>   issue I think
>>   doug
>>
>>   On 06/03/2013 02:20 PM, Erin Browning wrote:
>>   We use:
>>
>>   mri_convert N1029-anat+orig.BRIK
>>   freesurfer/mri/orig/001.mgz
>>
>>   where freesurfer is our freesurfer subject
>> folder.
>>
>>
>> On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve
>> > > >>
>> wrote:
>>
>> what is your mri_convert command line?
>>
>> On 06/03/2013 02:11 PM, Erin Browning wrote:
>> > Hi everyone--
>> >
>> > We have a series of scans with an hyperintense
>> artifact
>> cutting
>> > through the temporal and frontal lobe. When we
>> run
>> mri_convert to
>> > convert from AFNI .BRIK files to .mgz fles,
>> the results
>> look
>> like the
>> > attached image.
>> >
>> > How can I correct for this? We tried
>> skullstripping in
>> AFNI first to
>> > remove some of the artifact, but that didn't
>> seem to help
>> very much.
>> >
>> > Thank you,
>> > Erin Browning
>> >
>> >
>> >
>> >
>> __**_
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> 
>> > >
>> >
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>> freesurfer 
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> > >
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs:
>> 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>>
>> 
>> 
>> >
>> FileDrop:
>>   

Re: [Freesurfer] Recon-all difficulties off-site

[Douglas N Greve]

Hi Adam, if the subject folder exists and you pass recon-all a -i flag, 
then it will exit with error saying that the data exist (otherwise it 
would overwrite what is there). However, just because the subject folder 
exists does not mean that there is any data sitting in subject/mri/orig. 
Then it will tell you that it cannot find any data.

Note that when you run recon-all, you need to tell it to do something 
(eg, add the "-all" flag to do everything)

doug


On 06/03/2013 03:21 PM, Nitenson, Adam wrote:
> Hello users,
>
> I am trying to get Freesurfer (5.2) working properly off-site and am 
> encountering errors I did not have while working at the Martinos 
> center. We use the same Siemens 3T Tim Trio scanner at Brown, so I 
> would hope the data is similar to work with.
>
> I have been using dcmunpack since unpacksdcmdir is not identifying the 
> DICOM files properly. I have successfully unpacked the structural and 
> bold scans using the command (entered from the raw scan data folder:
>
> dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -run 2 
> MPRAGE nii struct (I also tried using mgz instead of nii, and also 
> changed struct to other things as it appears to be a naming argument)
>
> dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -fsfast 
> -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 
> 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 
> bold nii f.nii
>
> (path) just being an abbreviate piece of the relevant pathway
>
> These generate the MPRAGE and bold folders in the subject folder as 
> expected. I have difficulties with the next commands (environment has 
> been set).
>
> I try:
> recon-all -i  -s  -force
> recon-all -i (path)/FreesurferPractice/unpack/MPRAGE/002 -s unpack3
> (I got an error about using -force so I omitted that from my command)
>
> and get the following Error
> ERROR: You are trying to re-run an existing subject with (possibly)
>  new input data (-i). If this is truly new input data, you should delete
>  the subject folder and re-run, or specify a different subject name.
>  If you are just continuing an analysis of an existing subject, then
>  omit all -i flags.
>
> Yet when I omit -i and just use "recon-all -s unpack3", I get "ERROR: 
> nothing to do"
>
> I tried a different tactic and used
>
> "recon-all -s unpack3 -autorecon1" as well as "recon-all 
> -autorecon-all -s unpack3"
>
> which both created the various folders (bem, label, mri, surf, etc) 
> but failed with
> "ERROR: no run data found in (path)/FreesurferPractice/unpack3/mri. 
> Make sure to have a volume called 001.mgz in 
> (path)/FreesurferPractice/unpack3/mri/orig. If you have a second run 
> of data call it 002.mgz, etc."
>
> I have tried these commands in both bash and tcsh shells with the same 
> effect. So the problem, it seems, is that my "mri" file is blank, and 
> this was not a problem I had running these commands at Martinos. Any 
> idea what the issue might be?
>
> Best,
>
> Adam Nitenson
> Neuroscience Graduate Program
> Laboratory of Affective Neuroscience
> Brown University
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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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
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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.

Re: [Freesurfer] Fwd: Fwd: mir_convert produces a darkened file

[Bruce Fischl]

what does the 001.mgz look like? Do you have more than one input 
(otherwise you wouldn't need motion correction)? If so, you'll need to do 
this for each one

On Mon, 3 Jun 2013, Erin Browning wrote:


The orig.mgz is hyerintense (there's a screenshot of it in another post
now). The AFNI file is in float. 
I ran: 

mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz -odt float
--out-scale 1.5 -ns 1

and then I ran motioncor:

recon-all -subjid freesurfer -motioncor

Attached is what the scan looks like after each step; it's still coming out
hyperintense like before. I'm concerned it will segment poorly again. 





On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl 
wrote:
  Hi Erin

  that can happen if you lose too much dynamic range when
  "conforming". What does the orig.mgz look like? What voxel
  format is the afni file in (uchar? float?) mri_convert has a -ns
  1 flag to turn off intensity scaling ("no scale"). If the brik
  was in float you could use something like (from the mri dir)

  mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz
  --out-scale  -ns


  this will turn off auto scaling (-ns) then use the scale factor
  you supply isntead (), which you should estimate to bring
  white matter intensities to around 110.

  cheers
  Bruce



  On Mon, 3 Jun 2013, Erin Browning wrote:


It seems like it getting darker messes up the
normalization later on; could
this be the case? Here's what it looks like in AFNI
(1029-afni.jpg), and
here's what it looks like after we run motioncor
(1029-orig.jpg). 


On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve

wrote:

      that will not change the intensities at all.
It is probably just
      a display issue. Try changing the
brightness/contrast. The
      artifact might cause problems later on, but
this  is not an
      issue I think
      doug

      On 06/03/2013 02:20 PM, Erin Browning wrote:
      We use:

      mri_convert N1029-anat+orig.BRIK
      freesurfer/mri/orig/001.mgz

      where freesurfer is our freesurfer subject
folder.


On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>
wrote:

    what is your mri_convert command line?

    On 06/03/2013 02:11 PM, Erin Browning wrote:
    > Hi everyone--
    >
    > We have a series of scans with an hyperintense
artifact
cutting
    > through the temporal and frontal lobe. When we
run
mri_convert to
    > convert from AFNI .BRIK files to .mgz fles,
the results
look
    like the
    > attached image.
    >
    > How can I correct for this? We tried
skullstripping in
AFNI first to
    > remove some of the artifact, but that didn't
seem to help
very much.
    >
    > Thank you,
    > Erin Browning
    >
    >
    >
    >
___
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    
    >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

    --
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
    gr...@nmr.mgh.harvard.edu

    Phone Number: 617-724-2358
    Fax: 617-726-7422

    Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
   

    FileDrop:
https://gate.nmr.mgh.harvard.edu/filedrop2
   
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
   

    Outgoing:
   
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

    ___
    Freesurfer mailing list
    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-mai

Re: [Freesurfer] Fwd: Fwd: mir_convert produces a darkened file

[Bruce Fischl]

try what I suggested and see if that helps
On Mon, 3 Jun 2013, Erin Browning 
wrote:



Here is an example of what AR2 looks like (without playing with niterations
or anything like that to reduce the overall hypterintensity). The white
matter line is much closer to the pial line than it should be.




On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl 
wrote:
  Hi Erin

  that can happen if you lose too much dynamic range when
  "conforming". What does the orig.mgz look like? What voxel
  format is the afni file in (uchar? float?) mri_convert has a -ns
  1 flag to turn off intensity scaling ("no scale"). If the brik
  was in float you could use something like (from the mri dir)

  mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz
  --out-scale  -ns


  this will turn off auto scaling (-ns) then use the scale factor
  you supply isntead (), which you should estimate to bring
  white matter intensities to around 110.

  cheers
  Bruce



  On Mon, 3 Jun 2013, Erin Browning wrote:


It seems like it getting darker messes up the
normalization later on; could
this be the case? Here's what it looks like in AFNI
(1029-afni.jpg), and
here's what it looks like after we run motioncor
(1029-orig.jpg). 


On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve

wrote:

      that will not change the intensities at all.
It is probably just
      a display issue. Try changing the
brightness/contrast. The
      artifact might cause problems later on, but
this  is not an
      issue I think
      doug

      On 06/03/2013 02:20 PM, Erin Browning wrote:
      We use:

      mri_convert N1029-anat+orig.BRIK
      freesurfer/mri/orig/001.mgz

      where freesurfer is our freesurfer subject
folder.


On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>
wrote:

    what is your mri_convert command line?

    On 06/03/2013 02:11 PM, Erin Browning wrote:
    > Hi everyone--
    >
    > We have a series of scans with an hyperintense
artifact
cutting
    > through the temporal and frontal lobe. When we
run
mri_convert to
    > convert from AFNI .BRIK files to .mgz fles,
the results
look
    like the
    > attached image.
    >
    > How can I correct for this? We tried
skullstripping in
AFNI first to
    > remove some of the artifact, but that didn't
seem to help
very much.
    >
    > Thank you,
    > Erin Browning
    >
    >
    >
    >
___
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    
    >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

    --
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
    gr...@nmr.mgh.harvard.edu

    Phone Number: 617-724-2358
    Fax: 617-726-7422

    Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
   

    FileDrop:
https://gate.nmr.mgh.harvard.edu/filedrop2
   
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
   

    Outgoing:
   
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

    ___
    Freesurfer mailing list
    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
   

[Freesurfer] Recon-all difficulties off-site

[Nitenson, Adam]

Hello users,

I am trying to get Freesurfer (5.2) working properly off-site and am
encountering errors I did not have while working at the Martinos center. We
use the same Siemens 3T Tim Trio scanner at Brown, so I would hope the data
is similar to work with.

I have been using dcmunpack since unpacksdcmdir is not identifying the
DICOM files properly. I have successfully unpacked the structural and bold
scans using the command (entered from the raw scan data folder:

 dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -run 2 MPRAGE
nii struct (I also tried using mgz instead of nii, and also changed
struct to other things as it appears to be a naming argument)

 dcmunpack -src DICOM -targ (path)/FreesurferPractice/unpack3 -fsfast -run
3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold
nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii

(path) just being an abbreviate piece of the relevant pathway

These generate the MPRAGE and bold folders in the subject folder as
expected. I have difficulties with the next commands (environment has been
set).

I try:
recon-all -i  -s  -force
recon-all -i (path)/FreesurferPractice/unpack/MPRAGE/002 -s unpack3
(I got an error about using -force so I omitted that from my command)

and get the following Error
ERROR: You are trying to re-run an existing subject with (possibly)
 new input data (-i). If this is truly new input data, you should delete
 the subject folder and re-run, or specify a different subject name.
 If you are just continuing an analysis of an existing subject, then
 omit all -i flags.

Yet when I omit -i and just use "recon-all -s unpack3", I get "ERROR:
nothing to do"

I tried a different tactic and used

"recon-all -s unpack3 -autorecon1" as well as "recon-all -autorecon-all -s
unpack3"

which both created the various folders (bem, label, mri, surf, etc) but
failed with
"ERROR: no run data found in (path)/FreesurferPractice/unpack3/mri. Make
sure to have a volume called 001.mgz in
(path)/FreesurferPractice/unpack3/mri/orig. If
you have a second run of data call it 002.mgz, etc."

I have tried these commands in both bash and tcsh shells with the same
effect. So the problem, it seems, is that my "mri" file is blank, and this
was not a problem I had running these commands at Martinos. Any idea what
the issue might be?

Best,

Adam Nitenson
Neuroscience Graduate Program
Laboratory of Affective Neuroscience
Brown University
___
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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.

Re: [Freesurfer] Fwd: Fwd: mir_convert produces a darkened file

[Erin Browning]

Here is an example of what AR2 looks like (without playing with niterations
or anything like that to reduce the overall hypterintensity). The white
matter line is much closer to the pial line than it should be.




On Mon, Jun 3, 2013 at 2:00 PM, Bruce Fischl wrote:

> Hi Erin
>
> that can happen if you lose too much dynamic range when "conforming". What
> does the orig.mgz look like? What voxel format is the afni file in (uchar?
> float?) mri_convert has a -ns 1 flag to turn off intensity scaling ("no
> scale"). If the brik was in float you could use something like (from the
> mri dir)
>
> mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz --out-scale 
> -ns
>
>
> this will turn off auto scaling (-ns) then use the scale factor you supply
> isntead (), which you should estimate to bring white matter intensities
> to around 110.
>
> cheers
> Bruce
>
>
>
>
> On Mon, 3 Jun 2013, Erin Browning wrote:
>
>
>> It seems like it getting darker messes up the normalization later on;
>> could
>> this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and
>> here's what it looks like after we run motioncor (1029-orig.jpg).
>>
>>
>> On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu>
>> wrote:
>>
>>   that will not change the intensities at all. It is probably just
>>   a display issue. Try changing the brightness/contrast. The
>>   artifact might cause problems later on, but this  is not an
>>   issue I think
>>   doug
>>
>>   On 06/03/2013 02:20 PM, Erin Browning wrote:
>>   We use:
>>
>>   mri_convert N1029-anat+orig.BRIK
>>   freesurfer/mri/orig/001.mgz
>>
>>   where freesurfer is our freesurfer subject folder.
>>
>>
>> On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve
>> > > >>
>> wrote:
>>
>> what is your mri_convert command line?
>>
>> On 06/03/2013 02:11 PM, Erin Browning wrote:
>> > Hi everyone--
>> >
>> > We have a series of scans with an hyperintense artifact
>> cutting
>> > through the temporal and frontal lobe. When we run
>> mri_convert to
>> > convert from AFNI .BRIK files to .mgz fles, the results
>> look
>> like the
>> > attached image.
>> >
>> > How can I correct for this? We tried skullstripping in
>> AFNI first to
>> > remove some of the artifact, but that didn't seem to help
>> very much.
>> >
>> > Thank you,
>> > Erin Browning
>> >
>> >
>> >
>> > __**_
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > >
>> >
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> > >
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>> 
>> 
>> >
>> FileDrop: 
>> https://gate.nmr.mgh.harvard.**edu/filedrop2
>> 
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>>
>> 
>> >
>> Outgoing:
>>
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/
>>
>> __**_
>> Freesurfer mailing list
>> 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.
>>
>>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>> FileDrop: 
>> https://gate.nmr.mgh.harvard.**edu/filedrop2

Re: [Freesurfer] Group Analysis Question

[Fotiadis, Panagiotis]

Great, thanks for your help Doug!

Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, June 03, 2013 2:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis Question

yes, I think so. Maybe others can comment.

On 06/03/2013 02:49 PM, Fotiadis, Panagiotis wrote:
> Ok, great, it seems in this case that even though the overlays in both cases 
> are very similar, the kurtosis in the second analysis (Diseased vs Controls 
> no gender taken under consideration) is slightly better. Therefore would it 
> be correct to assume that the second analysis is more trustworthy?
>
> Thanks,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, June 03, 2013 2:34 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis Question
>
> yes
> On 06/03/2013 02:26 PM, Fotiadis, Panagiotis wrote:
>> I see. Would it be correct to say that better kurtosis would be illustrated 
>> as less significant clusters in the kurtosis.mgh overlay?
>>
>> Panos
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, June 03, 2013 1:53 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Group Analysis Question
>>
>> Not necessarily. It could have been in the FS analysis. You can run
>> mri_glmfit with  --kurtosis (a hidden option). This will create a
>> kurtosis.mgh and pkurtosis.mgh. Kurtosis is a measure of gaussianity of
>> the residuals (larger being less gaussian). The pkurtosis the the sig
>> (-log10(p)) of the probability of seeing the kurtosis under the null
>> (ie, the residuals are gaussian). So you can see if one model gives you
>> better kurtosis than another.
>>
>> doug
>>
>>
>> On 06/03/2013 01:20 PM, Fotiadis, Panagiotis wrote:
>>> I see. Yes from the one hand the results that I got make a lot more sense 
>>> in the second type of analysis, compared to the first one, however, there 
>>> are some somewhat important difference between the two analyses. If there 
>>> is an issue with the data, do you believe that it would be in the 
>>> acquisition? Because I checked the reconstructions and they look fine.
>>>
>>> Thanks,
>>> Panos
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Monday, June 03, 2013 11:24 AM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Group Analysis Question
>>>
>>> I would not expect them to be identical but similar.  If they change a
>>> lot there may be an issue with your data.
>>> doug
>>>
>>>
>>>
>>> On 6/3/13 11:11 AM, Fotiadis, Panagiotis wrote:
 Hey Doug,

 I have run a group analysis on my data with two different ways. (The input 
 is cortical thickness.) In the first analysis, I specified 4 groups 
 (Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas 
 in the second, just two groups (Diseased, Healthy). One of the comparisons 
 that I did was the age slope between Diseased and Healthy. Therefore in 
 the first analysis, I set the contrast vector to be [0 0 0 0 0.5 0.5 -0.5 
 -0.5] and in the second analysis I set it to [0 0 1 -1]. However, the 
 results that came up were somewhat different. For instance there were 
 clusters in the second analysis that were significant but were not 
 significant in the first analysis.
 Shouldn't the results be the same?

 Thank you,
 Panos
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.

Re: [Freesurfer] Fwd: Fwd: mir_convert produces a darkened file

[Douglas N Greve]

what is the problemexactly? how do the surfaces look?
doug

On 06/03/2013 02:54 PM, Erin Browning wrote:
>
> It seems like it getting darker messes up the normalization later on; 
> could this be the case? Here's what it looks like in AFNI 
> (1029-afni.jpg), and here's what it looks like after we run motioncor 
> (1029-orig.jpg).
>
>
> On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> that will not change the intensities at all. It is probably just a
> display issue. Try changing the brightness/contrast. The artifact
> might cause problems later on, but this  is not an issue I think
> doug
>
>
> On 06/03/2013 02:20 PM, Erin Browning wrote:
>
> We use:
>
> mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz
>
> where freesurfer is our freesurfer subject folder.
>
>
> On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
> what is your mri_convert command line?
>
> On 06/03/2013 02:11 PM, Erin Browning wrote:
> > Hi everyone--
> >
> > We have a series of scans with an hyperintense artifact
> cutting
> > through the temporal and frontal lobe. When we run
> mri_convert to
> > convert from AFNI .BRIK files to .mgz fles, the results look
> like the
> > attached image.
> >
> > How can I correct for this? We tried skullstripping in
> AFNI first to
> > remove some of the artifact, but that didn't seem to
> help very much.
> >
> > Thank you,
> > Erin Browning
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
>  >
>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
>  >
>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> 
>
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> 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.
>
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 6

Re: [Freesurfer] Fwd: Fwd: mir_convert produces a darkened file

[Bruce Fischl]

Hi Erin

that can happen if you lose too much dynamic range when "conforming". What 
does the orig.mgz look like? What voxel format is the afni file in (uchar? 
float?) mri_convert has a -ns 1 flag to turn off intensity scaling ("no 
scale"). If the brik was in float you could use something like (from the 
mri dir)


mri_convert file.BRIK orig/001.mgz -odt uchar -rl orig.mgz --out-scale  
-ns



this will turn off auto scaling (-ns) then use the scale factor you supply 
isntead (), which you should estimate to bring white matter intensities 
to around 110.


cheers
Bruce



On Mon, 3 Jun 2013, Erin Browning wrote:



It seems like it getting darker messes up the normalization later on; could
this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and
here's what it looks like after we run motioncor (1029-orig.jpg). 


On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve 
wrote:

  that will not change the intensities at all. It is probably just
  a display issue. Try changing the brightness/contrast. The
  artifact might cause problems later on, but this  is not an
  issue I think
  doug

  On 06/03/2013 02:20 PM, Erin Browning wrote:
  We use:

  mri_convert N1029-anat+orig.BRIK
  freesurfer/mri/orig/001.mgz

  where freesurfer is our freesurfer subject folder.


On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>
wrote:

    what is your mri_convert command line?

    On 06/03/2013 02:11 PM, Erin Browning wrote:
    > Hi everyone--
    >
    > We have a series of scans with an hyperintense artifact
cutting
    > through the temporal and frontal lobe. When we run
mri_convert to
    > convert from AFNI .BRIK files to .mgz fles, the results
look
    like the
    > attached image.
    >
    > How can I correct for this? We tried skullstripping in
AFNI first to
    > remove some of the artifact, but that didn't seem to help
very much.
    >
    > Thank you,
    > Erin Browning
    >
    >
    >
    > ___
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    
    >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

    --
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
    gr...@nmr.mgh.harvard.edu 
    Phone Number: 617-724-2358
    Fax: 617-726-7422

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    
    FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
   

    Outgoing:
   
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

    ___
    Freesurfer mailing list
    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.



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/




___
Freesurfer mailing list
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.

Re: [Freesurfer] Group Analysis Question

[Douglas N Greve]

yes, I think so. Maybe others can comment.

On 06/03/2013 02:49 PM, Fotiadis, Panagiotis wrote:
> Ok, great, it seems in this case that even though the overlays in both cases 
> are very similar, the kurtosis in the second analysis (Diseased vs Controls 
> no gender taken under consideration) is slightly better. Therefore would it 
> be correct to assume that the second analysis is more trustworthy?
>
> Thanks,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, June 03, 2013 2:34 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis Question
>
> yes
> On 06/03/2013 02:26 PM, Fotiadis, Panagiotis wrote:
>> I see. Would it be correct to say that better kurtosis would be illustrated 
>> as less significant clusters in the kurtosis.mgh overlay?
>>
>> Panos
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, June 03, 2013 1:53 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Group Analysis Question
>>
>> Not necessarily. It could have been in the FS analysis. You can run
>> mri_glmfit with  --kurtosis (a hidden option). This will create a
>> kurtosis.mgh and pkurtosis.mgh. Kurtosis is a measure of gaussianity of
>> the residuals (larger being less gaussian). The pkurtosis the the sig
>> (-log10(p)) of the probability of seeing the kurtosis under the null
>> (ie, the residuals are gaussian). So you can see if one model gives you
>> better kurtosis than another.
>>
>> doug
>>
>>
>> On 06/03/2013 01:20 PM, Fotiadis, Panagiotis wrote:
>>> I see. Yes from the one hand the results that I got make a lot more sense 
>>> in the second type of analysis, compared to the first one, however, there 
>>> are some somewhat important difference between the two analyses. If there 
>>> is an issue with the data, do you believe that it would be in the 
>>> acquisition? Because I checked the reconstructions and they look fine.
>>>
>>> Thanks,
>>> Panos
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Monday, June 03, 2013 11:24 AM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Group Analysis Question
>>>
>>> I would not expect them to be identical but similar.  If they change a
>>> lot there may be an issue with your data.
>>> doug
>>>
>>>
>>>
>>> On 6/3/13 11:11 AM, Fotiadis, Panagiotis wrote:
 Hey Doug,

 I have run a group analysis on my data with two different ways. (The input 
 is cortical thickness.) In the first analysis, I specified 4 groups 
 (Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas 
 in the second, just two groups (Diseased, Healthy). One of the comparisons 
 that I did was the age slope between Diseased and Healthy. Therefore in 
 the first analysis, I set the contrast vector to be [0 0 0 0 0.5 0.5 -0.5 
 -0.5] and in the second analysis I set it to [0 0 1 -1]. However, the 
 results that came up were somewhat different. For instance there were 
 clusters in the second analysis that were significant but were not 
 significant in the first analysis.
 Shouldn't the results be the same?

 Thank you,
 Panos
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Num

Re: [Freesurfer] Group Analysis Question

[Fotiadis, Panagiotis]

Ok, great, it seems in this case that even though the overlays in both cases 
are very similar, the kurtosis in the second analysis (Diseased vs Controls no 
gender taken under consideration) is slightly better. Therefore would it be 
correct to assume that the second analysis is more trustworthy?

Thanks,
Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, June 03, 2013 2:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis Question

yes
On 06/03/2013 02:26 PM, Fotiadis, Panagiotis wrote:
> I see. Would it be correct to say that better kurtosis would be illustrated 
> as less significant clusters in the kurtosis.mgh overlay?
>
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, June 03, 2013 1:53 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis Question
>
> Not necessarily. It could have been in the FS analysis. You can run
> mri_glmfit with  --kurtosis (a hidden option). This will create a
> kurtosis.mgh and pkurtosis.mgh. Kurtosis is a measure of gaussianity of
> the residuals (larger being less gaussian). The pkurtosis the the sig
> (-log10(p)) of the probability of seeing the kurtosis under the null
> (ie, the residuals are gaussian). So you can see if one model gives you
> better kurtosis than another.
>
> doug
>
>
> On 06/03/2013 01:20 PM, Fotiadis, Panagiotis wrote:
>> I see. Yes from the one hand the results that I got make a lot more sense in 
>> the second type of analysis, compared to the first one, however, there are 
>> some somewhat important difference between the two analyses. If there is an 
>> issue with the data, do you believe that it would be in the acquisition? 
>> Because I checked the reconstructions and they look fine.
>>
>> Thanks,
>> Panos
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, June 03, 2013 11:24 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Group Analysis Question
>>
>> I would not expect them to be identical but similar.  If they change a
>> lot there may be an issue with your data.
>> doug
>>
>>
>>
>> On 6/3/13 11:11 AM, Fotiadis, Panagiotis wrote:
>>> Hey Doug,
>>>
>>> I have run a group analysis on my data with two different ways. (The input 
>>> is cortical thickness.) In the first analysis, I specified 4 groups 
>>> (Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas 
>>> in the second, just two groups (Diseased, Healthy). One of the comparisons 
>>> that I did was the age slope between Diseased and Healthy. Therefore in the 
>>> first analysis, I set the contrast vector to be [0 0 0 0 0.5 0.5 -0.5 -0.5] 
>>> and in the second analysis I set it to [0 0 1 -1]. However, the results 
>>> that came up were somewhat different. For instance there were clusters in 
>>> the second analysis that were significant but were not significant in the 
>>> first analysis.
>>> Shouldn't the results be the same?
>>>
>>> Thank you,
>>> Panos
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/tr

Re: [Freesurfer] Group Analysis Question

[Douglas N Greve]

yes
On 06/03/2013 02:26 PM, Fotiadis, Panagiotis wrote:
> I see. Would it be correct to say that better kurtosis would be illustrated 
> as less significant clusters in the kurtosis.mgh overlay?
>
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, June 03, 2013 1:53 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis Question
>
> Not necessarily. It could have been in the FS analysis. You can run
> mri_glmfit with  --kurtosis (a hidden option). This will create a
> kurtosis.mgh and pkurtosis.mgh. Kurtosis is a measure of gaussianity of
> the residuals (larger being less gaussian). The pkurtosis the the sig
> (-log10(p)) of the probability of seeing the kurtosis under the null
> (ie, the residuals are gaussian). So you can see if one model gives you
> better kurtosis than another.
>
> doug
>
>
> On 06/03/2013 01:20 PM, Fotiadis, Panagiotis wrote:
>> I see. Yes from the one hand the results that I got make a lot more sense in 
>> the second type of analysis, compared to the first one, however, there are 
>> some somewhat important difference between the two analyses. If there is an 
>> issue with the data, do you believe that it would be in the acquisition? 
>> Because I checked the reconstructions and they look fine.
>>
>> Thanks,
>> Panos
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, June 03, 2013 11:24 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Group Analysis Question
>>
>> I would not expect them to be identical but similar.  If they change a
>> lot there may be an issue with your data.
>> doug
>>
>>
>>
>> On 6/3/13 11:11 AM, Fotiadis, Panagiotis wrote:
>>> Hey Doug,
>>>
>>> I have run a group analysis on my data with two different ways. (The input 
>>> is cortical thickness.) In the first analysis, I specified 4 groups 
>>> (Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas 
>>> in the second, just two groups (Diseased, Healthy). One of the comparisons 
>>> that I did was the age slope between Diseased and Healthy. Therefore in the 
>>> first analysis, I set the contrast vector to be [0 0 0 0 0.5 0.5 -0.5 -0.5] 
>>> and in the second analysis I set it to [0 0 1 -1]. However, the results 
>>> that came up were somewhat different. For instance there were clusters in 
>>> the second analysis that were significant but were not significant in the 
>>> first analysis.
>>> Shouldn't the results be the same?
>>>
>>> Thank you,
>>> Panos
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
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>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Fwd: mir_convert produces a darkened file

[Douglas N Greve]

that will not change the intensities at all. It is probably just a 
display issue. Try changing the brightness/contrast. The artifact might 
cause problems later on, but this  is not an issue I think
doug

On 06/03/2013 02:20 PM, Erin Browning wrote:
> We use:
>
> mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz
>
> where freesurfer is our freesurfer subject folder.
>
>
> On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> what is your mri_convert command line?
>
> On 06/03/2013 02:11 PM, Erin Browning wrote:
> > Hi everyone--
> >
> > We have a series of scans with an hyperintense artifact cutting
> > through the temporal and frontal lobe. When we run mri_convert to
> > convert from AFNI .BRIK files to .mgz fles, the results look
> like the
> > attached image.
> >
> > How can I correct for this? We tried skullstripping in AFNI first to
> > remove some of the artifact, but that didn't seem to help very much.
> >
> > Thank you,
> > Erin Browning
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
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>
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>
>
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> the e-mail
> contains patient information, please contact the Partners
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
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Re: [Freesurfer] autorecon3 error

[Claudia Dacquino]

Ok.
Thanks a lot!
Cheers
Claudia

Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:

> yes, you should be running
>
> recon-all -autorecon2-cp 
>
> cheers
> Bruce
>
> On Mon, 3 Jun 2013, Claudia Dacquino wrote:
>
>  Is this the problem? Is there an incorrect command?
>> Thanks.Cheers
>> Claudia
>>
>> Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:
>>   Hi Claudia
>>
>>   there is no autorecon3-cp, just autorecon2-cp
>>
>>   cheers
>>   Bruce
>>   On Mon, 3 Jun 2013, Claudia Dacquino wrote:
>>
>> Hi Freesurfers,
>> I did autorecon3-cp and exited with errors.
>> Ould anyone help me to understand what's the roblem?
>> You can find the recon-all.log attached.
>> Thanks in advance.
>> Claudia
>>
>>
>>
>>
>>
>>   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
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Re: [Freesurfer] Group Analysis Question

[Fotiadis, Panagiotis]

I see. Would it be correct to say that better kurtosis would be illustrated as 
less significant clusters in the kurtosis.mgh overlay?

Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, June 03, 2013 1:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis Question

Not necessarily. It could have been in the FS analysis. You can run
mri_glmfit with  --kurtosis (a hidden option). This will create a
kurtosis.mgh and pkurtosis.mgh. Kurtosis is a measure of gaussianity of
the residuals (larger being less gaussian). The pkurtosis the the sig
(-log10(p)) of the probability of seeing the kurtosis under the null
(ie, the residuals are gaussian). So you can see if one model gives you
better kurtosis than another.

doug


On 06/03/2013 01:20 PM, Fotiadis, Panagiotis wrote:
> I see. Yes from the one hand the results that I got make a lot more sense in 
> the second type of analysis, compared to the first one, however, there are 
> some somewhat important difference between the two analyses. If there is an 
> issue with the data, do you believe that it would be in the acquisition? 
> Because I checked the reconstructions and they look fine.
>
> Thanks,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, June 03, 2013 11:24 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis Question
>
> I would not expect them to be identical but similar.  If they change a
> lot there may be an issue with your data.
> doug
>
>
>
> On 6/3/13 11:11 AM, Fotiadis, Panagiotis wrote:
>> Hey Doug,
>>
>> I have run a group analysis on my data with two different ways. (The input 
>> is cortical thickness.) In the first analysis, I specified 4 groups 
>> (Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas 
>> in the second, just two groups (Diseased, Healthy). One of the comparisons 
>> that I did was the age slope between Diseased and Healthy. Therefore in the 
>> first analysis, I set the contrast vector to be [0 0 0 0 0.5 0.5 -0.5 -0.5] 
>> and in the second analysis I set it to [0 0 1 -1]. However, the results that 
>> came up were somewhat different. For instance there were clusters in the 
>> second analysis that were significant but were not significant in the first 
>> analysis.
>> Shouldn't the results be the same?
>>
>> Thank you,
>> Panos
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Fwd: mir_convert produces a darkened file

[Erin Browning]

We use:

mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz

where freesurfer is our freesurfer subject folder.


On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve
wrote:

> what is your mri_convert command line?
>
> On 06/03/2013 02:11 PM, Erin Browning wrote:
> > Hi everyone--
> >
> > We have a series of scans with an hyperintense artifact cutting
> > through the temporal and frontal lobe. When we run mri_convert to
> > convert from AFNI .BRIK files to .mgz fles, the results look like the
> > attached image.
> >
> > How can I correct for this? We tried skullstripping in AFNI first to
> > remove some of the artifact, but that didn't seem to help very much.
> >
> > Thank you,
> > Erin Browning
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
> ___
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>
>
> 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
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Re: [Freesurfer] possible to display data obtained through mri_segment as heatmap?

[Douglas N Greve]

we don't have a way to do this. With a little programming you could do 
this in matlab. let me know if you need pointers
doug

On 06/01/2013 04:43 PM, Salil Soman wrote:
> Dear Doug,
>
> Thank you for your response. I am not sure I understand what I would 
> be overlaying.
>
> I would like to display the T1 volume for the subject, but for each 
> voxel color value, I would like that to reflect the mean intensity 
> value that I calculated using mri_segstats. I do not see a way to do 
> this in freeview. Any pointers to further details would be greatly 
> appreciated.
>
> Best wishes,
>
> Sal
>
>
> On Fri, May 31, 2013 at 12:46 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> you can just specify an overlay on the freeview command line
>
>
> On 05/31/2013 03:26 PM, Salil Soman wrote:
>
> I have been able to generate the table. I was asking about an
> actual image (that could be visualized in freeview or
> something else).
>
> Thank you.
>
> -S
>
>
> On Fri, May 31, 2013 at 12:25 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
> Do you mean table data or data that you have on a map?
>
> On 05/31/2013 03:20 PM, Salil Soman wrote:
>
> Dear Doug,
>
> Thank you for your recent advise with using freesurfer to
> extract mean values from non structural image data. Is
> there a
> way to generate an image (e.g. heat map) displaying those
> values in free view?
>
> Best wishes,
>
> Sal
>
>
> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
>  >
> Phone Number: 617-724-2358 
> >
> Fax: 617-726-7422   >
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> 
>
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
> 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
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> but does not contain patient information, please contact the
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>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>
>

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Fwd: mir_convert produces a darkened file

[Douglas N Greve]

what is your mri_convert command line?

On 06/03/2013 02:11 PM, Erin Browning wrote:
> Hi everyone--
>
> We have a series of scans with an hyperintense artifact cutting 
> through the temporal and frontal lobe. When we run mri_convert to 
> convert from AFNI .BRIK files to .mgz fles, the results look like the 
> attached image.
>
> How can I correct for this? We tried skullstripping in AFNI first to 
> remove some of the artifact, but that didn't seem to help very much.
>
> Thank you,
> Erin Browning
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

[Douglas N Greve]

On 06/03/2013 02:03 PM, Ritobrato Datta wrote:
> Hi Doug,
>
> I looked that the morphometryStats table that you sent and looks like I need 
> the following measure.
>
> BrainSegNotVent - this I believe doesnt include cerebellum etc and no 
> ventricles.
It does include cerebellum. It does exclude ventricles
>
> But all my data are run through 5.1. How do I get this measure ? If I run the 
> 5.2 version of mri_segstats on the data that has been run through 5.1, will 
> it generate this volume ?
yes, you can run
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz 
--empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 
--excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab 
/usr/local/freesurfer/stable5/ASegStatsLUT.txt --subject subjectname

>
> Please let me know and sorry to keep pestering this.
>
> Thanks
>
> Rito
>
>
> - Original Message -
> From: Douglas N Greve 
> To: Ritobrato Datta 
> Cc: Freesurfer@nmr.mgh.harvard.edu
> Sent: Mon, 03 Jun 2013 13:54:01 -0400 (EDT)
> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
> brain vol.
>
> no, it does not include cerebellum
> On 06/03/2013 01:42 PM, Ritobrato Datta wrote:
>> In the website below,
>> lhCorticalWhiteMatter,rhCorticalWhiteMatter,CorticalWhiteMatter - volume 
>> inside the white surface minus anything that is not WM. CorticalWhiteMatter 
>> includes hypointensities. This uses the surface-based volume computation for 
>> part of the calculation and counts voxels to subtract "anything not in WM". 
>> It is approximately equal to the count of WM voxels in aparc+aseg.mgz.
>>
>> Since, cerebellar wm is in the aparc+aseg.mgz so that means its included in 
>> the CorticalWhiteMatter, correct ?
>>
>> - Original Message -
>> From: Douglas N Greve 
>> To: Ritobrato Datta 
>> Cc: Freesurfer@nmr.mgh.harvard.edu
>> Sent: Mon, 03 Jun 2013 13:19:54 -0400 (EDT)
>> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
>> brain vol.
>>
>>
>> See if this answers your question
>> http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
>> this is for v5.2 and beyond
>>
>> On 06/03/2013 01:07 PM, Ritobrato Datta wrote:
>>> ic thats rightI was getting confused. So the total gm vol includes 
>>> cerebellar gm vol but the cortical wm vol only includes the wm vol under 
>>> the cortical ribbon and around the subcortical gm structures?  Or does 
>>> that include wm under the cerebellar cortex as well ?
>>>
>>> Is there a table somewhere which specifies which of these freesurfer 
>>> parcellated structures contribute to these combined measures such has 
>>> supratentorial vol / whole gm vol etc etc
>>>
>>> That will be very helpful.
>>>
>>>
>>>
>>> - Original Message -
>>> From: Douglas N Greve 
>>> To: Ritobrato Datta , 
>>> Freesurfer@nmr.mgh.harvard.edu
>>> Sent: Mon, 03 Jun 2013 12:59:30 -0400 (EDT)
>>> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
>>> brain vol.
>>>
>>>
>>> Hi Rito, I don't think we report a total wm volume, do we?
>>> doug
>>>
>>>
>>>
>>>
>>> On 06/03/2013 12:56 PM, Ritobrato Datta wrote:
 Hi Doug,

 Just following up on your reply sometime back -
 Does total white volume include cerebellar wm vol also ?

 Please let me know.

 Thanks

 Rito

 - Original Message -
 From: Douglas N Greve 
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT)
 Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and 
 total brain vol.

 Total Gray includes the cerebellar gray
 doug
 On 05/24/2013 03:51 PM, Ritobrato Datta wrote:
> Hello All,
>
> Can someone address the following ? I sent this query yesterday but it 
> fell through the cracks.
>
> I am using freesurfer 5.1 for my analysis.
>
> I am interested in calculating the whole brain vol (total Gray vol + 
> total WM vol) excluding the CSF volume and cerebellum.
>
> Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol
>
> In all of the 79 subjects, when I compare the Total Brain Vol to 
> SupraTentorialVol, I find SupraTentorialVol is smaller than the Total 
> Brain Vol I have calculated.
>
> Here are some measures -
>
> For 79 subjects -
>
> Average Total Brain Vol = 1038395.291
>
> Average SupraTentorialVol = 979996.4684
>
> Is that expected ?
>
> Is it possible that CSF vol is part of Total Brain Vol ?
>
> Any insight will be helpful.
>
> Thanks
>
> Rito
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The informatio

[Freesurfer] Fwd: mir_convert produces a darkened file

[Erin Browning]

Hi everyone--

We have a series of scans with an hyperintense artifact cutting through the
temporal and frontal lobe. When we run mri_convert to convert from AFNI
.BRIK files to .mgz fles, the results look like the attached image.

How can I correct for this? We tried skullstripping in AFNI first to remove
some of the artifact, but that didn't seem to help very much.

Thank you,
Erin Browning
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Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

[Ritobrato Datta]

Hi Doug,

I looked that the morphometryStats table that you sent and looks like I need 
the following measure.

BrainSegNotVent - this I believe doesnt include cerebellum etc and no 
ventricles.

But all my data are run through 5.1. How do I get this measure ? If I run the 
5.2 version of mri_segstats on the data that has been run through 5.1, will it 
generate this volume ?

Please let me know and sorry to keep pestering this. 

Thanks

Rito


- Original Message -
From: Douglas N Greve 
To: Ritobrato Datta 
Cc: Freesurfer@nmr.mgh.harvard.edu
Sent: Mon, 03 Jun 2013 13:54:01 -0400 (EDT)
Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
brain vol.

no, it does not include cerebellum
On 06/03/2013 01:42 PM, Ritobrato Datta wrote:
> In the website below,
> lhCorticalWhiteMatter,rhCorticalWhiteMatter,CorticalWhiteMatter - volume 
> inside the white surface minus anything that is not WM. CorticalWhiteMatter 
> includes hypointensities. This uses the surface-based volume computation for 
> part of the calculation and counts voxels to subtract "anything not in WM". 
> It is approximately equal to the count of WM voxels in aparc+aseg.mgz.
>
> Since, cerebellar wm is in the aparc+aseg.mgz so that means its included in 
> the CorticalWhiteMatter, correct ?
>
> - Original Message -
> From: Douglas N Greve 
> To: Ritobrato Datta 
> Cc: Freesurfer@nmr.mgh.harvard.edu
> Sent: Mon, 03 Jun 2013 13:19:54 -0400 (EDT)
> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
> brain vol.
>
>
> See if this answers your question
> http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
> this is for v5.2 and beyond
>
> On 06/03/2013 01:07 PM, Ritobrato Datta wrote:
>> ic thats rightI was getting confused. So the total gm vol includes 
>> cerebellar gm vol but the cortical wm vol only includes the wm vol under the 
>> cortical ribbon and around the subcortical gm structures?  Or does that 
>> include wm under the cerebellar cortex as well ?
>>
>> Is there a table somewhere which specifies which of these freesurfer 
>> parcellated structures contribute to these combined measures such has 
>> supratentorial vol / whole gm vol etc etc
>>
>> That will be very helpful.
>>
>>
>>
>> - Original Message -
>> From: Douglas N Greve 
>> To: Ritobrato Datta , 
>> Freesurfer@nmr.mgh.harvard.edu
>> Sent: Mon, 03 Jun 2013 12:59:30 -0400 (EDT)
>> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
>> brain vol.
>>
>>
>> Hi Rito, I don't think we report a total wm volume, do we?
>> doug
>>
>>
>>
>>
>> On 06/03/2013 12:56 PM, Ritobrato Datta wrote:
>>> Hi Doug,
>>>
>>> Just following up on your reply sometime back -
>>> Does total white volume include cerebellar wm vol also ?
>>>
>>> Please let me know.
>>>
>>> Thanks
>>>
>>> Rito
>>>
>>> - Original Message -
>>> From: Douglas N Greve 
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT)
>>> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
>>> brain vol.
>>>
>>> Total Gray includes the cerebellar gray
>>> doug
>>> On 05/24/2013 03:51 PM, Ritobrato Datta wrote:
 Hello All,

 Can someone address the following ? I sent this query yesterday but it 
 fell through the cracks.

 I am using freesurfer 5.1 for my analysis.

 I am interested in calculating the whole brain vol (total Gray vol + total 
 WM vol) excluding the CSF volume and cerebellum.

 Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol

 In all of the 79 subjects, when I compare the Total Brain Vol to 
 SupraTentorialVol, I find SupraTentorialVol is smaller than the Total 
 Brain Vol I have calculated.

 Here are some measures -

 For 79 subjects -

 Average Total Brain Vol = 1038395.291

 Average SupraTentorialVol = 979996.4684

 Is that expected ?

 Is it possible that CSF vol is part of Total Brain Vol ?

 Any insight will be helpful.

 Thanks

 Rito

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 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 
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 properly
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-- 
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Re: [Freesurfer] autorecon3 error

[Bruce Fischl]

yes, you should be running

recon-all -autorecon2-cp 

cheers
Bruce

On Mon, 3 Jun 2013, Claudia Dacquino wrote:


Is this the problem? Is there an incorrect command?
Thanks.Cheers
Claudia

Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:
  Hi Claudia

  there is no autorecon3-cp, just autorecon2-cp

  cheers
  Bruce
  On Mon, 3 Jun 2013, Claudia Dacquino wrote:

Hi Freesurfers,
I did autorecon3-cp and exited with errors.
Ould anyone help me to understand what's the roblem?
You can find the recon-all.log attached.
Thanks in advance.
Claudia





  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
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

[Douglas N Greve]

no, it does not include cerebellum
On 06/03/2013 01:42 PM, Ritobrato Datta wrote:
> In the website below,
> lhCorticalWhiteMatter,rhCorticalWhiteMatter,CorticalWhiteMatter - volume 
> inside the white surface minus anything that is not WM. CorticalWhiteMatter 
> includes hypointensities. This uses the surface-based volume computation for 
> part of the calculation and counts voxels to subtract "anything not in WM". 
> It is approximately equal to the count of WM voxels in aparc+aseg.mgz.
>
> Since, cerebellar wm is in the aparc+aseg.mgz so that means its included in 
> the CorticalWhiteMatter, correct ?
>
> - Original Message -
> From: Douglas N Greve 
> To: Ritobrato Datta 
> Cc: Freesurfer@nmr.mgh.harvard.edu
> Sent: Mon, 03 Jun 2013 13:19:54 -0400 (EDT)
> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
> brain vol.
>
>
> See if this answers your question
> http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
> this is for v5.2 and beyond
>
> On 06/03/2013 01:07 PM, Ritobrato Datta wrote:
>> ic thats rightI was getting confused. So the total gm vol includes 
>> cerebellar gm vol but the cortical wm vol only includes the wm vol under the 
>> cortical ribbon and around the subcortical gm structures?  Or does that 
>> include wm under the cerebellar cortex as well ?
>>
>> Is there a table somewhere which specifies which of these freesurfer 
>> parcellated structures contribute to these combined measures such has 
>> supratentorial vol / whole gm vol etc etc
>>
>> That will be very helpful.
>>
>>
>>
>> - Original Message -
>> From: Douglas N Greve 
>> To: Ritobrato Datta , 
>> Freesurfer@nmr.mgh.harvard.edu
>> Sent: Mon, 03 Jun 2013 12:59:30 -0400 (EDT)
>> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
>> brain vol.
>>
>>
>> Hi Rito, I don't think we report a total wm volume, do we?
>> doug
>>
>>
>>
>>
>> On 06/03/2013 12:56 PM, Ritobrato Datta wrote:
>>> Hi Doug,
>>>
>>> Just following up on your reply sometime back -
>>> Does total white volume include cerebellar wm vol also ?
>>>
>>> Please let me know.
>>>
>>> Thanks
>>>
>>> Rito
>>>
>>> - Original Message -
>>> From: Douglas N Greve 
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT)
>>> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
>>> brain vol.
>>>
>>> Total Gray includes the cerebellar gray
>>> doug
>>> On 05/24/2013 03:51 PM, Ritobrato Datta wrote:
 Hello All,

 Can someone address the following ? I sent this query yesterday but it 
 fell through the cracks.

 I am using freesurfer 5.1 for my analysis.

 I am interested in calculating the whole brain vol (total Gray vol + total 
 WM vol) excluding the CSF volume and cerebellum.

 Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol

 In all of the 79 subjects, when I compare the Total Brain Vol to 
 SupraTentorialVol, I find SupraTentorialVol is smaller than the Total 
 Brain Vol I have calculated.

 Here are some measures -

 For 79 subjects -

 Average Total Brain Vol = 1038395.291

 Average SupraTentorialVol = 979996.4684

 Is that expected ?

 Is it possible that CSF vol is part of Total Brain Vol ?

 Any insight will be helpful.

 Thanks

 Rito

 ___
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 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
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Group Analysis Question

[Douglas N Greve]

Not necessarily. It could have been in the FS analysis. You can run 
mri_glmfit with  --kurtosis (a hidden option). This will create a 
kurtosis.mgh and pkurtosis.mgh. Kurtosis is a measure of gaussianity of 
the residuals (larger being less gaussian). The pkurtosis the the sig 
(-log10(p)) of the probability of seeing the kurtosis under the null 
(ie, the residuals are gaussian). So you can see if one model gives you 
better kurtosis than another.

doug


On 06/03/2013 01:20 PM, Fotiadis, Panagiotis wrote:
> I see. Yes from the one hand the results that I got make a lot more sense in 
> the second type of analysis, compared to the first one, however, there are 
> some somewhat important difference between the two analyses. If there is an 
> issue with the data, do you believe that it would be in the acquisition? 
> Because I checked the reconstructions and they look fine.
>
> Thanks,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, June 03, 2013 11:24 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Group Analysis Question
>
> I would not expect them to be identical but similar.  If they change a
> lot there may be an issue with your data.
> doug
>
>
>
> On 6/3/13 11:11 AM, Fotiadis, Panagiotis wrote:
>> Hey Doug,
>>
>> I have run a group analysis on my data with two different ways. (The input 
>> is cortical thickness.) In the first analysis, I specified 4 groups 
>> (Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas 
>> in the second, just two groups (Diseased, Healthy). One of the comparisons 
>> that I did was the age slope between Diseased and Healthy. Therefore in the 
>> first analysis, I set the contrast vector to be [0 0 0 0 0.5 0.5 -0.5 -0.5] 
>> and in the second analysis I set it to [0 0 1 -1]. However, the results that 
>> came up were somewhat different. For instance there were clusters in the 
>> second analysis that were significant but were not significant in the first 
>> analysis.
>> Shouldn't the results be the same?
>>
>> Thank you,
>> Panos
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

[Ritobrato Datta]

In the website below, 
lhCorticalWhiteMatter,rhCorticalWhiteMatter,CorticalWhiteMatter - volume inside 
the white surface minus anything that is not WM. CorticalWhiteMatter includes 
hypointensities. This uses the surface-based volume computation for part of the 
calculation and counts voxels to subtract "anything not in WM". It is 
approximately equal to the count of WM voxels in aparc+aseg.mgz.

Since, cerebellar wm is in the aparc+aseg.mgz so that means its included in the 
CorticalWhiteMatter, correct ?

- Original Message -
From: Douglas N Greve 
To: Ritobrato Datta 
Cc: Freesurfer@nmr.mgh.harvard.edu
Sent: Mon, 03 Jun 2013 13:19:54 -0400 (EDT)
Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
brain vol.


See if this answers your question
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
this is for v5.2 and beyond

On 06/03/2013 01:07 PM, Ritobrato Datta wrote:
> ic thats rightI was getting confused. So the total gm vol includes 
> cerebellar gm vol but the cortical wm vol only includes the wm vol under the 
> cortical ribbon and around the subcortical gm structures?  Or does that 
> include wm under the cerebellar cortex as well ?
>
> Is there a table somewhere which specifies which of these freesurfer 
> parcellated structures contribute to these combined measures such has 
> supratentorial vol / whole gm vol etc etc
>
> That will be very helpful.
>
>
>
> - Original Message -
> From: Douglas N Greve 
> To: Ritobrato Datta , 
> Freesurfer@nmr.mgh.harvard.edu
> Sent: Mon, 03 Jun 2013 12:59:30 -0400 (EDT)
> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
> brain vol.
>
>
> Hi Rito, I don't think we report a total wm volume, do we?
> doug
>
>
>
>
> On 06/03/2013 12:56 PM, Ritobrato Datta wrote:
>> Hi Doug,
>>
>> Just following up on your reply sometime back -
>> Does total white volume include cerebellar wm vol also ?
>>
>> Please let me know.
>>
>> Thanks
>>
>> Rito
>>
>> - Original Message -
>> From: Douglas N Greve 
>> To: freesurfer@nmr.mgh.harvard.edu
>> Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT)
>> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
>> brain vol.
>>
>> Total Gray includes the cerebellar gray
>> doug
>> On 05/24/2013 03:51 PM, Ritobrato Datta wrote:
>>> Hello All,
>>>
>>> Can someone address the following ? I sent this query yesterday but it fell 
>>> through the cracks.
>>>
>>> I am using freesurfer 5.1 for my analysis.
>>>
>>> I am interested in calculating the whole brain vol (total Gray vol + total 
>>> WM vol) excluding the CSF volume and cerebellum.
>>>
>>> Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol
>>>
>>> In all of the 79 subjects, when I compare the Total Brain Vol to 
>>> SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain 
>>> Vol I have calculated.
>>>
>>> Here are some measures -
>>>
>>> For 79 subjects -
>>>
>>> Average Total Brain Vol = 1038395.291
>>>
>>> Average SupraTentorialVol = 979996.4684
>>>
>>> Is that expected ?
>>>
>>> Is it possible that CSF vol is part of Total Brain Vol ?
>>>
>>> Any insight will be helpful.
>>>
>>> Thanks
>>>
>>> Rito
>>>
>>> ___
>>> Freesurfer mailing list
>>> 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
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] autorecon3 error

[Claudia Dacquino]

Is this the problem? Is there an incorrect command?
Thanks.
Cheers
Claudia

Il giorno lunedì 3 giugno 2013, Bruce Fischl ha scritto:

> Hi Claudia
>
> there is no autorecon3-cp, just autorecon2-cp
>
> cheers
> Bruce
> On Mon, 3 Jun 2013, Claudia Dacquino wrote:
>
>  Hi Freesurfers,
>> I did autorecon3-cp and exited with errors.
>> Ould anyone help me to understand what's the roblem?
>> You can find the recon-all.log attached.
>> Thanks in advance.
>> Claudia
>>
>>
>>
>>
>
> 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.
>
>
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

[Douglas N Greve]

See if this answers your question
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
this is for v5.2 and beyond

On 06/03/2013 01:07 PM, Ritobrato Datta wrote:
> ic thats rightI was getting confused. So the total gm vol includes 
> cerebellar gm vol but the cortical wm vol only includes the wm vol under the 
> cortical ribbon and around the subcortical gm structures?  Or does that 
> include wm under the cerebellar cortex as well ?
>
> Is there a table somewhere which specifies which of these freesurfer 
> parcellated structures contribute to these combined measures such has 
> supratentorial vol / whole gm vol etc etc
>
> That will be very helpful.
>
>
>
> - Original Message -
> From: Douglas N Greve 
> To: Ritobrato Datta , 
> Freesurfer@nmr.mgh.harvard.edu
> Sent: Mon, 03 Jun 2013 12:59:30 -0400 (EDT)
> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
> brain vol.
>
>
> Hi Rito, I don't think we report a total wm volume, do we?
> doug
>
>
>
>
> On 06/03/2013 12:56 PM, Ritobrato Datta wrote:
>> Hi Doug,
>>
>> Just following up on your reply sometime back -
>> Does total white volume include cerebellar wm vol also ?
>>
>> Please let me know.
>>
>> Thanks
>>
>> Rito
>>
>> - Original Message -
>> From: Douglas N Greve 
>> To: freesurfer@nmr.mgh.harvard.edu
>> Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT)
>> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
>> brain vol.
>>
>> Total Gray includes the cerebellar gray
>> doug
>> On 05/24/2013 03:51 PM, Ritobrato Datta wrote:
>>> Hello All,
>>>
>>> Can someone address the following ? I sent this query yesterday but it fell 
>>> through the cracks.
>>>
>>> I am using freesurfer 5.1 for my analysis.
>>>
>>> I am interested in calculating the whole brain vol (total Gray vol + total 
>>> WM vol) excluding the CSF volume and cerebellum.
>>>
>>> Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol
>>>
>>> In all of the 79 subjects, when I compare the Total Brain Vol to 
>>> SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain 
>>> Vol I have calculated.
>>>
>>> Here are some measures -
>>>
>>> For 79 subjects -
>>>
>>> Average Total Brain Vol = 1038395.291
>>>
>>> Average SupraTentorialVol = 979996.4684
>>>
>>> Is that expected ?
>>>
>>> Is it possible that CSF vol is part of Total Brain Vol ?
>>>
>>> Any insight will be helpful.
>>>
>>> Thanks
>>>
>>> Rito
>>>
>>> ___
>>> Freesurfer mailing list
>>> 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
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Group Analysis Question

[Fotiadis, Panagiotis]

I see. Yes from the one hand the results that I got make a lot more sense in 
the second type of analysis, compared to the first one, however, there are some 
somewhat important difference between the two analyses. If there is an issue 
with the data, do you believe that it would be in the acquisition? Because I 
checked the reconstructions and they look fine. 

Thanks,
Panos 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, June 03, 2013 11:24 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis Question

I would not expect them to be identical but similar.  If they change a
lot there may be an issue with your data.
doug



On 6/3/13 11:11 AM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> I have run a group analysis on my data with two different ways. (The input is 
> cortical thickness.) In the first analysis, I specified 4 groups 
> (Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas in 
> the second, just two groups (Diseased, Healthy). One of the comparisons that 
> I did was the age slope between Diseased and Healthy. Therefore in the first 
> analysis, I set the contrast vector to be [0 0 0 0 0.5 0.5 -0.5 -0.5] and in 
> the second analysis I set it to [0 0 1 -1]. However, the results that came up 
> were somewhat different. For instance there were clusters in the second 
> analysis that were significant but were not significant in the first analysis.
> Shouldn't the results be the same?
>
> Thank you,
> Panos
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>
>

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Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

[Ritobrato Datta]

ic thats rightI was getting confused. So the total gm vol includes 
cerebellar gm vol but the cortical wm vol only includes the wm vol under the 
cortical ribbon and around the subcortical gm structures?  Or does that 
include wm under the cerebellar cortex as well ?

Is there a table somewhere which specifies which of these freesurfer 
parcellated structures contribute to these combined measures such has 
supratentorial vol / whole gm vol etc etc

That will be very helpful. 



- Original Message -
From: Douglas N Greve 
To: Ritobrato Datta , Freesurfer@nmr.mgh.harvard.edu
Sent: Mon, 03 Jun 2013 12:59:30 -0400 (EDT)
Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
brain vol.


Hi Rito, I don't think we report a total wm volume, do we?
doug




On 06/03/2013 12:56 PM, Ritobrato Datta wrote:
> Hi Doug,
>
> Just following up on your reply sometime back -
> Does total white volume include cerebellar wm vol also ?
>
> Please let me know.
>
> Thanks
>
> Rito
>
> - Original Message -
> From: Douglas N Greve 
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT)
> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
> brain vol.
>
> Total Gray includes the cerebellar gray
> doug
> On 05/24/2013 03:51 PM, Ritobrato Datta wrote:
>> Hello All,
>>
>> Can someone address the following ? I sent this query yesterday but it fell 
>> through the cracks.
>>
>> I am using freesurfer 5.1 for my analysis.
>>
>> I am interested in calculating the whole brain vol (total Gray vol + total 
>> WM vol) excluding the CSF volume and cerebellum.
>>
>> Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol
>>
>> In all of the 79 subjects, when I compare the Total Brain Vol to 
>> SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain 
>> Vol I have calculated.
>>
>> Here are some measures -
>>
>> For 79 subjects -
>>
>> Average Total Brain Vol = 1038395.291
>>
>> Average SupraTentorialVol = 979996.4684
>>
>> Is that expected ?
>>
>> Is it possible that CSF vol is part of Total Brain Vol ?
>>
>> Any insight will be helpful.
>>
>> Thanks
>>
>> Rito
>>
>> ___
>> Freesurfer mailing list
>> 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
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] combination of different surfaces across the group for mri_glmfit statistics

[Douglas N Greve]

On 06/03/2013 12:37 PM, Robert Schulz wrote:
> Dear Douglas,
>
> thank you for your reply.
>
>> Hi,
>> I have two questions:
>> 1.
>> I have created specific surfaces in fsaverage rh for each of my 20
>> subjects. (xy.mgh)
>> I'd like to run statistical analysis within the common surface area
>> which is included in all subjects.
>> Therefore I wonder how to combine those surfaces.
>> My idea would be to add all surfaces and threshold the resulting
>> surface by 20 ==> giving a final surface common to all of them.
> I don't understand what you mean. What are you thresholding? The 
> thickness?
>
> No, to make it clear. Surfaces will include data derived from FSL 
> fiber tracking to investigate the structural connectivity of this 
> specific surface ("brain area"). So the actual surface is just a 
> binary (1) "mask". I'd like to know the common "core" surface hence 
> the surface common to all 20 subjects.
> How can I calculate this final surface whose area can be found in all 
> 20 subjects. It's just about the localization of the surface. It's 
> about where this surface is located in all subjects.
> I just thought to add all surfaces with their 1s in ther vertices and 
> see where I get 20. I hope this makes it clearer.
You can use
mri_concat xy.subj1.mgh xy.subj2.mgh ... --sum --o sum.mgh
mri_binarize --i sum.mgh --min 19.5 --o mask.mgh
then run mri_glmfit with --mask mask.mgh

doug
>
>
>> 2.
>> How can I limit mri_glmfit to this final surface to run the
>> statistical analysis only in this area, not in all of the hemisphere?
> You can run mri_glmfit with a --mask option to select only the voxels
> you want to use
>
> mri_glmfit will be conducted based on the surface. so as --mask, I can 
> use the finalmask.mhg?
>
>
>
> Thank you!
>
> doug
>> Can anybody provide the appropriate commands for both issues?
>> Thank you very much!
>> Best wishes, Robert
>
>
> -- 
> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und 
> Genossenschaftsregister sowie das Unternehmensregister (EHUG):
>
> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen 
> Rechts; Gerichtsstand: Hamburg
>
> Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. 
> Dr. Uwe Koch-Gromus, Astrid Lurati (Kommissarisch), Joachim Prölß, 
> Matthias Waldmann (Kommissarisch)
>
> Bitte erwägen Sie, ob diese Mail ausgedruckt werden muss - der Umwelt 
> zuliebe.
>
> Please consider whether this mail must be printed - please think of 
> the environment.
>
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

[Douglas N Greve]

Hi Rito, I don't think we report a total wm volume, do we?
doug




On 06/03/2013 12:56 PM, Ritobrato Datta wrote:
> Hi Doug,
>
> Just following up on your reply sometime back -
> Does total white volume include cerebellar wm vol also ?
>
> Please let me know.
>
> Thanks
>
> Rito
>
> - Original Message -
> From: Douglas N Greve 
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT)
> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total 
> brain vol.
>
> Total Gray includes the cerebellar gray
> doug
> On 05/24/2013 03:51 PM, Ritobrato Datta wrote:
>> Hello All,
>>
>> Can someone address the following ? I sent this query yesterday but it fell 
>> through the cracks.
>>
>> I am using freesurfer 5.1 for my analysis.
>>
>> I am interested in calculating the whole brain vol (total Gray vol + total 
>> WM vol) excluding the CSF volume and cerebellum.
>>
>> Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol
>>
>> In all of the 79 subjects, when I compare the Total Brain Vol to 
>> SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain 
>> Vol I have calculated.
>>
>> Here are some measures -
>>
>> For 79 subjects -
>>
>> Average Total Brain Vol = 1038395.291
>>
>> Average SupraTentorialVol = 979996.4684
>>
>> Is that expected ?
>>
>> Is it possible that CSF vol is part of Total Brain Vol ?
>>
>> Any insight will be helpful.
>>
>> Thanks
>>
>> Rito
>>
>> ___
>> Freesurfer mailing list
>> 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
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] Bug report: fslregister within reg-feat2anat

[Douglas N Greve]

Hi Chris, this problem was created because of a change in the way 
tcshell works. When fname2stem fails, it should not go on to set fsvol = 
tmp because status should be set to 1. This is the way tcshell used to 
work. With newer version of CentOS, it sets status=0 because the set tmp 
was successful even though fname2stem failed. This was a super annoying 
thing for them to do. I've put a new version of reg-feat2anat here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat

let me know if this works
doug



On 06/02/2013 10:16 PM, Chris Adamson wrote:
> During the reg-feat2anat script fslregister produces errors. I tracked
> it to the argument parsing code
>
> 419 case "--fsvol":
> 420 if ( $#argv < 1) goto arg1err;
> 421 set fsvol = $argv[1]; shift;
> 422 set tmp = `fname2stem $fsvol`;
> 423 if(! $status) set fsvol = $tmp;
> 424 breaksw
>
> The reg-feat2anat script uses the following call:
> ./fslregister --s *** --reg
> ***+.feat/reg/freesurfer/anat2exf.register.dat --mov
> ***+.feat/example_func.nii --dof 6 --bins 256 --cost corratio --fslmat
> ***+.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle
> 90 --initfslmat ***+.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp
> ***+.feat/reg/freesurfer/tmp --out
> ***+.feat/reg/freesurfer/tmp/exf-in-anat.nii
>
> and the fsvol variable is eventually set ERROR: because line 422 fails.
> fsvol originally is just "brainmask" but it requires the full filename
> for fname2stem to work. Also, if I change the line 422 to
> $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz the rest of the script fails
> because it expects to just have "brainmask" not the full path.
>
> FS VOL FIRST
> brainmask
> Before stem
> brainmask
> /data/***/mri/brainmask
> TMP
> ERROR: cannot determine stem
> FS VOL FIRST AFTER RETURN
> ERROR:
>
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] combination of different surfaces across the group for mri_glmfit statistics

[Robert Schulz]

Dear Douglas,

thank you for your reply.

> Hi,
> I have two questions:
> 1.
> I have created specific surfaces in fsaverage rh for each of my 20
> subjects. (xy.mgh)
> I'd like to run statistical analysis within the common surface area
> which is included in all subjects.
> Therefore I wonder how to combine those surfaces.
> My idea would be to add all surfaces and threshold the resulting
> surface by 20 ==> giving a final surface common to all of them.
I don't understand what you mean. What are you thresholding? The thickness?

No, to make it clear. Surfaces will include data derived from FSL fiber 
tracking to investigate the structural connectivity of this specific surface 
("brain area"). So the actual surface is just a binary (1) "mask". I'd like 
to know the common "core" surface hence the surface common to all 20 
subjects.
How can I calculate this final surface whose area can be found in all 20 
subjects. It's just about the localization of the surface. It's about where 
this surface is located in all subjects.
I just thought to add all surfaces with their 1s in ther vertices and see 
where I get 20. I hope this makes it clearer.


> 2.
> How can I limit mri_glmfit to this final surface to run the
> statistical analysis only in this area, not in all of the hemisphere?
You can run mri_glmfit with a --mask option to select only the voxels
you want to use

mri_glmfit will be conducted based on the surface. so as --mask, I can use 
the finalmask.mhg?



Thank you!

doug
> Can anybody provide the appropriate commands for both issues?
> Thank you very much!
> Best wishes, Robert


--
Pflichtangaben gemäß Gesetz über elektronische Handelsregister und 
Genossenschaftsregister sowie das Unternehmensregister (EHUG):

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; 
Gerichtsstand: Hamburg

Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe 
Koch-Gromus, Astrid Lurati (Kommissarisch), Joachim Prölß, Matthias Waldmann 
(Kommissarisch)

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Re: [Freesurfer] combination of different surfaces across the group for mri_glmfit statistics

[Douglas N Greve]

Hi Robert,
On 06/03/2013 12:12 PM, Robert Schulz wrote:
> Hi,
> I have two questions:
> 1.
> I have created specific surfaces in fsaverage rh for each of my 20 
> subjects. (xy.mgh)
> I'd like to run statistical analysis within the common surface area 
> which is included in all subjects.
> Therefore I wonder how to combine those surfaces.
> My idea would be to add all surfaces and threshold the resulting 
> surface by 20 ==> giving a final surface common to all of them.
I don't understand what you mean. What are you thresholding? The thickness?
> 2.
> How can I limit mri_glmfit to this final surface to run the 
> statistical analysis only in this area, not in all of the hemisphere?
You can run mri_glmfit with a --mask option to select only the voxels 
you want to use
doug
> Can anybody provide the appropriate commands for both issues?
> Thank you very much!
> Best wishes, Robert
>
>
> --
> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und 
> Genossenschaftsregister sowie das Unternehmensregister (EHUG):
>
> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen 
> Rechts; Gerichtsstand: Hamburg
>
> Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. 
> Dr. Uwe Koch-Gromus, Astrid Lurati (Kommissarisch), Joachim Prölß, 
> Matthias Waldmann (Kommissarisch)
>
> Bitte erwägen Sie, ob diese Mail ausgedruckt werden muss - der Umwelt 
> zuliebe.
>
> Please consider whether this mail must be printed - please think of 
> the environment.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] Fwd: autorecon3 error

[Bruce Fischl]

Hi Claudia

there is no autorecon3-cp, just autorecon2-cp

cheers
Bruce
On Mon, 3 Jun 2013, Claudia 
Dacquino wrote:

> Hi Freesurfers,
> I did autorecon3-cp and exited with errors.
> Ould anyone help me to understand what's the roblem?
> You can find the recon-all.log attached.
> Thanks in advance.
> Claudia
> 
> 
>
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Re: [Freesurfer] Defacing with mri_deface

[Bruce Fischl]

sure
On Mon, 3 Jun 2013, sle...@nmr.mgh.harvard.edu wrote:

> Hi Bruce,
>
> I see that somebody copied talairach_mixed_with_skull.gca to
>
> /usr/local/freesurfer/stable5/average/
>
> thank you, but FreeSurfer seems to be looking for it here:
>
> /usr/local/freesurfer/stable5_3_0/average/talairach_mixed_with_skull.gca
>
> Could you please have someone copy it there too?
>
> Here is the error.log from the mri/ directory:
>
> GCAread(/usr/local/freesurfer/stable5_3_0/average/talairach_mixed_with_skull.gca):
> could not open file
>
>
>  Steve
>
>> Hi Steve
>>
>> I think recon-all -deface only creates the orig_defaced.mgz which you can
>> then use with mri_mask to remove facial features from whatever volumes you
>> want.
>>
>> I don't have write permissions to that directory, but I'll see if I can
>> get
>> help to copy it.
>>
>> cheers
>> Bruce
>>
>>
>> On Wed, 29 May 2013,
>> sle...@nmr.mgh.harvard.edu wrote:
>>
>>> The script mri_deface which is called by recon-all with the -deface
>>> flag,
>>> requires the existence of two files
>>>
>>> /usr/local/freesurfer/stable5/average/face.gca
>>> /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
>>>
>>> The former exists where it should, the latter does not exist at that
>>> location, although it can be downloaded from
>>>
>>>  http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads
>>>
>>> and gunzipped. When I copy it into a directory and call mri_deface
>>> directly, it works OK because it can find that image locally. But when I
>>> call recon-all with the -deface flag, it looks for the file where it
>>> does
>>> not exist, i.e.
>>>
>>> /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
>>>
>>> Could someone with the appropriate permissions please copy that file to
>>> where recon-all expects to find it?
>>>
>>> Second question: If I call recon-all with the -deface flag, does it
>>> deface
>>> ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only
>>> deface a copy of orig.mgz to orig_defaced.mgz?
>>>
>>>
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>>>
>>>
>>>
>>
>>
>>
>
>
>
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Re: [Freesurfer] Defacing with mri_deface

[slehar]

Hi Bruce,

I see that somebody copied talairach_mixed_with_skull.gca to

/usr/local/freesurfer/stable5/average/

thank you, but FreeSurfer seems to be looking for it here:

/usr/local/freesurfer/stable5_3_0/average/talairach_mixed_with_skull.gca

Could you please have someone copy it there too?

Here is the error.log from the mri/ directory:

GCAread(/usr/local/freesurfer/stable5_3_0/average/talairach_mixed_with_skull.gca):
could not open file


  Steve

> Hi Steve
>
> I think recon-all -deface only creates the orig_defaced.mgz which you can
> then use with mri_mask to remove facial features from whatever volumes you
> want.
>
> I don't have write permissions to that directory, but I'll see if I can
> get
> help to copy it.
>
> cheers
> Bruce
>
>
> On Wed, 29 May 2013,
> sle...@nmr.mgh.harvard.edu wrote:
>
>> The script mri_deface which is called by recon-all with the -deface
>> flag,
>> requires the existence of two files
>>
>> /usr/local/freesurfer/stable5/average/face.gca
>> /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
>>
>> The former exists where it should, the latter does not exist at that
>> location, although it can be downloaded from
>>
>>  http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads
>>
>> and gunzipped. When I copy it into a directory and call mri_deface
>> directly, it works OK because it can find that image locally. But when I
>> call recon-all with the -deface flag, it looks for the file where it
>> does
>> not exist, i.e.
>>
>> /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
>>
>> Could someone with the appropriate permissions please copy that file to
>> where recon-all expects to find it?
>>
>> Second question: If I call recon-all with the -deface flag, does it
>> deface
>> ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only
>> deface a copy of orig.mgz to orig_defaced.mgz?
>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
>

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[Freesurfer] combination of different surfaces across the group for mri_glmfit statistics

[Robert Schulz]

Hi, 

I have two questions: 

1.
I have created specific surfaces in fsaverage rh for each of my 20 subjects. 
(xy.mgh)
I'd like to run statistical analysis within the common surface area which is 
included in all subjects. 
Therefore I wonder how to combine those surfaces. 
My idea would be to add all surfaces and threshold the resulting surface by 20 
==> giving a final surface common to all of them. 

2. 
How can I limit mri_glmfit to this final surface to run the statistical 
analysis only in this area, not in all of the hemisphere?

Can anybody provide the appropriate commands for both issues?

Thank you very much!

Best wishes, Robert

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Re: [Freesurfer] Group Analysis Question

[Douglas Greve]

I would not expect them to be identical but similar.  If they change a 
lot there may be an issue with your data.
doug



On 6/3/13 11:11 AM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> I have run a group analysis on my data with two different ways. (The input is 
> cortical thickness.) In the first analysis, I specified 4 groups 
> (Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas in 
> the second, just two groups (Diseased, Healthy). One of the comparisons that 
> I did was the age slope between Diseased and Healthy. Therefore in the first 
> analysis, I set the contrast vector to be [0 0 0 0 0.5 0.5 -0.5 -0.5] and in 
> the second analysis I set it to [0 0 1 -1]. However, the results that came up 
> were somewhat different. For instance there were clusters in the second 
> analysis that were significant but were not significant in the first analysis.
> Shouldn't the results be the same?
>
> Thank you,
> Panos
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Re: [Freesurfer] use of anot_2_label

[Douglas Greve]

brainstem is not part of cortex. Use mri_cor2label with the aseg. get 
the id from $FREESURFER_HOME/FreeSurferColorLUT.txt

doug






On 6/3/13 6:17 AM, LAOUCHEDI MAKHLOUF wrote:

Hi
  i used  mri_annotation2label to extract the cortical labels. for 
this command we must specify which hemisphere (--hemi ?h) and i want 
to extract the brainstem which is not a lateralized structure, is 
there any command like mri_annotation2label to extract the brainstem ?


thanks



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Re: [Freesurfer] Cortical thickness

[Douglas Greve]

Hi Joshua, when you add --fwhm 15 to the command line you are 
instructing mri_glmfit to smooth by 15mm. Is this what you want?  Or is 
the data already smoothed?

doug


On 6/3/13 12:26 AM, Joshua deSouza wrote:

Hi Doug,

The command line is mri_glmfit --y lh.t.15.mgh --fsgd t.txt dods --C 
t1.txt --surface fsaverage lh --cortex --fwhm 15 --glmdir lh.t.15.glmdir


I am doing a whole hemisphere analysis and am measuring cortical 
thickness. I do not have my own mask but I have doubts about the mask 
that has been produced because from previous studies, there has been 
significant thinning in the area around the hippocampus and parts of 
it are being left out in the mask, such as the para-hippocampal region.


Regards

Joshua

On Mon, Jun 3, 2013 at 10:54 AM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:



The residual FWHM is measured from the data itself. You apply a
certain amount of smoothing, but there is already some smoothness
to the data, so the final fwhm is a combination of what is already
there and what you apply. A fwhm of 47 is huge and may indicate
that something is wrong. What is the input? cortical thickness?
Are you using your own mask or is this a whole hemisphere analysis?

doug






On 6/2/13 10:29 PM, Joshua deSouza wrote:

Hello Doug,

Thank you for your quick replies to my queries. Really appreciate
it.

I have found the files containing the cortical thickness values.
Thank you. I assume that the order in which they follow are based
on the fsgd file and the cluster annotation numbers.

I was just slightly confused about the residual fwhm. I have
already done a smoothing of 15 on the file and have recieved a
residual value of 47, which I assume is extremely large. Since
I'm finding out values for the entire cortex I cannot do a
glmfit-sim as there are no fwhm cache values of 47. Could you
please tell me what the residual values mean?  What do you
recommend I do? Is there anything I can read up on to find out
more about this? (Please pardon my questions if they seem a
little trivial)

Thank you

Joshua

On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


This file is always created by mri_glmfit-sim. It might be
named something different depending on your parameters
(should always end in y.ocn.dat)
doug


On 6/2/13 3:57 AM, Joshua deSouza wrote:

Hi Doug,

This file that your saying, will be created after glmfit-sim
is done using the cache function and a threshold of 1.3 and
absolute ,with y being the fsgd file? Am I understanding
this correctly?

Thank you

Joshua

On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

There should be a file called something like
cache.th13.abs.y.ocn.dat.
This will have a column for each cluster and a row for
each subject. The
value in the row will be the input for each subject.
doug

On 05/30/2013 11:21 PM, Joshua deSouza wrote:
> Hello everyone,
>
> Please pardon my rather simple question
>
> I have done a GLM fit anlysis and have obtained a file
sig.mgh alonf
> with a few others after the analysis.As I know, I do
not have to
> create ROIs in order to do this. I also understand
that doing a
> multiple comparison analysis just compares the regions
of importance
> and evaluates them giving the most resilient cluster
depending on the
> threshold. So, this does not give a thickness
estimate. I would like
> to know how do I get the cortical thickness values
from the results?
> If so, can I do it after glmfit?
>
> And thanks Doug for your help in the other questions
that I had prior
> to this!
>
> Thank you
>
>
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[Freesurfer] Group Analysis Question

[Fotiadis, Panagiotis]

Hey Doug,

I have run a group analysis on my data with two different ways. (The input is 
cortical thickness.) In the first analysis, I specified 4 groups 
(Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas in 
the second, just two groups (Diseased, Healthy). One of the comparisons that I 
did was the age slope between Diseased and Healthy. Therefore in the first 
analysis, I set the contrast vector to be [0 0 0 0 0.5 0.5 -0.5 -0.5] and in 
the second analysis I set it to [0 0 1 -1]. However, the results that came up 
were somewhat different. For instance there were clusters in the second 
analysis that were significant but were not significant in the first analysis.
Shouldn't the results be the same?

Thank you,
Panos
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Re: [Freesurfer] motioncor

[Bruce Fischl]

if they are named orig/00[012345].mgz then I think they will be averaged 
but without motion correction, which is almost certainly not what you want

On Sun, 2 Jun 2013, 
obre...@nmr.mgh.harvard.edu wrote:

> Hi Bruce,
>
> Thanks for responding! For the sake of clarification, let's say I have
> multiple source volumes (XXX.mgz) in mri/orig/, and I don't use the -i
> switch in recon-all to point to one of them, exclusively. If I
> additionally include the -nomotioncor option, will the multiple source
> volumes be averaged without correcting for motion between them, yielding
> orig.mgz as output?
>
> Best,
>
> Gabriel
>
>
>> Hi Gabriel
>>
>> if you want to process only one volume, then point recon-all at it with
>> the -i switch. You can also use freeview instead of tkmedit for browsing
>> the volumes - it's much more flexible.
>>
>> The two volumes vs. one is an empirical question. I've found that a single
>> high-quality volume is better than motion-correcting and averaging two,
>> particularly if one of the two is lower quality, but that's an ad hoc
>> assessment on my part and depends a lot on field strength, coil, subject
>> motion, etc
>>
>> cheers
>> Bruce
>>
>> On Sun, 2 Jun 2013, Gabriel Obregon
>> wrote:
>>
>>> Hi,
>>>
>>> Could someone please help me with the following concerns:
>>>
>>> A. If I have multiple source volumes in mri/orig/ and run recon-all
>>> using the -nomotioncor option, how are these inputs processed compared
>>> to the case in which motion correction is employed, and what should I
>>> expect as my output?
>>>
>>> B. If I want to process only one of the multiple source volumes, i.e.,
>>> the "best", how should I proceed?
>>>
>>> C. I've been encountering displaying issues of the raw volumes using
>>> tkmedit. What other interfaces are readily available for browsing
>>> through the source volumes in order to assess their quality?
>>>
>>> D. Finally, if in one of my studies I could afford running only two
>>> MPRAGE sessions per subject, is motion correction advisable for
>>> segmenting the surfaces?
>>>
>>> Thanks!
>>>
>>> Gabriel
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>>>
>>>
>>
>>
>>
>
>
>
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Re: [Freesurfer] (no subject)

[Bruce Fischl]

Hi Shani

you'll need to send us some images and the recon-all.log for us to diagnose 
the problem
Bruce
On Mon, 3 Jun 2013, 
Shani Ben Amitay wrote:

> Hello all
> I have created white matter surface of a non primate brain and I'm trying to
> use mris_make_surfaces to position the pial surface.
> The problem is that the resulted pial surface is miss-positioned-the
> 'growing' stops very close to the white surface (no gradient visible where
> it stops)
> Any idea what could be the reasons ?
> 
> Thanks, Shani
> 
>
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Re: [Freesurfer] Bug report: fslregister within reg-feat2anat

[Z K]

Thank you Chris for pointing this potential bug and the possible culprit 
in the source code. We will take a closer look it and determine the best 
way to proceed.

-Zeke


On 06/02/2013 10:16 PM, Chris Adamson wrote:
> During the reg-feat2anat script fslregister produces errors. I tracked
> it to the argument parsing code
>
> 419 case "--fsvol":
> 420 if ( $#argv < 1) goto arg1err;
> 421 set fsvol = $argv[1]; shift;
> 422 set tmp = `fname2stem $fsvol`;
> 423 if(! $status) set fsvol = $tmp;
> 424 breaksw
>
> The reg-feat2anat script uses the following call:
> ./fslregister --s *** --reg
> ***+.feat/reg/freesurfer/anat2exf.register.dat --mov
> ***+.feat/example_func.nii --dof 6 --bins 256 --cost corratio --fslmat
> ***+.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle
> 90 --initfslmat ***+.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp
> ***+.feat/reg/freesurfer/tmp --out
> ***+.feat/reg/freesurfer/tmp/exf-in-anat.nii
>
> and the fsvol variable is eventually set ERROR: because line 422 fails.
> fsvol originally is just "brainmask" but it requires the full filename
> for fname2stem to work. Also, if I change the line 422 to
> $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz the rest of the script fails
> because it expects to just have "brainmask" not the full path.
>
> FS VOL FIRST
> brainmask
> Before stem
> brainmask
> /data/***/mri/brainmask
> TMP
> ERROR: cannot determine stem
> FS VOL FIRST AFTER RETURN
> ERROR:
>
>
>
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[Freesurfer] (no subject)

[Shani Ben Amitay]

Hello all

I have created white matter surface of a non primate brain and I'm trying
to use mris_make_surfaces to position the pial surface.
The problem is that the resulted pial surface is miss-positioned-the
'growing' stops very close to the white surface (no gradient visible where
it stops)
Any idea what could be the reasons ?

Thanks, Shani
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Re: [Freesurfer] bert recon-all errors, non-cuda

[Bruce Fischl]

Hi Graham,

I think the distance error is in the creation of the ?h.qsphere.nofix and 
can be ignored as can the others. It shouldn't be reported and I'll try to 
find the time to take it out as there is no metric perservation in the 
qsphere - it's only concerned with topology.


cheers
Bruce



On Mon, 3 Jun 2013, Graham Wideman wrote:


Hi all,

I'm testing recon-all using bert with the intent of ensuring that freesurfer
installation is good.

recon-all completes with a "finished without error" message, and the
resulting surfaces and parcellations look sensible.  However, a couple of
types of errors are showing up in the log whose significance I'd like to
understand.

I have attached the recon-all log, and there are snippets below. The two
types of error are:

1. mri_em_register: LINE SEARCH FAILED
---
I see that this has been reported to the list about a dozen times, and the
reply usually is that this message is seen occasionally for unknown reasons,
but it's not a concern. For me it pops up consistently for the bert sample
data, multiple times per run.

In case someone wants to investigate, or interpret the error message, I
found docs here:
http://www.dtcenter.org/com-GSI/users/docs/codeHTML/comGSIv2browser/html_co
de/subroutine/qnewton.f90.html

According to those docs, "INFO=3" means the function is complaining that it
didn't converge within a specified number of iterations. Which doesn't sound
desirable.

2. mris_sphere: distance error %10.0
--
An error of 100,000% sounds like a problem.  :-(

I'd appreciate hearing what the thinking is on these problems.

Thanks,

-- Graham

Subject bert2 recon-all.log

[Line 630 invoke]  mri_em_register -skull nu.mgz
/aaa_bin/freesurfer53c6/freesurfer/average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull.lta
...
[Line 746 error]  IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF
ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES:
FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof
QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.10
[Similar errors also at: ] 778, 1010, 1042, 2328, 2360

===
[Line 3135 invoke]  mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix
../surf/lh.qsphere.nofix
...
[Line 3232 error] distance error %10.00
[Similar error at:] 4927
===

#--

Started at Wed May 29 03:18:17 PDT 2013
Ended   at Wed May 29 09:18:38 PDT 2013
#@#%# recon-all-run-time-hours 6.006
recon-all -s bert2 finished without error at Wed May 29 09:18:38 PDT 2013
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Re: [Freesurfer] DEPRECATED warning in Freesurfers

[Christian Thode Larsen]

Hi,

While you're on the subject, there's a version 1.12 available from
http://packages.bic.mni.mcgill.ca/tgz/ (dated January 2011, Freesurfer
wraps and uses 1.10). I'm running tests with this version, and it also
produces the errors mentioned.

Best Regards,
Christian

On 06/03/2013 02:56 PM, Bruce Fischl wrote:
> Hi Peter
>
> I would try this:
>
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
> Bruce
> On Mon, 3 Jun 2013,
> Peter Wendorff wrote:
>
> Hi Brucel
> yes, sure - sorry.
> I followed your advice (your response to my first mail here), and found
> http://www.bic.mni.mcgill.ca/Research/Homepage which - if I'm not
> mistaken - is the MNI institute you pointed me to.
> As there's no John Sled listed on their website I wrote to Jennifer
> Chew, who is mentioned as general admnistrative questions or
> assistance, but I did not get an answer yet.
>
> I'll wait for a response further, but if there's any more direct
> contact, I would be happy to get an additional pointer ;)
>
> regards
> Peter
>
>
> Am 03.06.2013 14:29, schrieb Bruce Fischl:
> >>> Hi Peter,
> >>>
> >>> did you mean MNI when you said MRI? I think that they are still
> >>> maintaining it - I would be surprised otherwise Bruce On Mon, 3 Jun
> >>> 2013, Peter Wendorff wrote:
> >>>
> >>> Hi again.
> >>>
> >>> So: is the MRI stuff dead code? I wrote an email to Jennifer Chew
> >>> asking for the right contact for bugs/issues regarding that code.
> >>> That mail has been sent on May 22nd and I didn't get any response,
> >>> yet.
> >>>
> >>> Is that code ever updated by the freesurfer team? Or only if
> >>> there's anybody from MRI joining in by some kind of a pull request
> >>> (in git terms)? If the latter: Are pull requests accepted even by
> >>> other people than MRI stuff (e.g. by me, if I'm working out my
> >>> patch, which I haven't done yet)? How to apply that patch then?
> >>>
> >>> regards Peter
> >>>
> >>> Am 15.05.2013 16:18, schrieb Peter Wendorff:
> >> Hi Bruce.
> >>
> >> Thanks - kind of...
> >>
> >> Can you point me to anybody working on that stuff there
> >> currently? The cprresponding code is from 1996, and according
> >> to the MNI website, it's author John Sled isn't there any
> >> more.
> >>
> >> Who's the maintainer of these code parts in the freesurfer
> >> project? (Or isn't there anybody responsible?)
> >>
> >> Is there some kind of master repository/project for their
> >> code in Freesurfer (if the freesurfer project I hoped to
> >> address here isn't responsible for it)?
> >>
> >> If I were a pearl guru and know exactly what could and could
> >> not happen by this patch, I would probably ask for repository
> >> access, but I'm not, so any contact being responsible would
> >> be great.
> >>
> >> regards Peter
> >>
> >> Am 15.05.2013 15:04, schrieb Bruce Fischl:
> >>> thanks Peter,
> >>
> >>> that's actually MNI code, so you might want to report it
> >>> to them.
> >>
> >>> Bruce On Wed, 15 May 2013, Peter Wendorff wrote:
> >>
> >>> Hi.
> >>
> >>> I'm working with freesurfer as a software developer in a
> >>> cloud project. My task is to enable control of freesurfer
> >>> via network (e.g. REST interfaces).
> >>
> >>> That works fine so far, but I stumbled over the following
> >>> pearl deprecated warning:
> >>
> >>> "Use of ?PATTERN? without explicit operator is deprecated
> >>> at /usr/local/freesurfer//mni/bin/sharpen_volume line
> >>> 153."
> >>
> >>> Which has been printed to the log files repeatingly. I'm
> >>> not a pearl expert, but I think, it's due to a more up to
> >>> date pearl version used here, that deprecated the usage of
> >>> ? delimiters for patterns without explicit operator. Using
> >>> / as a delimiter works fine.
> >>
> >>> I changed that locally to (new line 153):
> >>
> >>> ($output_volume =~ /^([\S]+).mnc/) && ($base_name = $1) ||
> >>> die "sharpen_volume failed: output volume does not appear
> >>> to be" ." a minc volume.\n";
> >>
> >>> (the original code here was): ($output_volume =~
> >>> ?^([\S]+).mnc?) && ($base_name = $1) || die "sharpen_volume
> >>> failed: output volume does not appear to be" ." a minc
> >>> volume.\n";
> >>
> >>
> >>
> >>> I'm not sure this is the best solution. It's even not
> >>> strictly necessary to change this - it's only a warning
> >>> that's thrown; but I think, it's useful.
> >>
> >>> How can I submit this as a patch? Is it enough to report
> >>> here? What to do?
> >>
> >>> regards Peter Wendorff
> >>
> >>> P.S.: For referene the header parameters of my
> >>> sharpen_volume for revision comparison:
> >>
> >>>
> #
> >>>
> >>
> >>>
> >>
> >>
> >>>
> >

Re: [Freesurfer] DEPRECATED warning in Freesurfers

[Bruce Fischl]

Hi Peter

I would try this:

http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

Bruce
On Mon, 3 Jun 2013, 
Peter Wendorff wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Hi Brucel
> yes, sure - sorry.
> I followed your advice (your response to my first mail here), and found
> http://www.bic.mni.mcgill.ca/Research/Homepage which - if I'm not
> mistaken - is the MNI institute you pointed me to.
> As there's no John Sled listed on their website I wrote to Jennifer
> Chew, who is mentioned as general admnistrative questions or
> assistance, but I did not get an answer yet.
>
> I'll wait for a response further, but if there's any more direct
> contact, I would be happy to get an additional pointer ;)
>
> regards
> Peter
>
>
> Am 03.06.2013 14:29, schrieb Bruce Fischl:
>> Hi Peter,
>>
>> did you mean MNI when you said MRI? I think that they are still
>> maintaining it - I would be surprised otherwise Bruce On Mon, 3 Jun
>> 2013, Peter Wendorff wrote:
>>
>> Hi again.
>>
>> So: is the MRI stuff dead code? I wrote an email to Jennifer Chew
>> asking for the right contact for bugs/issues regarding that code.
>> That mail has been sent on May 22nd and I didn't get any response,
>> yet.
>>
>> Is that code ever updated by the freesurfer team? Or only if
>> there's anybody from MRI joining in by some kind of a pull request
>> (in git terms)? If the latter: Are pull requests accepted even by
>> other people than MRI stuff (e.g. by me, if I'm working out my
>> patch, which I haven't done yet)? How to apply that patch then?
>>
>> regards Peter
>>
>> Am 15.05.2013 16:18, schrieb Peter Wendorff:
> Hi Bruce.
>
> Thanks - kind of...
>
> Can you point me to anybody working on that stuff there
> currently? The cprresponding code is from 1996, and according
> to the MNI website, it's author John Sled isn't there any
> more.
>
> Who's the maintainer of these code parts in the freesurfer
> project? (Or isn't there anybody responsible?)
>
> Is there some kind of master repository/project for their
> code in Freesurfer (if the freesurfer project I hoped to
> address here isn't responsible for it)?
>
> If I were a pearl guru and know exactly what could and could
> not happen by this patch, I would probably ask for repository
> access, but I'm not, so any contact being responsible would
> be great.
>
> regards Peter
>
> Am 15.05.2013 15:04, schrieb Bruce Fischl:
>> thanks Peter,
>
>> that's actually MNI code, so you might want to report it
>> to them.
>
>> Bruce On Wed, 15 May 2013, Peter Wendorff wrote:
>
>> Hi.
>
>> I'm working with freesurfer as a software developer in a
>> cloud project. My task is to enable control of freesurfer
>> via network (e.g. REST interfaces).
>
>> That works fine so far, but I stumbled over the following
>> pearl deprecated warning:
>
>> "Use of ?PATTERN? without explicit operator is deprecated
>> at /usr/local/freesurfer//mni/bin/sharpen_volume line
>> 153."
>
>> Which has been printed to the log files repeatingly. I'm
>> not a pearl expert, but I think, it's due to a more up to
>> date pearl version used here, that deprecated the usage of
>> ? delimiters for patterns without explicit operator. Using
>> / as a delimiter works fine.
>
>> I changed that locally to (new line 153):
>
>> ($output_volume =~ /^([\S]+).mnc/) && ($base_name = $1) ||
>> die "sharpen_volume failed: output volume does not appear
>> to be" ." a minc volume.\n";
>
>> (the original code here was): ($output_volume =~
>> ?^([\S]+).mnc?) && ($base_name = $1) || die "sharpen_volume
>> failed: output volume does not appear to be" ." a minc
>> volume.\n";
>
>
>
>> I'm not sure this is the best solution. It's even not
>> strictly necessary to change this - it's only a warning
>> that's thrown; but I think, it's useful.
>
>> How can I submit this as a patch? Is it enough to report
>> here? What to do?
>
>> regards Peter Wendorff
>
>> P.S.: For referene the header parameters of my
>> sharpen_volume for revision comparison:
>
>> #
>>
>
>>
>
>
>>
>>
> #$RCSfile: sharpen_volume.in,v $ #$Revision: 1.1 $ #$Author:
>> bert $ #$Date: 2003/04/16 14:29:34 $ #$State: Exp $
>> #---
>>
>
>>
>>
> # -- MNI Header
>> -- #@NAME   :
>> sharpen_volume #@INPUT  : #@OUTPUT : #@RETURNS:
>> #@DESCRIPTION: modifies intensities so as to produce a
>> sharper histogram #@METHOD : #@GLOBALS: #@CALLS  :
>> #@CREATED: February 28, 1996 #@MODIFIED   :
>>

Re: [Freesurfer] DEPRECATED warning in Freesurfers

[Peter Wendorff]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Brucel
yes, sure - sorry.
I followed your advice (your response to my first mail here), and found
http://www.bic.mni.mcgill.ca/Research/Homepage which - if I'm not
mistaken - is the MNI institute you pointed me to.
As there's no John Sled listed on their website I wrote to Jennifer
Chew, who is mentioned as general admnistrative questions or
assistance, but I did not get an answer yet.

I'll wait for a response further, but if there's any more direct
contact, I would be happy to get an additional pointer ;)

regards
Peter


Am 03.06.2013 14:29, schrieb Bruce Fischl:
> Hi Peter,
> 
> did you mean MNI when you said MRI? I think that they are still 
> maintaining it - I would be surprised otherwise Bruce On Mon, 3 Jun
> 2013, Peter Wendorff wrote:
> 
> Hi again.
> 
> So: is the MRI stuff dead code? I wrote an email to Jennifer Chew
> asking for the right contact for bugs/issues regarding that code. 
> That mail has been sent on May 22nd and I didn't get any response,
> yet.
> 
> Is that code ever updated by the freesurfer team? Or only if
> there's anybody from MRI joining in by some kind of a pull request
> (in git terms)? If the latter: Are pull requests accepted even by
> other people than MRI stuff (e.g. by me, if I'm working out my
> patch, which I haven't done yet)? How to apply that patch then?
> 
> regards Peter
> 
> Am 15.05.2013 16:18, schrieb Peter Wendorff:
 Hi Bruce.
 
 Thanks - kind of...
 
 Can you point me to anybody working on that stuff there
 currently? The cprresponding code is from 1996, and according
 to the MNI website, it's author John Sled isn't there any
 more.
 
 Who's the maintainer of these code parts in the freesurfer 
 project? (Or isn't there anybody responsible?)
 
 Is there some kind of master repository/project for their
 code in Freesurfer (if the freesurfer project I hoped to
 address here isn't responsible for it)?
 
 If I were a pearl guru and know exactly what could and could
 not happen by this patch, I would probably ask for repository
 access, but I'm not, so any contact being responsible would
 be great.
 
 regards Peter
 
 Am 15.05.2013 15:04, schrieb Bruce Fischl:
> thanks Peter,
 
> that's actually MNI code, so you might want to report it
> to them.
 
> Bruce On Wed, 15 May 2013, Peter Wendorff wrote:
 
> Hi.
 
> I'm working with freesurfer as a software developer in a
> cloud project. My task is to enable control of freesurfer
> via network (e.g. REST interfaces).
 
> That works fine so far, but I stumbled over the following
> pearl deprecated warning:
 
> "Use of ?PATTERN? without explicit operator is deprecated
> at /usr/local/freesurfer//mni/bin/sharpen_volume line
> 153."
 
> Which has been printed to the log files repeatingly. I'm
> not a pearl expert, but I think, it's due to a more up to
> date pearl version used here, that deprecated the usage of
> ? delimiters for patterns without explicit operator. Using
> / as a delimiter works fine.
 
> I changed that locally to (new line 153):
 
> ($output_volume =~ /^([\S]+).mnc/) && ($base_name = $1) ||
> die "sharpen_volume failed: output volume does not appear
> to be" ." a minc volume.\n";
 
> (the original code here was): ($output_volume =~
> ?^([\S]+).mnc?) && ($base_name = $1) || die "sharpen_volume
> failed: output volume does not appear to be" ." a minc
> volume.\n";
 
 
 
> I'm not sure this is the best solution. It's even not
> strictly necessary to change this - it's only a warning
> that's thrown; but I think, it's useful.
 
> How can I submit this as a patch? Is it enough to report
> here? What to do?
 
> regards Peter Wendorff
 
> P.S.: For referene the header parameters of my
> sharpen_volume for revision comparison:
 
> #
>

>


>
> 
#$RCSfile: sharpen_volume.in,v $ #$Revision: 1.1 $ #$Author:
> bert $ #$Date: 2003/04/16 14:29:34 $ #$State: Exp $ 
> #---
>

>
> 
# -- MNI Header
> -- #@NAME   :
> sharpen_volume #@INPUT  : #@OUTPUT : #@RETURNS:
> #@DESCRIPTION: modifies intensities so as to produce a
> sharper histogram #@METHOD : #@GLOBALS: #@CALLS  :
> #@CREATED: February 28, 1996 #@MODIFIED   : 
> #-
>

>

>>
> 
___ Freesurfer
>> mailing list Freesurfer@nmr.mgh.harvard.edu 
>> https://mail.nmr.m

Re: [Freesurfer] mris_resample: Command not found.

[Lilla Zollei]

Hi Daniel,

All the information wrt memory and file naming conventions is described 
in:
mri_cvs_register --help

The final output file should be named final*norm.mgz

Lilla

On Mon, 3 Jun 2013, Barron, Daniel S wrote:

> Hi All,
>
> Was able to register 3 subjects to a common space with really great accuracy 
> (both of the overall volumes and of the aseg files).
>
> Note: cvs_register takes up quite a bit of RAM (how much exactly?) which 
> caused my desktop to slow and, essentially, crash.  Ended up running them on 
> the server.
>
> Question: While a description of the output is given on the wiki, I struggled 
> to tease out the details. Can I assume that el_reg_toXX.mgz is the final 
> output file?  I was somewhat confused because I assume "el" means elastic? I 
> am looking for the final registration file that incorporates both surfaces 
> and volumes.
>
> Again, thank you very much for the patch and for the excellent software.
>
> Cheers,
> Daniel
>
>
> On May 28, 2013, at 11:54 PM, Barron, Daniel S wrote:
>
>> Thanks for the path, Zeke.
>>
>> Because it didn't download as an executable file to my computer, I used 
>> "chmod +x ~/mris_resample" (FYI for others?)
>>
>> It looks to be running normally. Will report back when finished!
>>
>> Thanks again,
>> Daniel
>>
>>
>> On May 28, 2013, at 11:25 PM, 
>> wrote:
>>
>>> Daniel, Stefano, Others,
>>>
>>> A patch is now available for the "mris_resample : Command not found"
>>> error you encountered.
>>>
>>> Simply download the file from the following link and place it in your
>>> $FREESURFER_HOME/bin directory:
>>>
>>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample
>>>
>>> Feel free to contact me if you have any additional questions/issues.
>>>
>>> -Zeke
>>>
>>>
>>>  Original Message 
>>> Subject: Re: [Freesurfer] mris_resample: Command not found.
>>> Date: Tue, 28 May 2013 11:41:21 -0400
>>> From: Z K 
>>> To: Barron, Daniel S 
>>> CC: freesurfer@nmr.mgh.harvard.edu ,
>>>Lilla Zollei 
>>>
>>> Hello Daniel,
>>>
>>> This is a confirmed issue with the 64bit Mac build. A patch to fix the
>>> issue will be available shortly (~hours). I will email the list and you
>>> personally once it is available. Sorry for the inconvenience.
>>>
>>> -Zeke
>>>
>>> On 05/28/2013 11:36 AM, Barron, Daniel S wrote:
 Hi Lilla,
 I'm using OSX 10.8.3
 Thanks,
 Daniel
 
 From: Lilla Zollei [lzol...@nmr.mgh.harvard.edu]
 Sent: Tuesday, May 28, 2013 10:04 AM
 To: Barron, Daniel S
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: mris_resample: Command not found.
 Hi Daniel,
 What operating system are you using?
 Lilla
 On Tue, 28 May 2013, Barron, Daniel S wrote:
> Hello,
> I am trying to perform an inter-subject registration using
>>> mri_cvs_register on version 5.3.
> When I ran mri_cvs_check, my feedback was I needed to find
>>> "mri_cvs_register.settings.txt" but I didn't worry about this per
>>> Lilla's post:
>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html
> mri_cvs_register kicks off well, but eventually it ends with:
> "mris_resample: Command not found."
> I go into my $FREESURFER_HOME/bin directory and note that mris_resample
>>> is truly not there.  Did I not install 5.3 properly?
> I have attached a log file in case this helps.
> Cheers,
> Daniel
 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
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
>
>
>
>
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Re: [Freesurfer] autoreco3 error

[Bruce Fischl]

that usually means that the surfaces are inconsistent. Try running

recon-all -make all

instead. That should figure out what needs rebuilding and do so

cheers
Bruce



On Mon, 3 Jun 2013, LAOUCHEDI 
MAKHLOUF wrote:



Hi
   i run recon-all -autorecon3 on a normal subject and after a while, it
exited with errors, looking in the SUBJECTS_DIR/subj/scripts/error.log and
recon-all.error and recon-all.log i found the following messages :

error.log :

mrisReadTriangleFile(../surf/rh.smoothwm): surface doesn't match
../surf/rh.inflated

mrisReadTriangleFile failed.

MRISreadOriginalProperties: could not read surface file smoothwm

recon-all.error :
.
.
.
PWD /home_cluster/mlaouche/freesurf_makh/ctr5/scripts
CMD mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere

recon-all.log :

 mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere

setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
reading original vertex positions...
mrisReadTriangleFile(../surf/rh.smoothwm): surface doesn't match
../surf/rh.inflated

No such file or directory
mrisReadTriangleFile failed.

No such file or directory
MRISreadOriginalProperties: could not read surface file smoothwm
No such file or directory
Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s ctr5 exited with ERRORS at Mon Jun  3 11:38:58 CEST 2013

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

thank you for your help





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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.

Re: [Freesurfer] Volume acquisition

[Bruce Fischl]

Hi Elisa

usually we acquire sagitally as that is the shortest direction, but it 
shouldn't matter as long as your voxels are close to 1mm isotropic (just 
longer scans).

cheers
Bruce
On Mon, 
3 Jun 2013, elisa veronese wrote:

> Hi,
> I am a beginner in the use of Freesurfer. I was wondering if the T1w volume
> used as input for the recon-all has to be acquired in axial direction or
> not. In other words, is there a recommended acquisition direction?
> 
> Thank you,
> Elisa
> 
> --
> Elisa Veronese - PhD
> http://www.dei.unipd.it/~verones1/
> 
>
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] DEPRECATED warning in Freesurfers

[Bruce Fischl]

Hi Peter,

did you mean MNI when you said MRI? I think that they are still 
maintaining it - I would be surprised otherwise
Bruce
On Mon, 3 Jun 2013, Peter 
Wendorff wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Hi again.
>
> So: is the MRI stuff dead code?
> I wrote an email to Jennifer Chew asking for the right contact for
> bugs/issues regarding that code.
> That mail has been sent on May 22nd and I didn't get any response, yet.
>
> Is that code ever updated by the freesurfer team? Or only if there's
> anybody from MRI joining in by some kind of a pull request (in git terms)?
> If the latter: Are pull requests accepted even by other people than MRI
> stuff (e.g. by me, if I'm working out my patch, which I haven't done
> yet)? How to apply that patch then?
>
> regards
> Peter
>
> Am 15.05.2013 16:18, schrieb Peter Wendorff:
>> Hi Bruce.
>>
>> Thanks - kind of...
>>
>> Can you point me to anybody working on that stuff there currently?
>> The cprresponding code is from 1996, and according to the MNI
>> website, it's author John Sled isn't there any more.
>>
>> Who's the maintainer of these code parts in the freesurfer
>> project? (Or isn't there anybody responsible?)
>>
>> Is there some kind of master repository/project for their code in
>> Freesurfer (if the freesurfer project I hoped to address here
>> isn't responsible for it)?
>>
>> If I were a pearl guru and know exactly what could and could not
>> happen by this patch, I would probably ask for repository access,
>> but I'm not, so any contact being responsible would be great.
>>
>> regards Peter
>>
>> Am 15.05.2013 15:04, schrieb Bruce Fischl:
>>> thanks Peter,
>>
>>> that's actually MNI code, so you might want to report it to
>>> them.
>>
>>> Bruce On Wed, 15 May 2013, Peter Wendorff wrote:
>>
>>> Hi.
>>
>>> I'm working with freesurfer as a software developer in a cloud
>>> project. My task is to enable control of freesurfer via network
>>> (e.g. REST interfaces).
>>
>>> That works fine so far, but I stumbled over the following pearl
>>> deprecated warning:
>>
>>> "Use of ?PATTERN? without explicit operator is deprecated at
>>> /usr/local/freesurfer//mni/bin/sharpen_volume line 153."
>>
>>> Which has been printed to the log files repeatingly. I'm not a
>>> pearl expert, but I think, it's due to a more up to date pearl
>>> version used here, that deprecated the usage of ? delimiters for
>>> patterns without explicit operator. Using / as a delimiter works
>>> fine.
>>
>>> I changed that locally to (new line 153):
>>
>>> ($output_volume =~ /^([\S]+).mnc/) && ($base_name = $1) || die
>>> "sharpen_volume failed: output volume does not appear to be" ."
>>> a minc volume.\n";
>>
>>> (the original code here was): ($output_volume =~ ?^([\S]+).mnc?)
>>> && ($base_name = $1) || die "sharpen_volume failed: output volume
>>> does not appear to be" ." a minc volume.\n";
>>
>>
>>
>>> I'm not sure this is the best solution. It's even not strictly
>>> necessary to change this - it's only a warning that's thrown;
>>> but I think, it's useful.
>>
>>> How can I submit this as a patch? Is it enough to report here?
>>> What to do?
>>
>>> regards Peter Wendorff
>>
>>> P.S.: For referene the header parameters of my sharpen_volume for
>>>  revision comparison:
>>
>>> #
>>
>>>
>>
>>
>>> #$RCSfile: sharpen_volume.in,v $ #$Revision: 1.1 $ #$Author:
>>> bert $ #$Date: 2003/04/16 14:29:34 $ #$State: Exp $
>>> #---
>>
>>>  # -- MNI Header
>>> -- #@NAME   : sharpen_volume
>>>  #@INPUT  : #@OUTPUT : #@RETURNS: #@DESCRIPTION:
>>> modifies intensities so as to produce a sharper histogram
>>> #@METHOD : #@GLOBALS: #@CALLS  : #@CREATED: February
>>> 28, 1996 #@MODIFIED   :
>>> #-
>>
>>>
>>
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 mailing list 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
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>>
>
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Re: [Freesurfer] cortical thickness

[Bruce Fischl]

Hi Lucy

if you have a dicom series, you would run:

recon-all -s  -i  \
  -sd  -all

then wait 15 hours or so.
cheers
Bruce

On 
Mon, 3 Jun 2013, ?? wrote:

> Hi expert,
> If I want to get the cortical thickness,what will I do in the freesurfer?
> 
> 
> 
> 
> All suggestions welcome.
> Thanks in advance,
> Lucy
> 
>
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Re: [Freesurfer] mris_resample: Command not found.

[Barron, Daniel S]

Hi All,

Was able to register 3 subjects to a common space with really great accuracy 
(both of the overall volumes and of the aseg files).

Note: cvs_register takes up quite a bit of RAM (how much exactly?) which caused 
my desktop to slow and, essentially, crash.  Ended up running them on the 
server.

Question: While a description of the output is given on the wiki, I struggled 
to tease out the details. Can I assume that el_reg_toXX.mgz is the final output 
file?  I was somewhat confused because I assume "el" means elastic? I am 
looking for the final registration file that incorporates both surfaces and 
volumes. 

Again, thank you very much for the patch and for the excellent software.

Cheers,
Daniel


On May 28, 2013, at 11:54 PM, Barron, Daniel S wrote:

> Thanks for the path, Zeke. 
> 
> Because it didn't download as an executable file to my computer, I used 
> "chmod +x ~/mris_resample" (FYI for others?)
> 
> It looks to be running normally. Will report back when finished!
> 
> Thanks again,
> Daniel
> 
> 
> On May 28, 2013, at 11:25 PM, 
> wrote:
> 
>> Daniel, Stefano, Others,
>> 
>> A patch is now available for the "mris_resample : Command not found" 
>> error you encountered.
>> 
>> Simply download the file from the following link and place it in your
>> $FREESURFER_HOME/bin directory:
>> 
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample
>> 
>> Feel free to contact me if you have any additional questions/issues.
>> 
>> -Zeke
>> 
>> 
>>  Original Message 
>> Subject: Re: [Freesurfer] mris_resample: Command not found.
>> Date: Tue, 28 May 2013 11:41:21 -0400
>> From: Z K 
>> To: Barron, Daniel S 
>> CC: freesurfer@nmr.mgh.harvard.edu ,
>>Lilla Zollei 
>> 
>> Hello Daniel,
>> 
>> This is a confirmed issue with the 64bit Mac build. A patch to fix the
>> issue will be available shortly (~hours). I will email the list and you
>> personally once it is available. Sorry for the inconvenience.
>> 
>> -Zeke
>> 
>> On 05/28/2013 11:36 AM, Barron, Daniel S wrote:
>>> Hi Lilla,
>>> I'm using OSX 10.8.3
>>> Thanks,
>>> Daniel
>>> 
>>> From: Lilla Zollei [lzol...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, May 28, 2013 10:04 AM
>>> To: Barron, Daniel S
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: mris_resample: Command not found.
>>> Hi Daniel,
>>> What operating system are you using?
>>> Lilla
>>> On Tue, 28 May 2013, Barron, Daniel S wrote:
 Hello,
 I am trying to perform an inter-subject registration using
>> mri_cvs_register on version 5.3.
 When I ran mri_cvs_check, my feedback was I needed to find
>> "mri_cvs_register.settings.txt" but I didn't worry about this per
>> Lilla's post:
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.html
 mri_cvs_register kicks off well, but eventually it ends with:
 "mris_resample: Command not found."
 I go into my $FREESURFER_HOME/bin directory and note that mris_resample
>> is truly not there.  Did I not install 5.3 properly?
 I have attached a log file in case this helps.
 Cheers,
 Daniel
>>> 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
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
> 
> 
> ___
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> 



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[Freesurfer] autoreco3 error

[LAOUCHEDI MAKHLOUF]

Hi
   i run recon-all -autorecon3 on a normal subject and after a while, it exited 
with errors, looking in the SUBJECTS_DIR/subj/scripts/error.log and 
recon-all.error and recon-all.log i found the following messages :

error.log :

mrisReadTriangleFile(../surf/rh.smoothwm): surface doesn't match 
../surf/rh.inflated

mrisReadTriangleFile failed.

MRISreadOriginalProperties: could not read surface file smoothwm

recon-all.error :
.
.
.
PWD /home_cluster/mlaouche/freesurf_makh/ctr5/scripts
CMD mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere

recon-all.log :

 mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
reading original vertex positions...
mrisReadTriangleFile(../surf/rh.smoothwm): surface doesn't match 
../surf/rh.inflated

No such file or directory
mrisReadTriangleFile failed.

No such file or directory
MRISreadOriginalProperties: could not read surface file smoothwm
No such file or directory
Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 
x86_64 x86_64 GNU/Linux

recon-all -s ctr5 exited with ERRORS at Mon Jun  3 11:38:58 CEST 2013

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

thank you for your help




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[Freesurfer] use of anot_2_label

[LAOUCHEDI MAKHLOUF]

Hi
  i used  mri_annotation2label to extract the cortical labels. for this command 
we must specify which hemisphere (--hemi ?h) and i want to extract the 
brainstem which is not a lateralized structure, is there any command like 
mri_annotation2label to extract the brainstem ?

thanks
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[Freesurfer] cvs error

[Fernando Valle-Inclán]

Hi everyone,
 I´m trying to do cvs registration using freesurfer 5.3 and I get this
message:
"The following files are missing:
/Applications/freesurfer/bin/mri_cvs_register.settings.txt
You need to find these files or run reconall on the data in order to run
mri_cvs_register"

  Any idea would be wellcome

Thanks

Fernando
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[Freesurfer] Volume acquisition

[elisa veronese]

Hi,

I am a beginner in the use of Freesurfer. I was wondering if the T1w volume
used as input for the recon-all has to be acquired in axial direction or
not. In other words, is there a recommended acquisition direction?

Thank you,
Elisa

-- 
Elisa Veronese - PhD
http://www.dei.unipd.it/~verones1/
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Re: [Freesurfer] DEPRECATED warning in Freesurfers

[Peter Wendorff]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi again.

So: is the MRI stuff dead code?
I wrote an email to Jennifer Chew asking for the right contact for
bugs/issues regarding that code.
That mail has been sent on May 22nd and I didn't get any response, yet.

Is that code ever updated by the freesurfer team? Or only if there's
anybody from MRI joining in by some kind of a pull request (in git terms)?
If the latter: Are pull requests accepted even by other people than MRI
stuff (e.g. by me, if I'm working out my patch, which I haven't done
yet)? How to apply that patch then?

regards
Peter

Am 15.05.2013 16:18, schrieb Peter Wendorff:
> Hi Bruce.
> 
> Thanks - kind of...
> 
> Can you point me to anybody working on that stuff there currently? 
> The cprresponding code is from 1996, and according to the MNI
> website, it's author John Sled isn't there any more.
> 
> Who's the maintainer of these code parts in the freesurfer
> project? (Or isn't there anybody responsible?)
> 
> Is there some kind of master repository/project for their code in 
> Freesurfer (if the freesurfer project I hoped to address here
> isn't responsible for it)?
> 
> If I were a pearl guru and know exactly what could and could not 
> happen by this patch, I would probably ask for repository access,
> but I'm not, so any contact being responsible would be great.
> 
> regards Peter
> 
> Am 15.05.2013 15:04, schrieb Bruce Fischl:
>> thanks Peter,
> 
>> that's actually MNI code, so you might want to report it to
>> them.
> 
>> Bruce On Wed, 15 May 2013, Peter Wendorff wrote:
> 
>> Hi.
> 
>> I'm working with freesurfer as a software developer in a cloud 
>> project. My task is to enable control of freesurfer via network 
>> (e.g. REST interfaces).
> 
>> That works fine so far, but I stumbled over the following pearl 
>> deprecated warning:
> 
>> "Use of ?PATTERN? without explicit operator is deprecated at 
>> /usr/local/freesurfer//mni/bin/sharpen_volume line 153."
> 
>> Which has been printed to the log files repeatingly. I'm not a 
>> pearl expert, but I think, it's due to a more up to date pearl 
>> version used here, that deprecated the usage of ? delimiters for 
>> patterns without explicit operator. Using / as a delimiter works 
>> fine.
> 
>> I changed that locally to (new line 153):
> 
>> ($output_volume =~ /^([\S]+).mnc/) && ($base_name = $1) || die 
>> "sharpen_volume failed: output volume does not appear to be" ."
>> a minc volume.\n";
> 
>> (the original code here was): ($output_volume =~ ?^([\S]+).mnc?)
>> && ($base_name = $1) || die "sharpen_volume failed: output volume
>> does not appear to be" ." a minc volume.\n";
> 
> 
> 
>> I'm not sure this is the best solution. It's even not strictly 
>> necessary to change this - it's only a warning that's thrown;
>> but I think, it's useful.
> 
>> How can I submit this as a patch? Is it enough to report here?
>> What to do?
> 
>> regards Peter Wendorff
> 
>> P.S.: For referene the header parameters of my sharpen_volume for
>>  revision comparison:
> 
>> #
>
>> 
> 
> 
>> #$RCSfile: sharpen_volume.in,v $ #$Revision: 1.1 $ #$Author:
>> bert $ #$Date: 2003/04/16 14:29:34 $ #$State: Exp $ 
>> #---
>
>>  # -- MNI Header 
>> -- #@NAME   : sharpen_volume
>>  #@INPUT  : #@OUTPUT : #@RETURNS: #@DESCRIPTION: 
>> modifies intensities so as to produce a sharper histogram
>> #@METHOD : #@GLOBALS: #@CALLS  : #@CREATED: February
>> 28, 1996 #@MODIFIED   : 
>> #-
>
>> 
> 
>>> ___ Freesurfer 
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>>> 
> 
> 
>> The information in this e-mail is intended only for the person
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>> 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.
> 
> 
> 
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[Freesurfer] cortical thickness

[??????]

Hi expert,
If I want to get the cortical thickness,what will I do in the freesurfer?








All suggestions welcome.
Thanks in advance,
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