Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Anderson Winkler]

Hi Pedro,

Have a look at this article: 
http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours
I think this is the same you'd like to do (or you can change some steps 
easily).

Hope it helps!

All the best,

Anderson


On 05/07/12 20:44, Pedro Paulo de Magalhães Oliveira Junior wrote:

Doug,

I did

mri_annotation2label --subject bert --hemi lh --outdir 
$SUBJECTS_DIR/bert/label
mri_annotation2label --subject bert --hemi rh --outdir 
$SUBJECTS_DIR/bert/label


And then

mris_label2annot --s bert --hemi lh --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt --l lh.bankssts.label --l 
lh.caudalmiddlefrontal.label --l lh.entorhinal.label --l 
lh.paracentral.label --l lh.parstriangularis.label --l 
lh.postcentral.label --l lh.superiorfrontal.label --l 
lh.frontalpole.label --l lh.temporalpole.label --a myannot


and

mris_label2annot --s bert --hemi rh 
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --l rh.bankssts.label 
--l rh.isthmuscingulate.label --l rh.medialorbitofrontal.label --l 
rh.parstriangularis.label --l rh.rostralanteriorcingulate.label --l 
rh.superiorparietal.label --l rh.frontalpole.label --a myannot


If this is the right procedure I guess I'll have to modify the 
existing annot in matlab because all the surface is being labelled as 
Unknown.


Thanks

PPJ


On Thu, Jul 5, 2012 at 4:01 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


You can also break up the annot into labels (
mri_annotation2label) then
recombine them with a new color table with mris_label2annot.
doug

On 07/05/2012 02:57 PM, Bruce Fischl wrote:
> Hi PPJ,
>
> I think the color lut is embedded in the aparc.annot. If you want to
> change it you have to change the one that's in the .annot. I
would do
> it in matlab.
>
> cheers
> Bruce
>
> On Thu, 5 Jul 2012, Pedro Paulo de Magalhães Oliveira Junior wrote:
>
>> I'm trying to generate an image to a paper and I have to colorize
>> some areas of the cortex with specific
>> colors.
>> I have edited the FreeSurferColorLUT.txt changing the following
lines:
>> 1001 ctx-lh-bankssts 255 42 0 0
>> 1003 ctx-lh-caudalmiddlefrontal 255 14 0 0
>> 1006 ctx-lh-entorhinal 255 17 0 0
>> 1017 ctx-lh-paracentral 255 43 0 0
>> 1020 ctx-lh-parstriangularis 255 15 0 0
>> 1022 ctx-lh-postcentral 255 14 0 0
>> 1028 ctx-lh-superiorfrontal 255 79 0 0
>> 1032 ctx-lh-frontalpole 255 17 0 0
>> 1033 ctx-lh-temporalpole 255 14 0 0
>> 2001 ctx-rh-bankssts 255 18 0 0
>> 2010 ctx-rh-isthmuscingulate 255 39 0 0
>> 2014 ctx-rh-medialorbitofrontal 255 60 0 0
>> 2020 ctx-rh-parstriangularis 255 13 0 0
>> 2026 ctx-rh-rostralanteriorcingulate 255 40 0 0
>> 2029 ctx-rh-superiorparietal 255 48 0 0
>> 2032 ctx-rh-frontalpole 255 106 0 0
>>
>> all other regions are 127 127 127 0
>>
>> When I load the surface for some case with:
>> tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt
>>
>> I get the usual coloring scheme with the labels correct. TkSurfer
>> seems to be ignoring
>> FreeSurferColorLUT.txt, but the labels are placed in the right
spots.
>>
>> When I try to manually force the FreeSurferColorLUT.txt I'm
>> visualizing an all grey image. And the surface is
>> completely mislabeled, there is a 4th ventricle in the surface,
>> putamen in the surface, etc.
>>
>> What am I doing wrong?
>>
-
>> Pedro Paulo de Magalhães Oliveira Junior
>> Netfilter & SpeedComm Telecom-- www.netfilter.com.br

>> -- For mobile:
http://itunes.apple.com/br/artist/netfilter/id365306441
>>
>>
>>
>>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu

> 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

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


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[Freesurfer] overlapping labels

[David Grayson]

Hi freesurfers,

Can a .annot file include labels with overlapping vertices? If not, then when 
using mris_label2annot, how does freesurfer decide which label to assign the 
vertices to?

Thanks,

David
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Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Douglas N Greve]

Hi Pedro Paulo, it is not quite the right procedure, but I'm surprised 
that it gave unknown for all labels. Try
modifying the colortable.txt such that the first entry is the name and 
color for your first label, etc.
doug

On 07/05/2012 03:44 PM, Pedro Paulo de Magalhães Oliveira Junior wrote:
> Doug,
>
> I did
>
> mri_annotation2label --subject bert --hemi lh --outdir 
> $SUBJECTS_DIR/bert/label
> mri_annotation2label --subject bert --hemi rh --outdir 
> $SUBJECTS_DIR/bert/label
>
> And then
>
> mris_label2annot --s bert --hemi lh --ctab 
> $FREESURFER_HOME/FreeSurferColorLUT.txt --l lh.bankssts.label --l 
> lh.caudalmiddlefrontal.label --l lh.entorhinal.label --l 
> lh.paracentral.label --l lh.parstriangularis.label --l 
> lh.postcentral.label --l lh.superiorfrontal.label --l 
> lh.frontalpole.label --l lh.temporalpole.label --a myannot
>
> and
>
> mris_label2annot --s bert --hemi rh 
> --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --l rh.bankssts.label 
> --l rh.isthmuscingulate.label --l rh.medialorbitofrontal.label --l 
> rh.parstriangularis.label --l rh.rostralanteriorcingulate.label --l 
> rh.superiorparietal.label --l rh.frontalpole.label --a myannot
>
> If this is the right procedure I guess I'll have to modify the 
> existing annot in matlab because all the surface is being labelled as 
> Unknown.
>
> Thanks
>
> PPJ
>
>
> On Thu, Jul 5, 2012 at 4:01 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> You can also break up the annot into labels (
> mri_annotation2label) then
> recombine them with a new color table with mris_label2annot.
> doug
>
> On 07/05/2012 02:57 PM, Bruce Fischl wrote:
> > Hi PPJ,
> >
> > I think the color lut is embedded in the aparc.annot. If you want to
> > change it you have to change the one that's in the .annot. I
> would do
> > it in matlab.
> >
> > cheers
> > Bruce
> >
> > On Thu, 5 Jul 2012, Pedro Paulo de Magalhães Oliveira Junior wrote:
> >
> >> I'm trying to generate an image to a paper and I have to colorize
> >> some areas of the cortex with specific
> >> colors.
> >> I have edited the FreeSurferColorLUT.txt changing the following
> lines:
> >> 1001 ctx-lh-bankssts 255 42 0 0
> >> 1003 ctx-lh-caudalmiddlefrontal 255 14 0 0
> >> 1006 ctx-lh-entorhinal 255 17 0 0
> >> 1017 ctx-lh-paracentral 255 43 0 0
> >> 1020 ctx-lh-parstriangularis 255 15 0 0
> >> 1022 ctx-lh-postcentral 255 14 0 0
> >> 1028 ctx-lh-superiorfrontal 255 79 0 0
> >> 1032 ctx-lh-frontalpole 255 17 0 0
> >> 1033 ctx-lh-temporalpole 255 14 0 0
> >> 2001 ctx-rh-bankssts 255 18 0 0
> >> 2010 ctx-rh-isthmuscingulate 255 39 0 0
> >> 2014 ctx-rh-medialorbitofrontal 255 60 0 0
> >> 2020 ctx-rh-parstriangularis 255 13 0 0
> >> 2026 ctx-rh-rostralanteriorcingulate 255 40 0 0
> >> 2029 ctx-rh-superiorparietal 255 48 0 0
> >> 2032 ctx-rh-frontalpole 255 106 0 0
> >>
> >> all other regions are 127 127 127 0
> >>
> >> When I load the surface for some case with:
> >> tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt
> >>
> >> I get the usual coloring scheme with the labels correct. TkSurfer
> >> seems to be ignoring
> >> FreeSurferColorLUT.txt, but the labels are placed in the right
> spots.
> >>
> >> When I try to manually force the FreeSurferColorLUT.txt I'm
> >> visualizing an all grey image. And the surface is
> >> completely mislabeled, there is a 4th ventricle in the surface,
> >> putamen in the surface, etc.
> >>
> >> What am I doing wrong?
> >>
> -
> >> Pedro Paulo de Magalhães Oliveira Junior
> >> Netfilter & SpeedComm Telecom-- www.netfilter.com.br
> 
> >> -- For mobile:
> http://itunes.apple.com/br/artist/netfilter/id365306441
> >>
> >>
> >>
> >>
> >
> >
> > ___
> > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intende

Re: [Freesurfer] Image resolution and reliability of freesurfer measurements

[Bruce Fischl]

Hi Carolina

I don't know anyone who has ever tried. It will depend a lot on the CNR 
of the data

Bruce
On Thu, 5 Jul 2012, carolina.mr wrote:

> Hello,
> I would like to know if it is possible to process T1 images with a slice
> tickness of 5mm / 0.5mm of gap in freesurfer and obtain reliable cortical
> tickness measurements and parcelations?
> Thank you,
> Carolina Rimkus
> 
>
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[Freesurfer] Image resolution and reliability of freesurfer measurements

[carolina.mr]

Hello,

I would like to know if it is possible to process T1 images with a slice tickness of 5mm / 0.5mm of gap in freesurfer and obtain reliable cortical tickness measurements and parcelations?

Thank you,
Carolina Rimkus
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Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Pedro Paulo de Magalhães Oliveira Junior]

Doug,

I did

mri_annotation2label --subject bert --hemi lh --outdir
$SUBJECTS_DIR/bert/label
mri_annotation2label --subject bert --hemi rh --outdir $SUBJECTS_DIR
/bert/label

And then

mris_label2annot --s bert --hemi lh --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --l lh.bankssts.label --l
lh.caudalmiddlefrontal.label --l lh.entorhinal.label --l
lh.paracentral.label --l lh.parstriangularis.label --l lh.postcentral.label
--l lh.superiorfrontal.label --l lh.frontalpole.label --l
lh.temporalpole.label --a myannot

and

mris_label2annot --s bert --hemi rh
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --l rh.bankssts.label --l
rh.isthmuscingulate.label --l rh.medialorbitofrontal.label --l
rh.parstriangularis.label --l rh.rostralanteriorcingulate.label --l
rh.superiorparietal.label --l rh.frontalpole.label --a myannot

If this is the right procedure I guess I'll have to modify the existing
annot in matlab because all the surface is being labelled as Unknown.

Thanks

PPJ


On Thu, Jul 5, 2012 at 4:01 PM, Douglas N Greve
wrote:

> You can also break up the annot into labels ( mri_annotation2label) then
> recombine them with a new color table with mris_label2annot.
> doug
>
> On 07/05/2012 02:57 PM, Bruce Fischl wrote:
> > Hi PPJ,
> >
> > I think the color lut is embedded in the aparc.annot. If you want to
> > change it you have to change the one that's in the .annot. I would do
> > it in matlab.
> >
> > cheers
> > Bruce
> >
> > On Thu, 5 Jul 2012, Pedro Paulo de Magalhães Oliveira Junior wrote:
> >
> >> I'm trying to generate an image to a paper and I have to colorize
> >> some areas of the cortex with specific
> >> colors.
> >> I have edited the FreeSurferColorLUT.txt changing the following lines:
> >> 1001 ctx-lh-bankssts 255 42 0 0
> >> 1003 ctx-lh-caudalmiddlefrontal 255 14 0 0
> >> 1006 ctx-lh-entorhinal 255 17 0 0
> >> 1017 ctx-lh-paracentral 255 43 0 0
> >> 1020 ctx-lh-parstriangularis 255 15 0 0
> >> 1022 ctx-lh-postcentral 255 14 0 0
> >> 1028 ctx-lh-superiorfrontal 255 79 0 0
> >> 1032 ctx-lh-frontalpole 255 17 0 0
> >> 1033 ctx-lh-temporalpole 255 14 0 0
> >> 2001 ctx-rh-bankssts 255 18 0 0
> >> 2010 ctx-rh-isthmuscingulate 255 39 0 0
> >> 2014 ctx-rh-medialorbitofrontal 255 60 0 0
> >> 2020 ctx-rh-parstriangularis 255 13 0 0
> >> 2026 ctx-rh-rostralanteriorcingulate 255 40 0 0
> >> 2029 ctx-rh-superiorparietal 255 48 0 0
> >> 2032 ctx-rh-frontalpole 255 106 0 0
> >>
> >> all other regions are 127 127 127 0
> >>
> >> When I load the surface for some case with:
> >> tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt
> >>
> >> I get the usual coloring scheme with the labels correct. TkSurfer
> >> seems to be ignoring
> >> FreeSurferColorLUT.txt, but the labels are placed in the right spots.
> >>
> >> When I try to manually force the FreeSurferColorLUT.txt I'm
> >> visualizing an all grey image. And the surface is
> >> completely mislabeled, there is a 4th ventricle in the surface,
> >> putamen in the surface, etc.
> >>
> >> What am I doing wrong?
> >> -
> >> Pedro Paulo de Magalhães Oliveira Junior
> >> Netfilter & SpeedComm Telecom-- www.netfilter.com.br
> >> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
> >>
> >>
> >>
> >>
> >
> >
> > ___
> > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
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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
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Douglas N Greve]

You can also break up the annot into labels ( mri_annotation2label) then 
recombine them with a new color table with mris_label2annot.
doug

On 07/05/2012 02:57 PM, Bruce Fischl wrote:
> Hi PPJ,
>
> I think the color lut is embedded in the aparc.annot. If you want to 
> change it you have to change the one that's in the .annot. I would do 
> it in matlab.
>
> cheers
> Bruce
>
> On Thu, 5 Jul 2012, Pedro Paulo de Magalhães Oliveira Junior wrote:
>
>> I'm trying to generate an image to a paper and I have to colorize 
>> some areas of the cortex with specific
>> colors.
>> I have edited the FreeSurferColorLUT.txt changing the following lines:
>> 1001 ctx-lh-bankssts 255 42 0 0
>> 1003 ctx-lh-caudalmiddlefrontal 255 14 0 0
>> 1006 ctx-lh-entorhinal 255 17 0 0
>> 1017 ctx-lh-paracentral 255 43 0 0
>> 1020 ctx-lh-parstriangularis 255 15 0 0
>> 1022 ctx-lh-postcentral 255 14 0 0
>> 1028 ctx-lh-superiorfrontal 255 79 0 0
>> 1032 ctx-lh-frontalpole 255 17 0 0
>> 1033 ctx-lh-temporalpole 255 14 0 0
>> 2001 ctx-rh-bankssts 255 18 0 0
>> 2010 ctx-rh-isthmuscingulate 255 39 0 0
>> 2014 ctx-rh-medialorbitofrontal 255 60 0 0
>> 2020 ctx-rh-parstriangularis 255 13 0 0
>> 2026 ctx-rh-rostralanteriorcingulate 255 40 0 0
>> 2029 ctx-rh-superiorparietal 255 48 0 0
>> 2032 ctx-rh-frontalpole 255 106 0 0
>>
>> all other regions are 127 127 127 0
>>
>> When I load the surface for some case with:
>> tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt
>>
>> I get the usual coloring scheme with the labels correct. TkSurfer 
>> seems to be ignoring
>> FreeSurferColorLUT.txt, but the labels are placed in the right spots.
>>
>> When I try to manually force the FreeSurferColorLUT.txt I'm 
>> visualizing an all grey image. And the surface is
>> completely mislabeled, there is a 4th ventricle in the surface, 
>> putamen in the surface, etc.
>>
>> What am I doing wrong?
>> -
>> Pedro Paulo de Magalhães Oliveira Junior
>> Netfilter & SpeedComm Telecom-- www.netfilter.com.br
>> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>>
>>
>>
>>
>
>
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] TkSurfer and new color table. Mislabelling

[Bruce Fischl]

Hi PPJ,

I think the color lut is embedded in the aparc.annot. If you want to 
change it you have to change the one that's in the .annot. I would do it in 
matlab.


cheers
Bruce

On Thu, 5 Jul 2012, Pedro Paulo de Magalhães Oliveira 
Junior wrote:



I'm trying to generate an image to a paper and I have to colorize some areas of 
the cortex with specific
colors.
I have edited the FreeSurferColorLUT.txt changing the following lines:
1001 ctx-lh-bankssts 255 42 0 0
1003 ctx-lh-caudalmiddlefrontal 255 14 0 0
1006 ctx-lh-entorhinal 255 17 0 0
1017 ctx-lh-paracentral 255 43 0 0
1020 ctx-lh-parstriangularis 255 15 0 0
1022 ctx-lh-postcentral 255 14 0 0
1028 ctx-lh-superiorfrontal 255 79 0 0
1032 ctx-lh-frontalpole 255 17 0 0
1033 ctx-lh-temporalpole 255 14 0 0
2001 ctx-rh-bankssts 255 18 0 0
2010 ctx-rh-isthmuscingulate 255 39 0 0
2014 ctx-rh-medialorbitofrontal 255 60 0 0
2020 ctx-rh-parstriangularis 255 13 0 0
2026 ctx-rh-rostralanteriorcingulate 255 40 0 0
2029 ctx-rh-superiorparietal 255 48 0 0
2032 ctx-rh-frontalpole 255 106 0 0

all other regions are 127 127 127 0

When I load the surface for some case with:
tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt

I get the usual coloring scheme with the labels correct. TkSurfer seems to be 
ignoring
FreeSurferColorLUT.txt, but the labels are placed in the right spots.

When I try to manually force the FreeSurferColorLUT.txt I'm visualizing an all 
grey image. And the surface is
completely mislabeled, there is a 4th ventricle in the surface, putamen in the 
surface, etc.

What am I doing wrong?
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



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[Freesurfer] TkSurfer and new color table. Mislabelling

[Pedro Paulo de Magalhães Oliveira Junior]

I'm trying to generate an image to a paper and I have to colorize some
areas of the cortex with specific colors.

I have edited the FreeSurferColorLUT.txt changing the following lines:
1001 ctx-lh-bankssts 255 42 0 0
1003 ctx-lh-caudalmiddlefrontal 255 14 0 0
1006 ctx-lh-entorhinal 255 17 0 0
1017 ctx-lh-paracentral 255 43 0 0
1020 ctx-lh-parstriangularis 255 15 0 0
1022 ctx-lh-postcentral 255 14 0 0
1028 ctx-lh-superiorfrontal 255 79 0 0
1032 ctx-lh-frontalpole 255 17 0 0
1033 ctx-lh-temporalpole 255 14 0 0
2001 ctx-rh-bankssts 255 18 0 0
2010 ctx-rh-isthmuscingulate 255 39 0 0
2014 ctx-rh-medialorbitofrontal 255 60 0 0
2020 ctx-rh-parstriangularis 255 13 0 0
2026 ctx-rh-rostralanteriorcingulate 255 40 0 0
2029 ctx-rh-superiorparietal 255 48 0 0
2032 ctx-rh-frontalpole 255 106 0 0

all other regions are 127 127 127 0

When I load the surface for some case with:
tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt

I get the usual coloring scheme with the labels correct. TkSurfer seems to
be ignoring FreeSurferColorLUT.txt, but the labels are placed in the right
spots.

When I try to manually force the FreeSurferColorLUT.txt I'm visualizing an
all grey image. And the surface is completely mislabeled, there is a 4th
ventricle in the surface, putamen in the surface, etc.

What am I doing wrong?
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
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Re: [Freesurfer] multiple correction

[Douglas N Greve]

Hi Meng, if you are doing whole hemisphere correction, it will used 
already computed values which should only take a few seconds to run.
doug

On 07/05/2012 11:03 AM, Meng Li wrote:
>
> Hi, all,
>
> I have some questions about the multiple correction in qdec.
>
> I performed group analysis using qdec. There are 5 factors in the 
> qdec.table.dat file: 1 discrete, 4 continuous variables (covariates). 
> When I tried to perform the multiple correction, Whether I can choose 
> one of two ways (the fdr and monte carlo null-z simulation) only. And 
> if I use monte carlo null-z simulation, I have to pre-run 
> mri_glmfit-sim 1?
>
> Thanks,
>
> Meng
>
>
>
> --
>
> ++
>
> Meng Li
> major：Developmental and educational psychology
> South China Normal University
> Zhongshan Avenue West 55, Tianhe District
> Guangzhou 510631
> P. R. China
> Tel: +86 (0)13824486409
>
> ++
> 李盟
> 华南师范大学
> 发展与教育心理学专业
> 地址：
> 广东省 广州市 天河区 中山大道 西55号
> 邮编：510631
> 电话： 13824486409 (手机, 广州)
> +
>
>
>
>
>
>
> ___
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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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[Freesurfer] multiple correction

[Meng Li]

Hi, all,

I have some questions about the multiple correction in qdec.

I performed group analysis using qdec. There are 5 factors in the 
qdec.table.dat file: 1 discrete, 4 continuous variables (covariates). When I 
tried to perform the multiple correction, Whether I can choose one of two ways 
(the fdr and monte carlo null-z simulation) only. And if I use monte carlo 
null-z simulation, I have to pre-run mri_glmfit-sim 1?

Thanks,

Meng

 





--


++

Meng Li
major：Developmental and educational psychology
South China Normal University
Zhongshan Avenue West 55, Tianhe District
Guangzhou 510631
P. R. China
Tel: +86 (0)13824486409

++
李盟
华南师范大学
发展与教育心理学专业
 地址：
广东省 广州市 天河区 中山大道 西55号
邮编：510631
电话： 13824486409 (手机, 广州)
+


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Re: [Freesurfer] Parallel vs. Sequential part

[R Edgar]

On Tue, Jul 3, 2012 at 5:56 PM, Akio Yamamoto
 wrote:

> Yes, as Richard pointed out, I just wanted to know the numbers for input
> to Amdahl's law, if you have already something, to figure out the maximum
> expected speedup using multiple processors/cores.
>
> As for improvements of em_reg, I'll try to split each transform as well as
> parallelize the energy evaluation.

Parallelising the energy evaluation is the lowest hanging fruit, and
is what happens in the 'slow' GPU version. But for highest
performance, I would convert the nested transform loops into a single
one, and farm those out between OpenMP threads (I wouldn't bother
trying nested parallelism of the energy evaluation, although you might
want to do some SSE tinkering). That is effectively what happens in
the 'fast' GPU version - you can use the same basic structure. But be
aware that the slightly different transforms which result can cause
you to converge to a different solution.

HTH,

Richard
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Re: [Freesurfer] label transformation to MNI space

[Anders Hougaard]

Of course, you are right...It fits perfectly now. Thank you so much!

Best,
Anders

2012/7/4 Douglas Greve 

>  Where did rh.v1.probl.label come from? The way you call mri_label2vol, it
> should be in fsaverage space. If it is in an individual space, then the
> registration is wrong. Try running mni152reg to create a registration from
> the individual to mni152, then use that reg instead.
> doug
>
>
> On 7/4/12 5:32 AM, Anders Hougaard wrote:
>
> Dear Doug,
>
>
>  I have problem similar to this:
> I am trying to convert V1 labels from the Hinds method to volumes and
> transform them to MNI152 space for use in FSL.
> I tried using this command:
> mri_label2vol --label rh.v1.prob.label --reg
> $FREESURFER_HOME/average/mni152.register.dat --temp MNI152_T1_2mm.nii.gz
> --o rh_v1_prob.nii.gz --label-stat rh_v1_prob_stat.nii.gz
>
> ...but the output is not registered correctly. It seems to be shift
> downward as Linda described.
>
>  Label conversion using the cmd
> mri_label2label --srclabel rh.v1.prob.label --s 
> --regmethod surface --trglabel rh.v1.prob.new.label --hemi rh
> does not solve it.
>
>  Any suggestions?
>
>  Best regards,
> Anders Hougaard
>
>
>
> 2011/10/18 Douglas N Greve 
>
> The problem appears to be with the label itself. Try this conversion:
>
> mri_label2label --srclabel lh.entorhinal.label --s fsaverage --regmethod
> surface --trglabel lh.entorhinal.new.label --hemi lh
>
> Also, you might want to use the entorhinal label define in the
> aparc+aseg since it fills in the ribbon:
> mri_binarize --i aparc+aseg.mgz --match 1006 --o lh_entorhinal.nii.gz
> 1006 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt
>
> doug
>
>
>
>
> Linda Douw wrote:
> > Hi Doug,
> > Thanks for the reply. This cmd makes it slightly better I guess, but
> still
> > definetely off target. It seems to be shift downward, towards inferior,
> > and therefore sometimes outside the skull. Any other ideas?
> > Linda
> >
> >
> >> The way the reg is set up, the targ is your mask. Try this cmd:
> >> mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz
> >> --o lh_entorhinal_MNI.nii.gz --reg
> >> $FREESURFER_HOME/average/mni152.register.dat --inv
> >>
> >> doug
> >>
> >> Linda Douw wrote:
> >>
> >>> Hi all,
> >>>
> >>> I am trying to transform some labels from the aparc to masks in MNI
> >>> space.
> >>> Ideally, I would like to do this for each subject in my study
> >>> individually
> >>> (using their own rawavg.mgz and labels), but for now I started out with
> >>> fsaverage. I first converted the label file into a nifti:
> >>>
> >>> mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject
> >>> fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz
> >>> --identity
> >>>
> >>> And then put the nifti file containing the label into MNI space:
> >>>
> >>> mri_vol2vol --mov lh_entorhinal.nii.gz --targ
> MNI152_T1_2mm.brain.nii.gz
> >>> --o lh_entorhinal_MNI.nii.gz --reg
> >>> $FREESURFER_HOME/average/mni152.register.dat
> >>>
> >>> But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is
> >>> completely wrong. I checked the location with tkregister as well:
> >>>
> >>> tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg
> >>> /$FREESURFER_HOME/average/mni152.register.dat
> >>>
> >>> But here the entorhinal was also in the wrong place.
> >>>
> >>> Do you know how to fix this?
> >>>
> >>> Thanks,
> >>>
> >>>
> >> --
> >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >>
> >>
> >>
> >>
> >
> >
> >
>
> --
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
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Re: [Freesurfer] Hippocampal segmentation doubts

[Gabriel Gonzalez Escamilla]

Thank you so much for your answer Koen,I understand, but now I'm having some trouble when running the command on one subject, hope you can help me.I have tried to perform the hippocampal subfields segmentation by running:recon-all -s MySubject -hippo-subfields and also:kvlSegmentHippocampalSubfields.sh MySubject left /root/trabajo/freesurfer/subjects /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults 
But I always get the following error:maximalDeformation: 75.1793Transforming meshDone transforming meshRasterizing Levenberg-Marquardt...numberOfEntries: 24131/root/trabajo/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 23175 Segmentation fault      kvlSegmentWithoutGUI configurationFileDeformableRegistration.txtfailed to do kvlSegmentWithoutGUI configurationFileDeformableRegistration.txtLinux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s MySubject exited with ERRORS at Tue Jul  3 15:54:39 CEST 2012For more details, see the log file /root/trabajo/freesurfer/subjects/MySubject/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportingThe recon-all.log says:##@# Hippocampal Subfields processing Tue Jul  3 15:48:33 CEST 2012 mkdir -p /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults kvlSegmentHippocampalSubfields.sh MySubject left /root/trabajo/freesurfer/subjects /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s MySubject exited with ERRORS at Tue Jul  3 15:54:39 CEST 2012To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting This error occurres only on this subject and for the left hemisphere, not like this for the right hemisphere, which ends perfectly when running the second command. I'm sending you the configurationFileDeformation for the left hemisphere, in case it may help. Any help will be so appreciatedBest Regards,GabrielEl 04/07/12, Koen Van Leemput   escribió:Hi Gabriel,1. Using pre-processed data obtained with an older version ofFreeSurfer should be OK, as long as you remember that the obtainedresults might/will be different from the ones you'd get if you had runthe whole analysis from scratch.2. The generic label "hippocampus" is used to denote the tail of thehippocampus, where no attempt is made to further subdivide between thedifferent subfields. This is admittedly not a great naming convention- sorry for the confusion.3. You should not do any correction on the obtained volumes: "partialvolume" here merely means the effect of voxels containing a mix ofdifferent subfields simultaneously. The "non-partial volume" resultshere only indicate that this effect is not explicitly modeled when youcall the hippocampal subfield segmentation routine with its defaultsettings.Hope this helps,KoenOn Thu, Jun 28, 2012 at 5:29 AM, Gabriel Gonzalez Escamilla wrote:>> Dear Freesurfer experts>> I'm starting to deal with the FS v5.1 hippocampal subfields segmentation,> and I have a couple doubts...>> If I have my subjects segmented from an older FS version, Would be any> problem when running the -hippo-subfields?> I'm guessing not, but I wanna be sure. Because, as I've looked the> -hippo-subfields recon seems to not modify the whole brain segmentation, am> I right?>> second, when I apply the "kvlQuantifyHippocampalSubfieldSegmentations.sh" I> do obtain two txt files containing such segmentation of the 8 hippocampal> subfields, but at the beggining it appear a field for the left and right> hippocampus, but I don't know exactly what does this column represents,> because if I sum the other colums the subfield sums are so much bigger than> the hippocampus field; i.e.> volume_in_number_of_voxels   Left-Hippocampus   left_presubiculum   left_CA1> left_CA2-3   left_fimbria   left_subiculum   left_CA4-DG> left_hippocampal_fissure> c_12_hipo    3789.97    3215.08    2654.65    7705.2    336.857    4841.63> 4158.49    356.626>>> and last. Do I need to somehow do some partial volume corrections to this> output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw> on the page that the output is "0.5*0.5*0.5mm^3".>>> Many thanks in advanced,> Gabriel>> --> --> PhD. student Gabriel González-Escamilla> Laboratory of Functional Neuroscience> Department of Physiology, Anatomy, and Cell Biology> University Pablo de Olavide> Ctra. de Utrera, Km.1> 41013 - Seville> - Spain ->> Email: ggon...@upo.es> http://www.upo.es/neuroaging/es/>> ___> 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>