date:20111025

Re: [Freesurfer] Segmentation error?

2011-10-25 Thread Gergely Orsi

Dear Bruce and others,

We have just ran into strange ICV volumes.

For all our 100+ subjets, the total icv is around 1500cm3  (around
1300-1700).

For the new group (only 7 subjects) the average ICV is around 1200  (ranging
from 900-1500).

This is almost microcephalia, but they are normal.

If we take a look at the brainseg volume or brain mask volumes they are
larger than the total ICV (for e.g. subject 5 has brainmaskvol: 1440;
brainseg vol: 1021; ICV 1036)

This is not right. It's kind'a strange that someone has bigger brain than
skull :)

I was using freesurfer 4.5 for both groups.

Do you have any idea what did I miss?

Thanks,

Gergo

2011/10/3 Bruce Fischl 

> The stuff outside the pial surface won't affect things, which is one of the
> reasons we prefer the surface-based measured of cortical morphometry.
>
> Similarly, we don't use the surface-based stuff in the hippocampus, so you
> should be all set (since many of the cortical assumptions aren't valid
> there)
>
> cheers
> Bruce
>
>
>
> On Mon, 3 Oct 2011, Gergely Orsi wrote:
>
>  Dear Freesurfers!!
>>
>> I've encountered two strange segmentation "errors", if they are errors at
>> all.
>>
>>
>>
>> Please see the attached fs.png:
>>
>> You can see that there are excess pial tissues on the superior part of the
>> brain. The pial surface is
>> defined correctly and the excess pial tissue is outside the red line yet
>> it
>> is coloured pink. My question, is :
>>
>> Does this have any impact on the results?
>>
>>
>> The second is related to the hippocampus.
>>
>> Please see the attached fs2.png:
>>
>> The pial surface around the hippocampus looks a bit weird.
>> It actually discards 1/3 of the hippocampus (it is outside the red line).
>>
>> Do you have any suggestions regarding the two problems.
>>
>> I'm using FS 4.5 on several 64bit linux distributions.
>>
>>
>> --
>> Gergely Orsi
>> biologist - research associate
>> Diagnostic Center of Pécs
>> H-7623 Pécs, Rét str. 2.
>> Tel.: 0036-70-3174676
>> E-mail: gergo.o...@gmail.com
>>
>>
>>
>
> 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.
>

-- 
Gergely Orsi
biologist - research associate
Diagnostic Center of Pécs
H-7623 Pécs, Rét str. 2.
Tel.: 0036-70-3174676
E-mail: gergo.o...@gmail.com
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[Freesurfer] Diffusion tensor estimation method

2011-10-25 Thread Ed Gronenschild

Hi,

There are various methods to estimate the diffusion tensor, like
linear-least squares, non-linear least-squares, German-McClure
M-estimator.
I would like to know which method is used by FreeSurfer in
the dt_recon command?

Cheers,
Ed

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[Freesurfer] Question on mris_pmake

2011-10-25 Thread Jungwon Ryu

Hi,

 

I'm trying to get distances on a cortical surface between sets of voxels in
visual areas and I have two questions;

 

1) I have the following error message so often;

 

===

System error: Address already in use

 

Fatal error encountered.

   SSocket `Unnamed SSocket_UDP_receive' (id: 0)

   Current function: c_SSocket_UDP_receive::c_SSocket_UDP_receive

   Problem binding to socket 1701

Error returned from system: Address already in use

Throwing exception to (this) with code 1

 

terminate called after throwing an instance of 'c_SSocket*'

runSh_Ori_1_02_01.sh: line 5789: 93334 Abort trap  mris_pmake
--subject JR20110819 --hemi rh --surface0 white --curv0 sulc --curv1 sulc
--mpmOverlay euclidean --mpmProg pathFind --mpmArgs
startVertex:907,endVertex:731 >> result_Ori_1_02_01.txt

 

===

 

I have around 10,000 voxel pairs to run mris_pmake( ) command. Since I have
to call mris_pmake( ) so many times (one pair by one pair), I splitted the
whole list of voxel pairs into four script files, containing many mris_pmake
commands with 2,500 voxel pairs as arguments, then I ran scripts with four
terminal windows saparately to parallelize the processing. All script files
are located in the same diretory. Then I had the message as above. What
might be the problem? (It seems as if multiple terminal instances share the
socket port number)

 

2) How can I get interhemispheric distances between visual areas across
hemispheres?

 

Ryu

 

PhD student

Department of Brain and Cognitive Sciences,

Seoul National University, Korea

 

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Re: [Freesurfer] CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line 92 : invalid texture reference

2011-10-25 Thread R Edgar

On Mon, Oct 24, 2011 at 9:28 PM, Hemant Bokil  wrote:

> Thanks for the response. Does this mean that I should use CUDA 3.2 ? There
> was some discussion on the group recently about Freesurfer not working with
> CUDA 4 and one suggestion made was to switch to CUDA 3.2. Thanks,

Probably. NVIDIA always like to claim full backwards compatibility,
but I've never been fully convinced.

Richard
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Re: [Freesurfer] Segmentation error?

2011-10-25 Thread Bruce Fischl


can you send us an example of one that is way off?
On Tue, 25 Oct 2011, 
Gergely Orsi wrote:



Dear Bruce and others,

We have just ran into strange ICV volumes.

For all our 100+ subjets, the total icv is around 1500cm3  (around 1300-1700).

For the new group (only 7 subjects) the average ICV is around 1200  (ranging 
from 900-1500).

This is almost microcephalia, but they are normal.

If we take a look at the brainseg volume or brain mask volumes they are larger 
than the total ICV (for e.g. subject 5 has brainmaskvol: 1440; brainseg
vol: 1021; ICV 1036)

This is not right. It's kind'a strange that someone has bigger brain than skull 
:)

I was using freesurfer 4.5 for both groups.


Do you have any idea what did I miss?

Thanks,

Gergo







2011/10/3 Bruce Fischl 
  The stuff outside the pial surface won't affect things, which is one of 
the reasons we prefer the surface-based measured of cortical
  morphometry.

  Similarly, we don't use the surface-based stuff in the hippocampus, so 
you should be all set (since many of the cortical assumptions aren't
  valid there)

  cheers
  Bruce



On Mon, 3 Oct 2011, Gergely Orsi wrote:

  Dear Freesurfers!!

  I've encountered two strange segmentation "errors", if they are errors at
  all.



  Please see the attached fs.png:

  You can see that there are excess pial tissues on the superior part of the
  brain. The pial surface is
  defined correctly and the excess pial tissue is outside the red line yet 
it
  is coloured pink. My question, is :

  Does this have any impact on the results?


  The second is related to the hippocampus.

  Please see the attached fs2.png:

  The pial surface around the hippocampus looks a bit weird.
  It actually discards 1/3 of the hippocampus (it is outside the red line).

  Do you have any suggestions regarding the two problems.

  I'm using FS 4.5 on several 64bit linux distributions.


  --
  Gergely Orsi
  biologist - research associate
  Diagnostic Center of Pécs
  H-7623 Pécs, Rét str. 2.
  Tel.: 0036-70-3174676
  E-mail: gergo.o...@gmail.com




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.




--
Gergely Orsi
biologist - research associate
Diagnostic Center of Pécs
H-7623 Pécs, Rét str. 2.
Tel.: 0036-70-3174676
E-mail: gergo.o...@gmail.com

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Re: [Freesurfer] Segmentation error?

2011-10-25 Thread Gergely Orsi

Here you are:

# Title Segmentation Statistics
#
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp $
# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask
mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --subject SZEMAN2 --surf-wm-vol --ctab
/home/kutato/freesurfer/ASegStatsLUT.txt
# sysname  Linux
# hostname kutato16
# machine  x86_64
# user kutato16
# anatomy_type volume
#
# SUBJECTS_DIR /home/kutato/freesurfer/subjects
# subjectname SZEMAN2
# BrainMaskFile  mri/brainmask.mgz
# BrainMaskFileTimeStamp  2011/09/30 14:48:41
# Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1460346,
unitless
# Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1460346.00, mm^3
# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume
Without Ventricles, 964476.00, mm^3
# Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels,
986721, unitless
# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 986721.00,
mm^3
# Measure IntraCranialVol, ICV, Intracranial Volume, 900902.902900, mm^3
# SegVolFile mri/aseg.mgz
# SegVolFileTimeStamp  2011/09/30 21:17:55
# ColorTable /home/kutato/freesurfer/ASegStatsLUT.txt
# ColorTableTimeStamp 2009/08/11 14:24:37
# InVolFile  mri/norm.mgz
# InVolFileTimeStamp  2011/09/30 15:23:28
# InVolFrame 0
# PVVolFile  mri/norm.mgz
# PVVolFileTimeStamp  2011/09/30 15:23:28
# surface-based-volume mm3 lh-cerebral-white-matter 199672.312500
# surface-based-volume mm3 rh-cerebral-white-matter 200666.875000
# surface-based-volume mm3 tot-cerebral-white-matter 400339.187500
# ExcludeSegId 0
# VoxelVolume_mm3 1
# TableCol  1 ColHeader Index
# TableCol  1 FieldName Index
# TableCol  1 Units NA
# TableCol  2 ColHeader SegId
# TableCol  2 FieldName Segmentation Id
# TableCol  2 Units NA
# TableCol  3 ColHeader NVoxels
# TableCol  3 FieldName Number of Voxels
# TableCol  3 Units unitless
# TableCol  4 ColHeader Volume_mm3
# TableCol  4 FieldName Volume
# TableCol  4 Units mm^3
# TableCol  5 ColHeader StructName
# TableCol  5 FieldName Structure Name
# TableCol  5 Units NA
# TableCol  6 ColHeader normMean
# TableCol  6 FieldName Intensity normMean
# TableCol  6 Units MR
# TableCol  7 ColHeader normStdDev
# TableCol  7 FieldName Itensity normStdDev
# TableCol  7 Units MR
# TableCol  8 ColHeader normMin
# TableCol  8 FieldName Intensity normMin
# TableCol  8 Units MR
# TableCol  9 ColHeader normMax
# TableCol  9 FieldName Intensity normMax
# TableCol  9 Units MR
# TableCol 10 ColHeader normRange
# TableCol 10 FieldName Intensity normRange
# TableCol 10 Units MR
# NRows 49
# NTableCols 10
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev
normMin normMax normRange
  1   2181224   181224.0  Left-Cerebral-White-Matter   103.0824
7.827337.   124.87.
  2   3220289   220289.0  Left-Cerebral-Cortex  73.9965
10.054725.   109.84.
  3   4  9827 9827.0  Left-Lateral-Ventricle38.7152
10.831121.89.68.
  4   5   472  472.0  Left-Inf-Lat-Vent 58.1272
10.072936.97.61.
  5   7 1186611866.0  Left-Cerebellum-White-Matter  85.2734
7.639641.   110.69.
  6   8 2966929669.0  Left-Cerebellum-Cortex62.3768
10.679417.94.77.
  7  10  6422 6422.0  Left-Thalamus-Proper  97.5967
8.182554.   114.60.
  8  11  3645 3645.0  Left-Caudate  86.3108
8.235652.   110.58.
  9  12  5670 5670.0  Left-Putamen  93.1821
5.743062.   111.49.
 10  13  1860 1860.0  Left-Pallidum105.5083
3.892085.   116.31.
 11  14  1023 1023.0  3rd-Ventricle 46.9565
12.755528.78.50.
 12  15  1027 1027.0  4th-Ventricle 34.1996
12.367211.73.62.
 13  16 1208112081.0  Brain-Stem91.9390
11.856744.   113.69.
 14  17  2538 2538.0  Left-Hippocampus  80.2219
8.167129.   109.80.
 15  18   952  952.0  Left-Amygdala 80.3787
7.140455.   105.50.
 16  24  1785 1785.0  CSF   57.1199
13.185029.95.66.
 17  26   592  592.0  Left-Accumbens-area   84.8315
5.736460.   104.44.
 18  28  3806 3806.0  Left-VentralDC   101.0622
9.684851.   115.64.
 19  30   190  190.0  Left-vessel   71.0

Re: [Freesurfer] Segmentation error?

2011-10-25 Thread Bruce Fischl


I meant canyou tar and gzip the subject and ftp it to us
On Tue, 25 Oct 
2011, Gergely Orsi wrote:



Here you are:

# Title Segmentation Statistics
#
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp $
# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask
mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --subject SZEMAN2 --surf-wm-vol --ctab
/home/kutato/freesurfer/ASegStatsLUT.txt
# sysname  Linux
# hostname kutato16
# machine  x86_64
# user kutato16
# anatomy_type volume
#
# SUBJECTS_DIR /home/kutato/freesurfer/subjects
# subjectname SZEMAN2
# BrainMaskFile  mri/brainmask.mgz
# BrainMaskFileTimeStamp  2011/09/30 14:48:41
# Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1460346,
unitless
# Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1460346.00, mm^3
# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume
Without Ventricles, 964476.00, mm^3
# Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 
986721, unitless
# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 986721.00,
mm^3
# Measure IntraCranialVol, ICV, Intracranial Volume, 900902.902900, mm^3
# SegVolFile mri/aseg.mgz
# SegVolFileTimeStamp  2011/09/30 21:17:55
# ColorTable /home/kutato/freesurfer/ASegStatsLUT.txt
# ColorTableTimeStamp 2009/08/11 14:24:37
# InVolFile  mri/norm.mgz
# InVolFileTimeStamp  2011/09/30 15:23:28
# InVolFrame 0
# PVVolFile  mri/norm.mgz
# PVVolFileTimeStamp  2011/09/30 15:23:28
# surface-based-volume mm3 lh-cerebral-white-matter 199672.312500
# surface-based-volume mm3 rh-cerebral-white-matter 200666.875000
# surface-based-volume mm3 tot-cerebral-white-matter 400339.187500
# ExcludeSegId 0
# VoxelVolume_mm3 1
# TableCol  1 ColHeader Index
# TableCol  1 FieldName Index
# TableCol  1 Units NA
# TableCol  2 ColHeader SegId
# TableCol  2 FieldName Segmentation Id
# TableCol  2 Units NA
# TableCol  3 ColHeader NVoxels
# TableCol  3 FieldName Number of Voxels
# TableCol  3 Units unitless
# TableCol  4 ColHeader Volume_mm3
# TableCol  4 FieldName Volume
# TableCol  4 Units mm^3
# TableCol  5 ColHeader StructName
# TableCol  5 FieldName Structure Name
# TableCol  5 Units NA
# TableCol  6 ColHeader normMean
# TableCol  6 FieldName Intensity normMean
# TableCol  6 Units MR
# TableCol  7 ColHeader normStdDev
# TableCol  7 FieldName Itensity normStdDev
# TableCol  7 Units MR
# TableCol  8 ColHeader normMin
# TableCol  8 FieldName Intensity normMin
# TableCol  8 Units MR
# TableCol  9 ColHeader normMax
# TableCol  9 FieldName Intensity normMax
# TableCol  9 Units MR
# TableCol 10 ColHeader normRange
# TableCol 10 FieldName Intensity normRange
# TableCol 10 Units MR
# NRows 49
# NTableCols 10
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev
normMin normMax normRange 
  1   2    181224   181224.0  Left-Cerebral-White-Matter   103.0824
7.8273    37.   124.    87.
  2   3    220289   220289.0  Left-Cerebral-Cortex  73.9965   
10.0547    25.   109.    84.
  3   4  9827 9827.0  Left-Lateral-Ventricle    38.7152   
10.8311    21.    89.    68.
  4   5   472  472.0  Left-Inf-Lat-Vent 58.1272   
10.0729    36.    97.    61.
  5   7 11866    11866.0  Left-Cerebellum-White-Matter  85.2734
7.6396    41.   110.    69.
  6   8 29669    29669.0  Left-Cerebellum-Cortex    62.3768   
10.6794    17.    94.    77.
  7  10  6422 6422.0  Left-Thalamus-Proper  97.5967
8.1825    54.   114.    60.
  8  11  3645 3645.0  Left-Caudate  86.3108
8.2356    52.   110.    58.
  9  12  5670 5670.0  Left-Putamen  93.1821
5.7430    62.   111.    49.
 10  13  1860 1860.0  Left-Pallidum    105.5083
3.8920    85.   116.    31.
 11  14  1023 1023.0  3rd-Ventricle 46.9565   
12.7555    28.    78.    50.
 12  15  1027 1027.0  4th-Ventricle 34.1996   
12.3672    11.    73.    62.
 13  16 12081    12081.0  Brain-Stem    91.9390   
11.8567    44.   113.    69.
 14  17  2538 2538.0  Left-Hippocampus  80.2219
8.1671    29.   109.    80.
 15  18   952  952.0  Left-Amygdala 80.3787
7.1404    55.   105.    50.
 16  24  1785 1785.0  CSF   57.1199   
13.1850    29.    95.    66.
 17  26   592  592.0  Left-Accumbens-area   84.8315
5.7364    60.   104.    44.
 18  28  38

Re: [Freesurfer] Segmentation error?

2011-10-25 Thread Gergely Orsi

Yes of course, just a minute.

2011/10/25 Bruce Fischl 

> I meant canyou tar and gzip the subject and ftp it to us
>
> On Tue, 25 Oct 2011, Gergely Orsi wrote:
>
>  Here you are:
>>
>> # Title Segmentation Statistics
>> #
>> # generating_program mri_segstats
>> # cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp
>> $
>> # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
>> mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask
>> mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm
>> --in-intensity-units MR --etiv --subject SZEMAN2 --surf-wm-vol --ctab
>> /home/kutato/freesurfer/**ASegStatsLUT.txt
>> # sysname  Linux
>> # hostname kutato16
>> # machine  x86_64
>> # user kutato16
>> # anatomy_type volume
>> #
>> # SUBJECTS_DIR /home/kutato/freesurfer/**subjects
>> # subjectname SZEMAN2
>> # BrainMaskFile  mri/brainmask.mgz
>> # BrainMaskFileTimeStamp  2011/09/30 14:48:41
>> # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1460346,
>> unitless
>> # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1460346.00, mm^3
>> # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume
>> Without Ventricles, 964476.00, mm^3
>> # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels,
>> 986721, unitless
>> # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 986721.00,
>> mm^3
>> # Measure IntraCranialVol, ICV, Intracranial Volume, 900902.902900, mm^3
>> # SegVolFile mri/aseg.mgz
>> # SegVolFileTimeStamp  2011/09/30 21:17:55
>> # ColorTable /home/kutato/freesurfer/**ASegStatsLUT.txt
>> # ColorTableTimeStamp 2009/08/11 14:24:37
>> # InVolFile  mri/norm.mgz
>> # InVolFileTimeStamp  2011/09/30 15:23:28
>> # InVolFrame 0
>> # PVVolFile  mri/norm.mgz
>> # PVVolFileTimeStamp  2011/09/30 15:23:28
>> # surface-based-volume mm3 lh-cerebral-white-matter 199672.312500
>> # surface-based-volume mm3 rh-cerebral-white-matter 200666.875000
>> # surface-based-volume mm3 tot-cerebral-white-matter 400339.187500
>> # ExcludeSegId 0
>> # VoxelVolume_mm3 1
>> # TableCol  1 ColHeader Index
>> # TableCol  1 FieldName Index
>> # TableCol  1 Units NA
>> # TableCol  2 ColHeader SegId
>> # TableCol  2 FieldName Segmentation Id
>> # TableCol  2 Units NA
>> # TableCol  3 ColHeader NVoxels
>> # TableCol  3 FieldName Number of Voxels
>> # TableCol  3 Units unitless
>> # TableCol  4 ColHeader Volume_mm3
>> # TableCol  4 FieldName Volume
>> # TableCol  4 Units mm^3
>> # TableCol  5 ColHeader StructName
>> # TableCol  5 FieldName Structure Name
>> # TableCol  5 Units NA
>> # TableCol  6 ColHeader normMean
>> # TableCol  6 FieldName Intensity normMean
>> # TableCol  6 Units MR
>> # TableCol  7 ColHeader normStdDev
>> # TableCol  7 FieldName Itensity normStdDev
>> # TableCol  7 Units MR
>> # TableCol  8 ColHeader normMin
>> # TableCol  8 FieldName Intensity normMin
>> # TableCol  8 Units MR
>> # TableCol  9 ColHeader normMax
>> # TableCol  9 FieldName Intensity normMax
>> # TableCol  9 Units MR
>> # TableCol 10 ColHeader normRange
>> # TableCol 10 FieldName Intensity normRange
>> # TableCol 10 Units MR
>> # NRows 49
>> # NTableCols 10
>> # ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean
>> normStdDev
>> normMin normMax normRange
>>   1   2181224   181224.0  Left-Cerebral-White-Matter**
>> 103.0824
>> 7.827337.   124.87.
>>   2   3220289   220289.0  Left-Cerebral-Cortex  **
>> 73.9965
>> 10.054725.   109.84.
>>   3   4  9827 9827.0  Left-Lateral-Ventricle**
>> 38.7152
>> 10.831121.89.68.
>>   4   5   472  472.0  Left-Inf-Lat-Vent **
>> 58.1272
>> 10.072936.97.61.
>>   5   7 1186611866.0  Left-Cerebellum-White-Matter  **
>> 85.2734
>> 7.639641.   110.69.
>>   6   8 2966929669.0  Left-Cerebellum-Cortex**
>> 62.3768
>> 10.679417.94.77.
>>   7  10  6422 6422.0  Left-Thalamus-Proper  **
>> 97.5967
>> 8.182554.   114.60.
>>   8  11  3645 3645.0  Left-Caudate  **
>> 86.3108
>> 8.235652.   110.58.
>>   9  12  5670 5670.0  Left-Putamen  **
>> 93.1821
>> 5.743062.   111.49.
>>  10  13  1860 1860.0  Left-Pallidum **
>> 105.5083
>> 3.892085.   116.31.
>>  11  14  1023 1023.0  3rd-Ventricle **
>> 46.9565
>> 12.755528.78.50.
>>  12  15  1027 1027.0  4th-Ventricle **
>> 34.1996
>> 12.367211.73.62.
>>  13  16 1208112081.0  Brain-Stem**
>> 91.9390
>> 11.856744.   113.69.
>>  14  17  2538 2538.0  Left-Hippocampus  **
>> 80.2219
>> 8.167129.   109.

Re: [Freesurfer] Segmentation error?

2011-10-25 Thread Gergely Orsi

SZEMAN2.tar.gz have just been uploaded.

Thank you

Gergo

2011/10/25 Gergely Orsi 

> Yes of course, just a minute.
>
>
> 2011/10/25 Bruce Fischl 
>
>> I meant canyou tar and gzip the subject and ftp it to us
>>
>> On Tue, 25 Oct 2011, Gergely Orsi wrote:
>>
>>  Here you are:
>>>
>>> # Title Segmentation Statistics
>>> #
>>> # generating_program mri_segstats
>>> # cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks
>>> Exp $
>>> # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
>>> mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask
>>> mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm
>>> --in-intensity-units MR --etiv --subject SZEMAN2 --surf-wm-vol --ctab
>>> /home/kutato/freesurfer/**ASegStatsLUT.txt
>>> # sysname  Linux
>>> # hostname kutato16
>>> # machine  x86_64
>>> # user kutato16
>>> # anatomy_type volume
>>> #
>>> # SUBJECTS_DIR /home/kutato/freesurfer/**subjects
>>> # subjectname SZEMAN2
>>> # BrainMaskFile  mri/brainmask.mgz
>>> # BrainMaskFileTimeStamp  2011/09/30 14:48:41
>>> # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1460346,
>>> unitless
>>> # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1460346.00,
>>> mm^3
>>> # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume
>>> Without Ventricles, 964476.00, mm^3
>>> # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels,
>>> 986721, unitless
>>> # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume,
>>> 986721.00,
>>> mm^3
>>> # Measure IntraCranialVol, ICV, Intracranial Volume, 900902.902900, mm^3
>>> # SegVolFile mri/aseg.mgz
>>> # SegVolFileTimeStamp  2011/09/30 21:17:55
>>> # ColorTable /home/kutato/freesurfer/**ASegStatsLUT.txt
>>> # ColorTableTimeStamp 2009/08/11 14:24:37
>>> # InVolFile  mri/norm.mgz
>>> # InVolFileTimeStamp  2011/09/30 15:23:28
>>> # InVolFrame 0
>>> # PVVolFile  mri/norm.mgz
>>> # PVVolFileTimeStamp  2011/09/30 15:23:28
>>> # surface-based-volume mm3 lh-cerebral-white-matter 199672.312500
>>> # surface-based-volume mm3 rh-cerebral-white-matter 200666.875000
>>> # surface-based-volume mm3 tot-cerebral-white-matter 400339.187500
>>> # ExcludeSegId 0
>>> # VoxelVolume_mm3 1
>>> # TableCol  1 ColHeader Index
>>> # TableCol  1 FieldName Index
>>> # TableCol  1 Units NA
>>> # TableCol  2 ColHeader SegId
>>> # TableCol  2 FieldName Segmentation Id
>>> # TableCol  2 Units NA
>>> # TableCol  3 ColHeader NVoxels
>>> # TableCol  3 FieldName Number of Voxels
>>> # TableCol  3 Units unitless
>>> # TableCol  4 ColHeader Volume_mm3
>>> # TableCol  4 FieldName Volume
>>> # TableCol  4 Units mm^3
>>> # TableCol  5 ColHeader StructName
>>> # TableCol  5 FieldName Structure Name
>>> # TableCol  5 Units NA
>>> # TableCol  6 ColHeader normMean
>>> # TableCol  6 FieldName Intensity normMean
>>> # TableCol  6 Units MR
>>> # TableCol  7 ColHeader normStdDev
>>> # TableCol  7 FieldName Itensity normStdDev
>>> # TableCol  7 Units MR
>>> # TableCol  8 ColHeader normMin
>>> # TableCol  8 FieldName Intensity normMin
>>> # TableCol  8 Units MR
>>> # TableCol  9 ColHeader normMax
>>> # TableCol  9 FieldName Intensity normMax
>>> # TableCol  9 Units MR
>>> # TableCol 10 ColHeader normRange
>>> # TableCol 10 FieldName Intensity normRange
>>> # TableCol 10 Units MR
>>> # NRows 49
>>> # NTableCols 10
>>> # ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean
>>> normStdDev
>>> normMin normMax normRange
>>>   1   2181224   181224.0  Left-Cerebral-White-Matter**
>>> 103.0824
>>> 7.827337.   124.87.
>>>   2   3220289   220289.0  Left-Cerebral-Cortex  **
>>> 73.9965
>>> 10.054725.   109.84.
>>>   3   4  9827 9827.0  Left-Lateral-Ventricle**
>>> 38.7152
>>> 10.831121.89.68.
>>>   4   5   472  472.0  Left-Inf-Lat-Vent **
>>> 58.1272
>>> 10.072936.97.61.
>>>   5   7 1186611866.0  Left-Cerebellum-White-Matter  **
>>> 85.2734
>>> 7.639641.   110.69.
>>>   6   8 2966929669.0  Left-Cerebellum-Cortex**
>>> 62.3768
>>> 10.679417.94.77.
>>>   7  10  6422 6422.0  Left-Thalamus-Proper  **
>>> 97.5967
>>> 8.182554.   114.60.
>>>   8  11  3645 3645.0  Left-Caudate  **
>>> 86.3108
>>> 8.235652.   110.58.
>>>   9  12  5670 5670.0  Left-Putamen  **
>>> 93.1821
>>> 5.743062.   111.49.
>>>  10  13  1860 1860.0  Left-Pallidum **
>>> 105.5083
>>> 3.892085.   116.31.
>>>  11  14  1023 1023.0  3rd-Ventricle **
>>> 46.9565
>>> 12.755528.78.50.
>>>  12  15  1027 1027.0  4th-Ventricle **
>>> 34.1996
>>> 12.367211.73.62.
>>>  13  16

Re: [Freesurfer] Segmentation error?

2011-10-25 Thread Bruce Fischl

I think your acquisition is cutting off some cerebellum, and in any case 
has a very steep intensity drop off in the cerebellum and brainstem. Is it 
slab selective in that direction? You might try increasing the size of the 
slab or lengthening your slab-select pulse, or including some oversampling 
in that direction.


On Tue, 25 Oct 2011, Gergely Orsi wrote:


SZEMAN2.tar.gz have just been uploaded.

Thank you

Gergo

2011/10/25 Gergely Orsi 
  Yes of course, just a minute.


2011/10/25 Bruce Fischl 
  I meant canyou tar and gzip the subject and ftp it to us

On Tue, 25 Oct 2011, Gergely Orsi wrote:

  Here you are:

  # Title Segmentation Statistics
  #
  # generating_program mri_segstats
  # cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks 
Exp $
  # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
  mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask
  mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm
  --in-intensity-units MR --etiv --subject SZEMAN2 --surf-wm-vol --ctab
  /home/kutato/freesurfer/ASegStatsLUT.txt
  # sysname  Linux
  # hostname kutato16
  # machine  x86_64
  # user kutato16
  # anatomy_type volume
  #
  # SUBJECTS_DIR /home/kutato/freesurfer/subjects
  # subjectname SZEMAN2
  # BrainMaskFile  mri/brainmask.mgz
  # BrainMaskFileTimeStamp  2011/09/30 14:48:41
  # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1460346,
  unitless
  # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1460346.00, mm^3
  # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume
  Without Ventricles, 964476.00, mm^3
  # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 
  986721, unitless
  # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 986721.00,
  mm^3
  # Measure IntraCranialVol, ICV, Intracranial Volume, 900902.902900, mm^3
  # SegVolFile mri/aseg.mgz
  # SegVolFileTimeStamp  2011/09/30 21:17:55
  # ColorTable /home/kutato/freesurfer/ASegStatsLUT.txt
  # ColorTableTimeStamp 2009/08/11 14:24:37
  # InVolFile  mri/norm.mgz
  # InVolFileTimeStamp  2011/09/30 15:23:28
  # InVolFrame 0
  # PVVolFile  mri/norm.mgz
  # PVVolFileTimeStamp  2011/09/30 15:23:28
  # surface-based-volume mm3 lh-cerebral-white-matter 199672.312500
  # surface-based-volume mm3 rh-cerebral-white-matter 200666.875000
  # surface-based-volume mm3 tot-cerebral-white-matter 400339.187500
  # ExcludeSegId 0
  # VoxelVolume_mm3 1
  # TableCol  1 ColHeader Index
  # TableCol  1 FieldName Index
  # TableCol  1 Units NA
  # TableCol  2 ColHeader SegId
  # TableCol  2 FieldName Segmentation Id
  # TableCol  2 Units NA
  # TableCol  3 ColHeader NVoxels
  # TableCol  3 FieldName Number of Voxels
  # TableCol  3 Units unitless
  # TableCol  4 ColHeader Volume_mm3
  # TableCol  4 FieldName Volume
  # TableCol  4 Units mm^3
  # TableCol  5 ColHeader StructName
  # TableCol  5 FieldName Structure Name
  # TableCol  5 Units NA
  # TableCol  6 ColHeader normMean
  # TableCol  6 FieldName Intensity normMean
  # TableCol  6 Units MR
  # TableCol  7 ColHeader normStdDev
  # TableCol  7 FieldName Itensity normStdDev
  # TableCol  7 Units MR
  # TableCol  8 ColHeader normMin
  # TableCol  8 FieldName Intensity normMin
  # TableCol  8 Units MR
  # TableCol  9 ColHeader normMax
  # TableCol  9 FieldName Intensity normMax
  # TableCol  9 Units MR
  # TableCol 10 ColHeader normRange
  # TableCol 10 FieldName Intensity normRange
  # TableCol 10 Units MR
  # NRows 49
  # NTableCols 10
  # ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean 
normStdDev
  normMin normMax normRange 
    1   2    181224   181224.0  Left-Cerebral-White-Matter   
103.0824
  7.8273    37.   124.    87.
    2   3    220289   220289.0  Left-Cerebral-Cortex  73.9965   
  10.0547    25.   109.    84.
    3   4  9827 9827.0  Left-Lateral-Ventricle    38.7152   
  10.8311    21.    89.    68.
    4   5   472  472.0  Left-Inf-Lat-Vent 58.1272   
  10.0729    36.    97.    61.
    5   7 11866    11866.0  Left-Cerebellum-White-Matter  
85.2734
  7.6396    41.   110.    69.
    6   8 29669    29669.0  Left-Cerebellum-Cortex    62.3768   
  10.6794    17.    94.    77.
    7  10  6422 6422.0  Left-Thalamus-Proper  
97.5967
  8.1825    54.   114.    60.
    8  11  3645 3645.0  Left-Caudate  
86.3108
  8.2356    52.

[Freesurfer] mris_pmake error

2011-10-25 Thread Steph Bickel

Hi,

when trying to use mris_pmake I get error messages:
when I run:mris_pmake
I get:
sh: cannot create lock: Permission denied

mris_pmake
I'm sorry, but an error condition has occurred.
While I was checking on the options file,
I couldn't access the options file. Does it exist?

Exiting to system with code 40


When I run: sudo ./bin/mris_pmake
I get:
mris_pmake
I'm sorry, but an error condition has occurred.
While I was processing environment,
it seems that the SUBJECTS_DIR env variable is not set.

Exiting to system with code 10


I did specify SUBJECTS_DIR in SetUpFreesurfer.sh that I source in the bashrc
file and the variable is set for the other freesurfer functions.

I am using   freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on ubuntu
11.04.

Any help is much appreciated.

thanks,

Stephan
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Re: [Freesurfer] mris_pmake error

2011-10-25 Thread Rudolph Pienaar

'mris_pmake' is still very experimental. It's not run as part of the 
standard recon-all stream, and is more of a post-processing surface 
tool. It has a somewhat complicated set of dependencies at this stage 
(among them, a file called 'options.txt' that controls its behavior).

What are you looking to do with it?

Best
-=R

On 10/25/11 10:51 , Steph Bickel wrote:
> Hi,
>
> when trying to use mris_pmake I get error messages:
> when I run:mris_pmake
> I get:
> sh: cannot create lock: Permission denied
>
> mris_pmake
> I'm sorry, but an error condition has occurred.
> While I was checking on the options file,
> I couldn't access the options file. Does it exist?
>
> Exiting to system with code 40
>
>
> When I run: sudo ./bin/mris_pmake
> I get:
> mris_pmake
> I'm sorry, but an error condition has occurred.
> While I was processing environment,
> it seems that the SUBJECTS_DIR env variable is not set.
>
> Exiting to system with code 10
>
>
> I did specify SUBJECTS_DIR in SetUpFreesurfer.sh that I source in the
> bashrc file and the variable is set for the other freesurfer functions.
>
> I am using   freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on ubuntu
> 11.04.
>
> Any help is much appreciated.
>
> thanks,
>
> Stephan
>
>
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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-- 
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Re: [Freesurfer] Segmentation error?

2011-10-25 Thread Douglas N Greve

you can also check the accuracy of the registration used to compute the 
eTIV with:

cd $SUBJECTS_DIR/$subject/mri/transforms

tkregister2 --lta talairach_with_skull.lta \
  --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \
   --mov ../nu_noneck.mgz --reg junk.reg.dat

doug


Gergely Orsi wrote:
> Dear Bruce and others,
>
> We have just ran into strange ICV volumes.
>
> For all our 100+ subjets, the total icv is around 1500cm3  (around 
> 1300-1700).
>
> For the new group (only 7 subjects) the average ICV is around 1200  
> (ranging from 900-1500).
>
> This is almost microcephalia, but they are normal.
>
> If we take a look at the brainseg volume or brain mask volumes they 
> are larger than the total ICV (for e.g. subject 5 has brainmaskvol: 
> 1440; brainseg vol: 1021; ICV 1036)
>
> This is not right. It's kind'a strange that someone has bigger brain 
> than skull :)
>
> I was using freesurfer 4.5 for both groups.
>
>
> Do you have any idea what did I miss?
>
> Thanks,
>
> Gergo
>
>
>
>
>
>
>
> 2011/10/3 Bruce Fischl  >
>
> The stuff outside the pial surface won't affect things, which is
> one of the reasons we prefer the surface-based measured of
> cortical morphometry.
>
> Similarly, we don't use the surface-based stuff in the
> hippocampus, so you should be all set (since many of the cortical
> assumptions aren't valid there)
>
> cheers
> Bruce
>
>
>
> On Mon, 3 Oct 2011, Gergely Orsi wrote:
>
> Dear Freesurfers!!
>
> I've encountered two strange segmentation "errors", if they
> are errors at
> all.
>
>
>
> Please see the attached fs.png:
>
> You can see that there are excess pial tissues on the superior
> part of the
> brain. The pial surface is
> defined correctly and the excess pial tissue is outside the
> red line yet it
> is coloured pink. My question, is :
>
> Does this have any impact on the results?
>
>
> The second is related to the hippocampus.
>
> Please see the attached fs2.png:
>
> The pial surface around the hippocampus looks a bit weird.
> It actually discards 1/3 of the hippocampus (it is outside the
> red line).
>
> Do you have any suggestions regarding the two problems.
>
> I'm using FS 4.5 on several 64bit linux distributions.
>
>
> --
> Gergely Orsi
> biologist - research associate
> Diagnostic Center of Pécs
> H-7623 Pécs, Rét str. 2.
> Tel.: 0036-70-3174676
> E-mail: gergo.o...@gmail.com 
>
>
>
>
> 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.
>
>
>
>
> -- 
> Gergely Orsi
> biologist - research associate
> Diagnostic Center of Pécs
> H-7623 Pécs, Rét str. 2.
> Tel.: 0036-70-3174676
> E-mail: gergo.o...@gmail.com 
> 
>
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] mris_pmake error

2011-10-25 Thread Steph Bickel

Hi Rudolph,

thanks for your speedy response.
I want to get distance along vertices (the surface) between two vertex
points. Is there maybe a matlab function doing this?

Thanks,

Stephan

On Tue, Oct 25, 2011 at 10:54 AM, Rudolph Pienaar <
rudo...@nmr.mgh.harvard.edu> wrote:

> 'mris_pmake' is still very experimental. It's not run as part of the
> standard recon-all stream, and is more of a post-processing surface tool. It
> has a somewhat complicated set of dependencies at this stage (among them, a
> file called 'options.txt' that controls its behavior).
>
> What are you looking to do with it?
>
> Best
> -=R
>
>
> On 10/25/11 10:51 , Steph Bickel wrote:
>
>> Hi,
>>
>> when trying to use mris_pmake I get error messages:
>> when I run:mris_pmake
>> I get:
>> sh: cannot create lock: Permission denied
>>
>> mris_pmake
>> I'm sorry, but an error condition has occurred.
>> While I was checking on the options file,
>> I couldn't access the options file. Does it exist?
>>
>> Exiting to system with code 40
>>
>>
>> When I run: sudo ./bin/mris_pmake
>> I get:
>> mris_pmake
>> I'm sorry, but an error condition has occurred.
>> While I was processing environment,
>> it seems that the SUBJECTS_DIR env variable is not set.
>>
>> Exiting to system with code 10
>>
>>
>> I did specify SUBJECTS_DIR in SetUpFreesurfer.sh that I source in the
>> bashrc file and the variable is set for the other freesurfer functions.
>>
>> I am using   freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 on
>> ubuntu
>> 11.04.
>>
>> Any help is much appreciated.
>>
>> thanks,
>>
>> Stephan
>>
>>
>>
>>
>>
>>
>>
>>
>> __**_
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
>>
>
>
> --
> Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
> 149 (2301) 13th Street, Charlestown, MA 02129 USA
>
>
> 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] roi analysis from label or annotation

2011-10-25 Thread Douglas N Greve

Did you try passing --olab a full path?

Knut J Bjuland wrote:
> Hi
>
> I use mri_surfcluster -olab --subject fsaverage --in sig.mgh --hemi ?h 
> to produce label for the areas indicated by mri_glmfit. Then I use 
> label and mean follow by the python script.
>
>
> cheers
> Knut J
>
> I use
>
> > Date: Mon, 24 Oct 2011 10:43:02 -0400
> > From: gr...@nmr.mgh.harvard.edu
> > To: knut...@hotmail.com
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] roi analysis from label or annotation
> >
> > It's very hard to tell what you are doing without a command-line.
> > Generally, you can pass the full path of a label to surfcluster to make
> > it save it in a particular location.
> > doug
> >
> > Knut J Bjuland wrote:
> > > I am working on roi analysis. I have made a label using 
> mri_surdcluster and used mri_label2label to
> > > copy the label from fsaverage to each individual subject. The next 
> step would be to use
> > > mris_anatomical_stats to calculate stats for each subject. I used 
> a Python to merge the txt file from
> > > mris_anatomical_stats.
> > >
> > > Is it possible to force mri_surfcluster to save the label another 
> dir than fsaverage?
> > > Can I use convert roi label to annotation and then use aparc2stats
> > > or similar command to get group statics?
> > >
> > >
> > > Cheers
> > > Knut J
> > > 
> 
> > >
> > > ___
> > > 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
> >
> >
> >
> > 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
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Re: [Freesurfer] white matter volume in a ROI

2011-10-25 Thread Douglas N Greve


Yes, I see what you mean. mri_aparc2aseg is hard coded to accept both 
hemis. The easiest way around it is just to create a dummy label for the 
right hemisphere.
doug

dolphin...@aol.com wrote:
> Hi Doug,
>
> thanks a lot your advice.
>
> I created an annnotation of my ROI-label as called 
> lh.cluster1.labe.label with the command line:
>
> /mris_label2annot --s ZPN20 --h lh --ctab 
> //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab --a 
> myaparc --l lh.cluster1.labe/.label --nhits nhits.mgh
>
> This works fine. After that i have used your commmand in this way:
>
> m/ri_aparc2aseg --s ZPN20 --labelwm --hypo-as-wm --rip-unknown 
> --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot myaparc/
>
> and i get the following error, which is cause that i have no 
> lh.cluster1.labe.label in the right hemisphere:
>
> /Loading lh annotations from 
> /Users/dolphinede/Desktop/Probanden/ZPN20/label/lh.myaparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally 
> //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab)
>
> Reading rh white surface
>  /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.white
>
> Reading rh pial surface
>  /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.pial
>
> Loading rh annotations from 
> /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot
> could not read annot file 
> /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot
> No such file or directory
> ERROR: MRISreadAnnotation() failed 
> /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot/
>
> The question i have is if all these steps are right and/if i have to 
> do some more steps to get white matter volume of my annotation and 
> where i can find it?
>
> Excuse my numerous questions but I am just a freesurfer-beginner...
>
> Best regards
>
> Daniel
>
>
>
>
>
>
>
>
>
> -Ursprüngliche Mitteilung-
> Von: Douglas N Greve 
> An: dolphinede ; freesurfer 
> 
> Verschickt: Mo, 24 Okt 2011 10:04 pm
> Betreff: Re: [Freesurfer] white matter volume in a ROI
>
> It will be more involved than that. You will need to create an 
> annotation that contains your label (maybe in addition to other labels), 
> then uses mri_aparc2aseg with the --labelwm option, something like
>
> mri_aparc2aseg --s subject-anat --labelwm --hypo-as-wm --rip-unknown 
> --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot yourannot
>
> doug
>
> dolphin...@aol.com  wrote:
> > Hi Doug,
> >
> > thanks a lot for your answer.
> >
> > So i understand you right that i can get "exact" knowledge about the 
> > thickness, grey matter volume and pial surface area in my ROI, but in 
> > case of "the" ROI white matter volume, i have to look to which 
> > cortical label my ROI counts and then I use the wmparc.files for this 
> > label?
> >
> > Best regards
> >
> > Daniel Klein
> >
> >
> >
> >  
> >
> >
> >
> >
> >
> > -Ursprüngliche Mitteilung-
> > Von: Douglas N Greve  > >
> > An: dolphinede mailto:dolphin...@aol.com>>
> > Cc: freesurfer  > >
> > Verschickt: Mo, 24 Okt 2011 4:48 pm
> > Betreff: Re: [Freesurfer] white matter volume in a ROI
> >
> > For GM area and volume, you can use mris_anatomical_stats. See the 
> > recent thread on how. For the WM volume, how would you define the WM 
> > volume that corresponds to you label? We have a routine that parcellates 
> > WM based on closest proximity to a cortical label.
> > doug
> >
> > dolphin...@aol.com  wrote:
> > > Dear FreeSurfer experts,
> > >
> > > i have created  a ROI in qdec  , where i have found a significant 
> > > correlation between lgi and age.
> > >
> > > I mapped this ROI to all subjects.
> > >
> > > I am interested to compare in this ROI the pial-surface area, the grey 
> > > matter volume and if possible the white matter volume for this 
> > > specific region and i am not sure how to do this?
> > >
> > > Best regards
> > >
> > > Daniel Klein
> > > 
> > >
> > > ___
> > > 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 
> > 
> >
> >
> >
> > 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 Par

Re: [Freesurfer] Diffusion tensor estimation method

2011-10-25 Thread Douglas N Greve

It uses a linear least squares method.
doug

Ed Gronenschild wrote:
> Hi,
>
> There are various methods to estimate the diffusion tensor, like
> linear-least squares, non-linear least-squares, German-McClure
> M-estimator.
> I would like to know which method is used by FreeSurfer in
> the dt_recon command?
>
> Cheers,
> Ed
>
> ___
> 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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Re: [Freesurfer] mris_pmake error

2011-10-25 Thread Bruce Fischl

an easy way to do this to within 15% or so is to compute the great circle 
distance between the two vertices on the ?h.sphere file.
On Tue, 25 Oct 
2011, Steph Bickel wrote:



Hi Rudolph,
thanks for your speedy response. 
I want to get distance along vertices (the surface) between two vertex points. 
Is there maybe a matlab function doing this?

Thanks,

Stephan

On Tue, Oct 25, 2011 at 10:54 AM, Rudolph Pienaar  
wrote:
  'mris_pmake' is still very experimental. It's not run as part of the 
standard recon-all stream, and is more of a post-processing surface
  tool. It has a somewhat complicated set of dependencies at this stage 
(among them, a file called 'options.txt' that controls its behavior).

  What are you looking to do with it?

  Best
  -=R


On 10/25/11 10:51 , Steph Bickel wrote:
Hi,

when trying to use mris_pmake I get error messages:
when I run:mris_pmake
I get:
sh: cannot create lock: Permission denied

mris_pmake
I'm sorry, but an error condition has occurred.
While I was checking on the options file,
I couldn't access the options file. Does it exist?

Exiting to system with code 40


When I run: sudo ./bin/mris_pmake
I get:
mris_pmake
I'm sorry, but an error condition has occurred.
While I was processing environment,
it seems that the SUBJECTS_DIR env variable is not set.

Exiting to system with code 10


I did specify SUBJECTS_DIR in SetUpFreesurfer.sh that I source in the
bashrc file and the variable is set for the other freesurfer functions.

I am using   freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on ubuntu
11.04.

Any help is much appreciated.

thanks,

Stephan








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--
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA


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[Freesurfer] Fwd: BEM surface generation questions

2011-10-25 Thread Dan G Wakeman

Hi,

I have a couple of questions about the two different ways to generate BEM 
surfaces available in FreeSurfer. I have done a comparison of the techniques 
available in 
mri_watershed -surf
mri_make_bem_surfaces
(Version 4.3.0)
with another algorithm (which I know the algorithm)
I have received a request from reviewers to briefly describe how each of the 
first two techniques develops the surfaces. 
I have read all of the Ségonne 2004 paper several times and while I believe I 
can explain how the "brain"/"inner skull" surface is generated. I cannot figure 
out how the other two surfaces are generated: "outer skull" and "outer skin" 
surfaces.

Additionally, I cannot find any information about mri_make_bem_surfaces either 
on the wiki or in the email archives (I realize this software may be kept in as 
a courtesy to the MEG users: my tests suggest this is very useful). Is there 
anyone who can provide even a brief description of how this tool generates the 
surfaces?

Thank You,
Dan


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Re: [Freesurfer] mris_pmake error

2011-10-25 Thread Rudolph Pienaar

On 10/25/11 10:57 , Steph Bickel wrote:
> Hi Rudolph,
>
> thanks for your speedy response.
> I want to get distance along vertices (the surface) between two vertex
> points.

OK -- 'mris_pmake' works for this. Say you have a subject called 'test' 
and you want to calculate the distance on the lh 'smoothwm' from vertex 
1000 to 2:

mris_pmake --subject test --hemi lh --surface0 smoothwm --surface1 
smoothwm --curv0 curv --curv1 curv --mpmProg pathFind --mpmOverlay 
distance --mpmArgs startVertex:1000,endVertex:2

The only important options are '--surface0 smoothwm --mpmProg pathFind 
--mpmOverlab distance --mpmArgs startVertex:1000,endVertex:2'

The other args, '--surface 1 smoothwm --curv0 curv --curv1 curv' are not 
used for finding the path, but do nonetheless need to be filled in. As I 
indicated, "mris_pmake" is more developer than user friendly.

So, the above will generate in your terminal:

Start->End vertices[ 1000->2 ]
Total path cost  [ 55.957047 ]
LabelWrite: saving to ./dijk.label

Where the "Total path cost" corresponds to the distance along the mesh 
(using the "distance" overlay in the "pathFind" module between vertices 
1000 and 2 means that the minimum cost in moving between those 
locations is the minimum distance).

You can load the 'dijk.label' into Freeview to see the path itself.

If you want to use the 'inflated' surface instead, change the arg to 
'--surface0':

mris_pmake --subject test --hemi lh --surface0 inflated --surface1 
smoothwm --curv0 curv --curv1 curv --mpmProg pathFind --mpmOverlay 
distance --mpmArgs startVertex:1000,endVertex:2

which outputs:

Start->End vertices[ 1000->2 ]
Total path cost  [ 57.521545 ]
LabelWrite: saving to ./dijk.label

Oh, and I have a strong suspicion that you need to use the current 'dev' 
version of 'mris_pmake'. If you are using the 'stable' version and it 
won't work, let me know and we can get the 'dev' version out to you.

Best
-=R

-- 
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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[Freesurfer] hippocampal subfields

2011-10-25 Thread Lugar, Heather

If I were to run the hippocampal subfields command on data that had been 
previously processed using Freesurfer 5.0 (rather than 5.1), would the results 
be valid?

Thanks,
Heather
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Re: [Freesurfer] CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line 92 : invalid texture reference

2011-10-25 Thread Hemant Bokil

Hi Richard and others,
I installed the earlier driver and the toolkit, but I sill have the same
crash. A portion of the log just before the crash is below. Any thoughts ?
Hemant
 mri_em_register_cuda -skull nu.mgz
/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull.lta

nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2010 NVIDIA Corporation
Built on Thu_Nov__4_12:44:17_PDT_2010
Cuda compilation tools, release 3.2, V0.2.1221

Driver : 3.20
Runtime : 3.20

Acquiring CUDA device
Using default device
CUDA device: Quadro FX 4600
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'...
gcaAllocMax: node dims 64 64 64
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
average std = 23.1   using min determinant for regularization = 53.4
0 singular and 5702 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 20.2 or > 943.7
total sample mean = 92.0 (1443 zeros)

spacing=8, using 3481 sample points, tol=1.00e-05...

CUDA Error in file
'/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line
92 : invalid texture reference.
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3481, passno 0, spacing 8
Abort (core dumped)
Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27
19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 209 exited with ERRORS at Tue Oct 25 17:13:11 EDT 2011

For more details, see the log file
/home/hemant/FreeSurferSubjects/209/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

On Tue, Oct 25, 2011 at 8:41 AM, R Edgar  wrote:

> On Mon, Oct 24, 2011 at 9:28 PM, Hemant Bokil 
> wrote:
>
> > Thanks for the response. Does this mean that I should use CUDA 3.2 ?
> There
> > was some discussion on the group recently about Freesurfer not working
> with
> > CUDA 4 and one suggestion made was to switch to CUDA 3.2. Thanks,
>
> Probably. NVIDIA always like to claim full backwards compatibility,
> but I've never been fully convinced.
>
> Richard
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> dispose of the e-mail.
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Re: [Freesurfer] mris_pmake error

2011-10-25 Thread Steph Bickel

Hi Rudolph and Bruce,

thanks for your responses.

rudolph, your example works great. just 2 questions:
what dimension is the total path cost in the mris_pmake output?
is there a way to input a file with several vertex point pairs to compute
the distance between, or do I have to loop through the pairs I would like to
compute?

Bruce, thank you very much for your suggestion. it would be easier for me to
compute it this way and I would like to compare results with mris_pmake
results. I am currently looking for a way to compute the distance on the
sphere, if you have a suggestion how to do this it would be much
appreciated.

Thank you,

Stephan


On Tue, Oct 25, 2011 at 2:26 PM, Rudolph Pienaar <
rudo...@nmr.mgh.harvard.edu> wrote:

> On 10/25/11 10:57 , Steph Bickel wrote:
>
>> Hi Rudolph,
>>
>> thanks for your speedy response.
>> I want to get distance along vertices (the surface) between two vertex
>> points.
>>
>
> OK -- 'mris_pmake' works for this. Say you have a subject called 'test' and
> you want to calculate the distance on the lh 'smoothwm' from vertex 1000 to
> 2:
>
> mris_pmake --subject test --hemi lh --surface0 smoothwm --surface1 smoothwm
> --curv0 curv --curv1 curv --mpmProg pathFind --mpmOverlay distance --mpmArgs
> startVertex:1000,endVertex:**2
>
> The only important options are '--surface0 smoothwm --mpmProg pathFind
> --mpmOverlab distance --mpmArgs startVertex:1000,endVertex:**2'
>
> The other args, '--surface 1 smoothwm --curv0 curv --curv1 curv' are not
> used for finding the path, but do nonetheless need to be filled in. As I
> indicated, "mris_pmake" is more developer than user friendly.
>
> So, the above will generate in your terminal:
>
> Start->End vertices[ 1000->2 ]
> Total path cost  [ 55.957047 ]
> LabelWrite: saving to ./dijk.label
>
> Where the "Total path cost" corresponds to the distance along the mesh
> (using the "distance" overlay in the "pathFind" module between vertices 1000
> and 2 means that the minimum cost in moving between those locations is
> the minimum distance).
>
> You can load the 'dijk.label' into Freeview to see the path itself.
>
> If you want to use the 'inflated' surface instead, change the arg to
> '--surface0':
>
> mris_pmake --subject test --hemi lh --surface0 inflated --surface1 smoothwm
> --curv0 curv --curv1 curv --mpmProg pathFind --mpmOverlay distance --mpmArgs
> startVertex:1000,endVertex:**2
>
> which outputs:
>
> Start->End vertices[ 1000->2 ]
> Total path cost  [ 57.521545 ]
> LabelWrite: saving to ./dijk.label
>
> Oh, and I have a strong suspicion that you need to use the current 'dev'
> version of 'mris_pmake'. If you are using the 'stable' version and it won't
> work, let me know and we can get the 'dev' version out to you.
>
> Best
> -=R
>
>
>
>
> --
> Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
> 149 (2301) 13th Street, Charlestown, MA 02129 USA
>
>
> 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] mris_pmake error

2011-10-25 Thread Bruce Fischl


find the angle between the vectors connecting each point with (0,0,0).

compute the fraction of the circle that it represents, and multiply it by:

K * PI * D

where

D = diameter of ?h.sphere
K = sqrt(surface area of surface you are interested in)
---
sqrt(surface area of sphere)

cheers
Bruce

On 
Tue, 25 Oct 2011, Steph Bickel wrote:



Hi Rudolph and Bruce,
thanks for your responses. 

rudolph, your example works great. just 2 questions: 
what dimension is the total path cost in the mris_pmake output? 
is there a way to input a file with several vertex point pairs to compute
the distance between, or do I have to loop through the pairs I would like to
compute?

Bruce, thank you very much for your suggestion. it would be easier for me to
compute it this way and I would like to compare results with mris_pmake
results. I am currently looking for a way to compute the distance on the
sphere, if you have a suggestion how to do this it would be much
appreciated.  

Thank you,

Stephan


On Tue, Oct 25, 2011 at 2:26 PM, Rudolph Pienaar
 wrote:
  On 10/25/11 10:57 , Steph Bickel wrote:
Hi Rudolph,

thanks for your speedy response.
I want to get distance along vertices (the surface)
between two vertex
points.


OK -- 'mris_pmake' works for this. Say you have a subject called
'test' and you want to calculate the distance on the lh 'smoothwm'
from vertex 1000 to 2:

mris_pmake --subject test --hemi lh --surface0 smoothwm --surface1
smoothwm --curv0 curv --curv1 curv --mpmProg pathFind --mpmOverlay
distance --mpmArgs startVertex:1000,endVertex:2

The only important options are '--surface0 smoothwm --mpmProg pathFind
--mpmOverlab distance --mpmArgs startVertex:1000,endVertex:2'

The other args, '--surface 1 smoothwm --curv0 curv --curv1 curv' are
not used for finding the path, but do nonetheless need to be filled
in. As I indicated, "mris_pmake" is more developer than user friendly.

So, the above will generate in your terminal:

Start->End vertices                                    [ 1000->2 ]
Total path cost                                          [ 55.957047 ]
LabelWrite: saving to ./dijk.label

Where the "Total path cost" corresponds to the distance along the mesh
(using the "distance" overlay in the "pathFind" module between
vertices 1000 and 2 means that the minimum cost in moving between
those locations is the minimum distance).

You can load the 'dijk.label' into Freeview to see the path itself.

If you want to use the 'inflated' surface instead, change the arg to
'--surface0':

mris_pmake --subject test --hemi lh --surface0 inflated --surface1
smoothwm --curv0 curv --curv1 curv --mpmProg pathFind --mpmOverlay
distance --mpmArgs startVertex:1000,endVertex:2

which outputs:

Start->End vertices                                    [ 1000->2 ]
Total path cost                                          [ 57.521545 ]
LabelWrite: saving to ./dijk.label

Oh, and I have a strong suspicion that you need to use the current
'dev' version of 'mris_pmake'. If you are using the 'stable' version
and it won't work, let me know and we can get the 'dev' version out to
you.

Best
-=R




--
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA


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