Re: [Freesurfer] Hippocampal segmentation doubts

2012-07-05 Thread 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  k...@nmr.mgh.harvard.edu 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 Escamillaggon...@upo.es 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 e-mail contains patient 

Re: [Freesurfer] Parallel vs. Sequential part

2012-07-05 Thread R Edgar
On Tue, Jul 3, 2012 at 5:56 PM, Akio Yamamoto
yamam...@tkl.iis.u-tokyo.ac.jp 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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[Freesurfer] multiple correction

2012-07-05 Thread 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] multiple correction

2012-07-05 Thread 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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[Freesurfer] TkSurfer and new color table. Mislabelling

2012-07-05 Thread 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] TkSurfer and new color table. Mislabelling

2012-07-05 Thread 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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Re: [Freesurfer] TkSurfer and new color table. Mislabelling

2012-07-05 Thread 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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Fax: 617-726-7422

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

2012-07-05 Thread 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
gr...@nmr.mgh.harvard.eduwrote:

 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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 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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 e-mail
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[Freesurfer] Image resolution and reliability of freesurfer measurements

2012-07-05 Thread 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] Image resolution and reliability of freesurfer measurements

2012-07-05 Thread 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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Re: [Freesurfer] TkSurfer and new color table. Mislabelling

2012-07-05 Thread 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 
 gr...@nmr.mgh.harvard.edu 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
 http://www.netfilter.com.br
  -- For mobile:
 http://itunes.apple.com/br/artist/netfilter/id365306441
 
 
 
 
 
 
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 tel:617-724-2358
 Fax: 617-726-7422 tel:617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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 the e-mail
 contains patient information, please contact the Partners
  

[Freesurfer] overlapping labels

2012-07-05 Thread 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

2012-07-05 Thread 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 
gr...@nmr.mgh.harvard.edu 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
http://www.netfilter.com.br
 -- For mobile:
http://itunes.apple.com/br/artist/netfilter/id365306441






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

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

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