date:20110706

Hi again,

I found out that, if I change the flip4fsl line
printf '%s ' `cat $inbvecs | awk -v sgn=$sign[$k]1 -v n=$k 
'{print sgn*$n}'` \
to
printf '%s ' `cat $inbvecs | awk -v sgn=$sign[$k]1 -v n=$k 
'{print $n}'` \
(deleting the sgn*) the values in the out-bvecs are correct, i.e. the numbers 
after the decimal separator are there.

Could you please help me to figure out what this line does.
In my case: sign = + + + (my image orientation is LAS)
therefore sgn is +1
What is the difference in my case between  '{print sgn*$n}'`  and  '{print 
$n}'` ?

Thank you very much,
Franz

Am 06.07.2011 um 21:32 schrieb Anastasia Yendiki:

> 
> I'm attaching what I get when I run it. Only the trailing zeros are missing.
> 
> On Wed, 6 Jul 2011, Franz Liem wrote:
> 
>> If i flip4fsl my fake file the the numbers after the decimal point are 
>> missing in the output (bvecs_bvecs_onezero3decpoint1_western_out).
>> 
>> I have attached a fake bvecs fitting your tutorial data (70 lines). Would 
>> you be so kind, as to run this.
>> 
>> Thank you so much for your help,
>> Franz
>> 
>> 
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Re: [Freesurfer] glibc detected *** mris_make_surfaces: double free or corruption (!prev): 0x000000003710cc10

Hi Knut,

if you upload the subject we'll see if we can replicate this.

Bruce
On Wed, 6 Jul 
2011, Knut J Bjuland wrote:

> The name of the subjects is 3. The command that was used were  recon-all
> -autorecon2-pial -s 3. I then issued the bugr and got this output. I
> have also included the error message. I belive that there were an double
> free or an corruption detected by glibc. The recon-all files is available 
> upon request.
>
>
> Cheers
> Knut J
>
>
>
>
> --
> FREESURFER_HOME: /usr/local/freesurfer
>
> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
>
> RedHat release: Fedora release 15 (Lovelock)
>
> Kernel info: Linux 2.6.38.8-32.fc15.x86_64 x86_64
>
> 
>
>
>
>
> *** glibc detected *** mris_make_surfaces: double free or corruption
> (!prev): 0x3710cc10 ***
> === Backtrace: =
> /lib64/libc.so.6[0x3cdf07703a]
> mris_make_surfaces[0x518a39]
> mris_make_surfaces[0x5a7e3c]
> mris_make_surfaces[0x40f172]
> /lib64/libc.so.6(__libc_start_main+0xed)[0x3cdf02139d]
> mris_make_surfaces(__gxx_personality_v0+0x18a)[0x40bf5a]
> === Memory map: 
> 0040-00cf1000 r-xp  00:00 0
> 00cf1000-00df ---p  00:00 0
> 00df-26b79000 rwxp  00:00 0
> 26eb9000-383d5000 rwxp  00:00 0
> [heap]
> 3cdec0-3cdec1f000 r-xp  fd:01 71696709
> /lib64/ld-2.14.so
> 3cdec1f000-3cdee1e000 ---p  00:00 0
> 3cdee1e000-3cdee1f000 r-xp 0001e000 fd:01 71696709
> /lib64/ld-2.14.so
> 3cdee1f000-3cdee2 rwxp 0001f000 fd:01 71696709
> /lib64/ld-2.14.so
> 3cdee2-3cdee21000 rwxp  00:00 0
> 3cdf00-3cdf18f000 r-xp  fd:01 71696719
> /lib64/libc-2.14.so
> 3cdf18f000-3cdf38e000 ---p 0018f000 fd:01 71696719
> /lib64/libc-2.14.so
> 3cdf38e000-3cdf392000 r-xp 0018e000 fd:01 71696719
> /lib64/libc-2.14.so
> 3cdf392000-3cdf393000 rwxp 00192000 fd:01 71696719
> /lib64/libc-2.14.so
> 3cdf393000-3cdf399000 rwxp  00:00 0
> 3cdf40-3cdf483000 r-xp  fd:01 71696792
> /lib64/libm-2.14.so
> 3cdf483000-3cdf682000 ---p 00083000 fd:01 71696792
> /lib64/libm-2.14.so
> 3cdf682000-3cdf683000 r-xp 00082000 fd:01 71696792
> /lib64/libm-2.14.so
> 3cdf683000-3cdf684000 rwxp 00083000 fd:01 71696792
> /lib64/libm-2.14.so
> 3cdf80-3cdf816000 r-xp  fd:01 71696723
> /lib64/libpthread-2.14.so
> 3cdf816000-3cdfa15000 ---p 00016000 fd:01 71696723
> /lib64/libpthread-2.14.so
> 3cdfa15000-3cdfa16000 r-xp 00015000 fd:01 71696723
> /lib64/libpthread-2.14.so
> 3cdfa16000-3cdfa17000 rwxp 00016000 fd:01 71696723
> /lib64/libpthread-2.14.so
> 3cdfa17000-3cdfa1b000 rwxp  00:00 0
> 3cdfc0-3cdfc02000 r-xp  fd:01 71696776
> /lib64/libdl-2.14.so
> 3cdfc02000-3cdfe02000 ---p 2000 fd:01 71696776
> /lib64/libdl-2.14.so
> 3cdfe02000-3cdfe03000 r-xp 2000 fd:01 71696776
> /lib64/libdl-2.14.so
> 3cdfe03000-3cdfe04000 rwxp 3000 fd:01 71696776
> /lib64/libdl-2.14.so
> 3ce000-3ce0015000 r-xp  fd:01 71696796
> /lib64/libgcc_s-4.6.0-20110603.so.1
> 3ce0015000-3ce0214000 ---p 00015000 fd:01 71696796
> /lib64/libgcc_s-4.6.0-20110603.so.1
> 3ce0214000-3ce0215000 rwxp 00014000 fd:01 71696796
> /lib64/libgcc_s-4.6.0-20110603.so.1
> 3ce040-3ce0416000 r-xp  fd:01 71696774
> /lib64/libz.so.1.2.5
> 3ce0416000-3ce0616000 ---p 00016000 fd:01 71696774
> /lib64/libz.so.1.2.5
> 3ce0616000-3ce0617000 rwxp 00016000 fd:01 71696774
> /lib64/libz.so.1.2.5
> 3ce200-3ce20e8000 r-xp  fd:01 891
> /usr/lib64/libstdc++.so.6.0.16
> 3ce20e8000-3ce22e8000 ---p 000e8000 fd:01 891
> /usr/lib64/libstdc++.so.6.0.16
> 3ce22e8000-3ce22f r-xp 000e8000 fd:01 891
> /usr/lib64/libstdc++.so.6.0.16
> 3ce22f-3ce22f2000 rwxp 000f fd:01 891
> /usr/lib64/libstdc++.so.6.0.16
> 3ce22f2000-3ce2307000 rwxp  00:00 0
> 3cea00-3cea05c000 r-xp  fd:01 71698673
> /lib64/libfreebl3.so
> 3cea05c000-3cea25b000 ---p 0005c000 fd:01 71698673
> /lib64/libfreebl3.so
> 3cea25b000-3cea25d000 rwxp 0005b000 fd:01 71698673
> /lib64/libfreebl3.so
> 3cea25d000-3cea261000 rwxp  00:00 0
> 3cea40-3cea408000 r-xp  fd:01 71698674
> /lib64/libcrypt-2.14.so
> 3cea408000-3cea607000 ---p 8000 fd:01 71698674
> /lib64/libcrypt-2.14.so
> 3cea607000-3cea608000 r-xp 7000 fd:01 71698674
> /lib64/libcrypt-2.14.so
> 3cea608000-3cea609000 rwxp 8000 fd:01 71698674
> /lib64/libcrypt-2.14.so
> 3cea609000-3cea637000 rwxp  00:00 0
> 7f0e126d9000-7f0e189ec000 rwxp  00:00 0
> 7f0e189ec000-7f0e189f8000 r-xp  fd:01 71696450
> /lib64/libnss_files-2.14.so
> 7f0e189f8000-7f0e18bf7000 ---p c000 fd:01 71696450
> /lib64/libnss_files-2.14.so
> 7f0e18bf7000-7f0e18bf8000 r-xp b000 fd:01 71696450
> /lib64/libnss_files-2.14.so
> 7f0e18bf8000-7f0e18bf9000 rwxp c000 fd:01 71696450
> /lib64/libnss_files-2.14.so
> 7f0

Re: [Freesurfer] repost: error using recon-all function

what does the file 2645166/mri/transforms/talairach_avi.log say?  or you
can send it to me.

n.

On Wed, 2011-07-06 at 14:10 -0500, Ryan Hutten wrote:
> Freesurfer Experts,
> 
> I am reposting an error message that I receive when using the
> recon-all function to analyze my own data. 
> 
> The command which I am trying to execute is:
> recon-all -s 2645166 -all
> 
> 2645166 is the patient ID. 
> 
> Running this gives an error: 
> ERROR: avi2talxfm failed, see transforms/talairach_avi.log
> Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC
> 2010 x86_64 x86_64 x86_64 GNU/Linux
> 
> recon-all -s 2645166 exited with ERRORS at Wed Jul  6 14:06:34 CDT
> 2011
> 
> 
> bugr gives this:
> -
> 
> FREESURFER_HOME: /usr/local/freesurfer
> 
> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
> 
> RedHat release: Fedora release 14 (Laughlin)
> 
> Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64
> 
> -
> 
> I apologize to keep asking the same questions, but until this is
> resolved, I am unable to process the new data obtained in my lab. I am
> relatively new to using this software, so any guidance would be much
> appreciated!
> 
> Thanks!
> ___
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Re: [Freesurfer] QDEC : Error loading the data table.

Ignacio,

I think it is the dashes in the factor name, try changing this:

Left-Cerebral-Cortical-Thickness

to this:

Left_Cerebral_Cortical_Thickness

n.

On Wed, 2011-07-06 at 14:50 -0400, Ignacio Letelier wrote:
> Hi 
> 
> I have recently tried to create a new  table and I received the
> following message after loading it in QDEC:
> 
> Loading data
> table /home/virtualuser/apps/freesurfer/subjects/qdec.table.dat...
> Number of columns:  5
> fsid column:1
> Number of factors:  4
> Number of subjects: 10
> ERROR3: QdecDataTable::Load failed to tokenize string:
>  
> on line 4 of /home/virtualuser/apps/freesurfer/subjects/qdec.table.dat
> Error loading the data table.
> 
> All the information above is right except the last one since the my
> number of subject is not 10.
> 
> Can anyone help me solving this problem ? 
> 
> 
> Best regards.
> -- 
> Ignacio 
> ___
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[Freesurfer] more on fieldsign problems-

2011-07-06 Thread Michelle Umali

Dear all,
I've been having issues with my fieldsign images all I get are  
speckles. I did the following and did not get any errors:

1) ran recon-all -all
2) cut and saved occipital patches (rh.occip.patch.3d) from inflated surface
3) ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d rh.occip.patch.flat
4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy 48  
paradigm
rtopy.par -nskip 4 fwhm 0
5) selxavg3-sess -a rtopy.self.rh -s sj09
6) fieldsign-sess -a rtopy.self.rh -occip -s sj09

When I looked at the fieldsign map using:
7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign

all I got were blue and red speckles.  The polar and eccentricity maps  
seemed ok.


Any help would be great.

Michelle
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Re: [Freesurfer] Subject information


mri_info 

should do the trick

cheers
Bruce
On Wed, 6 Jul 2011, 
leonardo kay wrote:




Hi all


Is there someway (command line) to get direct information on each  subject  
acquisition parameters?

Best regards.
--
Leo Kay.


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Re: [Freesurfer] Error while loading qdec project file

what is your operating system?  linux and mac typically have a /tmp dir,
unless you're running on a cluster?

n.

On Wed, 2011-07-06 at 15:46 +0200, Tetiana Dadakova wrote:
> Dear experts,
> 
> When I try to load a saved Project File, I get an error:
> 
> Loading data table /tmp/qdec_project_archive/qdec.table.dat...
> ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat
> Error loading the project file.
> 
> I do not have any /tmp subdirectory. Should it appear when I save the
> Project File? Should it be in /qdec directory?
> 
> Thank you,
> Tanja.
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> 
> 

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Re: [Freesurfer] QDEC : Error loading the data table.

can you email me the qdec.table.dat file?  probably something is not
being parsed properly and i'll have to eyeball what it might be.

n.

On Wed, 2011-07-06 at 14:50 -0400, Ignacio Letelier wrote:
> Hi 
> 
> I have recently tried to create a new  table and I received the
> following message after loading it in QDEC:
> 
> Loading data
> table /home/virtualuser/apps/freesurfer/subjects/qdec.table.dat...
> Number of columns:  5
> fsid column:1
> Number of factors:  4
> Number of subjects: 10
> ERROR3: QdecDataTable::Load failed to tokenize string:
>  
> on line 4 of /home/virtualuser/apps/freesurfer/subjects/qdec.table.dat
> Error loading the data table.
> 
> All the information above is right except the last one since the my
> number of subject is not 10.
> 
> Can anyone help me solving this problem ? 
> 
> 
> Best regards.
> -- 
> Ignacio 
> ___
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Re: [Freesurfer] tracula bvecs problem



I'm attaching what I get when I run it. Only the trailing zeros are 
missing.


On Wed, 6 Jul 2011, Franz Liem wrote:


If i flip4fsl my fake file the the numbers after the decimal point are missing 
in the output (bvecs_bvecs_onezero3decpoint1_western_out).

I have attached a fake bvecs fitting your tutorial data (70 lines). Would you 
be so kind, as to run this.

Thank you so much for your help,
Franz


0 0 0 0 0 0 0 0 0 0 -1.1 -0.1 -0.1 -1 -1 0 0 -1 -1 0 0 -1 -1 0 0 -1 -1 0 0 -1 
-1 0 0 -1 -1 0 0 -1 -1 0 0 -1 -1.1 -0.1 -0.1 -1 -1 0 0 -1 -1 0 0 -1 -1 0 0 -1 
-1 0 0 -1 -1 0 0 -1 -1 0 0 -1 
0 0 0 0 0 0 0 0 0 0 0 -1.1 0 -1.2 -0.2 -1.2 0 -1 0 -1 0 -1 0 -1 0 -1 0 -1 0 -1 
0 -1 0 -1 0 -1 0 -1 0 -1 0 -1 0 -1.1 0 -1.2 -0.2 -1.2 0 -1 0 -1 0 -1 0 -1 0 -1 
0 -1 0 -1 0 -1 0 -1 0 -1 0 -1 
0 0 0 0 0 0 0 0 0 0 0 0 1 1.1 0 0 1.3 1.3 0.3 0 1 1 0 0 1 1 0 0 1 1 0 0 1 1 0 0 
1 1 0 0 1 1 0 0 1 1.1 0 0 1.3 1.3 0.3 0 1 1 0 0 1 1 0 0 1 1 0 0 1 1 0 0 1 1 
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[Freesurfer] repost: error using recon-all function

2011-07-06 Thread Ryan Hutten

Freesurfer Experts,

I am reposting an error message that I receive when using the recon-all
function to analyze my own data.

The command which I am trying to execute is:
recon-all -s 2645166 -all

2645166 is the patient ID.

Running this gives an error:
ERROR: avi2talxfm failed, see transforms/talairach_avi.log
Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC 2010
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 2645166 exited with ERRORS at Wed Jul  6 14:06:34 CDT 2011


bugr gives this:
-

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

RedHat release: Fedora release 14 (Laughlin)

Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64

-

I apologize to keep asking the same questions, but until this is resolved, I
am unable to process the new data obtained in my lab. I am relatively new to
using this software, so any guidance would be much appreciated!

Thanks!
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[Freesurfer] QDEC : Error loading the data table.

2011-07-06 Thread Ignacio Letelier

Hi

I have recently tried to create a new  table and I received the following
message after loading it in QDEC:

Loading data table
/home/virtualuser/apps/freesurfer/subjects/qdec.table.dat...
Number of columns:  5
fsid column:1
Number of factors:  4
Number of subjects: 10
ERROR3: QdecDataTable::Load failed to tokenize string:

on line 4 of /home/virtualuser/apps/freesurfer/subjects/qdec.table.dat
Error loading the data table.

All the information above is right except the last one since the my number
of subject is not 10.

Can anyone help me solving this problem ?


Best regards.
-- 
Ignacio
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[Freesurfer] recon-all abort with glibc error

2011-07-06 Thread Knut J Bjuland

The name of the subjects is 3. The command that was used were  recon-all
-autorecon2-pial -s 3. I then issued the bugr and got this output. I
have also included the error message. I belive that there were an double
free or an corruption detected by glibc. The recon-all files is available upon 
request.


Cheers
Knut J 




--
FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

RedHat release: Fedora release 15 (Lovelock)

Kernel info: Linux 2.6.38.8-32.fc15.x86_64 x86_64






*** glibc detected *** mris_make_surfaces: double free or corruption
(!prev): 0x3710cc10 ***
=== Backtrace: =
/lib64/libc.so.6[0x3cdf07703a]
mris_make_surfaces[0x518a39]
mris_make_surfaces[0x5a7e3c]
mris_make_surfaces[0x40f172]
/lib64/libc.so.6(__libc_start_main+0xed)[0x3cdf02139d]
mris_make_surfaces(__gxx_personality_v0+0x18a)[0x40bf5a]
=== Memory map: 
0040-00cf1000 r-xp  00:00 0
00cf1000-00df ---p  00:00 0
00df-26b79000 rwxp  00:00 0
26eb9000-383d5000 rwxp  00:00 0 
[heap]
3cdec0-3cdec1f000 r-xp  fd:01 71696709  
/lib64/ld-2.14.so
3cdec1f000-3cdee1e000 ---p  00:00 0
3cdee1e000-3cdee1f000 r-xp 0001e000 fd:01 71696709  
/lib64/ld-2.14.so
3cdee1f000-3cdee2 rwxp 0001f000 fd:01 71696709  
/lib64/ld-2.14.so
3cdee2-3cdee21000 rwxp  00:00 0
3cdf00-3cdf18f000 r-xp  fd:01 71696719  
/lib64/libc-2.14.so
3cdf18f000-3cdf38e000 ---p 0018f000 fd:01 71696719  
/lib64/libc-2.14.so
3cdf38e000-3cdf392000 r-xp 0018e000 fd:01 71696719  
/lib64/libc-2.14.so
3cdf392000-3cdf393000 rwxp 00192000 fd:01 71696719  
/lib64/libc-2.14.so
3cdf393000-3cdf399000 rwxp  00:00 0
3cdf40-3cdf483000 r-xp  fd:01 71696792  
/lib64/libm-2.14.so
3cdf483000-3cdf682000 ---p 00083000 fd:01 71696792  
/lib64/libm-2.14.so
3cdf682000-3cdf683000 r-xp 00082000 fd:01 71696792  
/lib64/libm-2.14.so
3cdf683000-3cdf684000 rwxp 00083000 fd:01 71696792  
/lib64/libm-2.14.so
3cdf80-3cdf816000 r-xp  fd:01 71696723  
/lib64/libpthread-2.14.so
3cdf816000-3cdfa15000 ---p 00016000 fd:01 71696723  
/lib64/libpthread-2.14.so
3cdfa15000-3cdfa16000 r-xp 00015000 fd:01 71696723  
/lib64/libpthread-2.14.so
3cdfa16000-3cdfa17000 rwxp 00016000 fd:01 71696723  
/lib64/libpthread-2.14.so
3cdfa17000-3cdfa1b000 rwxp  00:00 0
3cdfc0-3cdfc02000 r-xp  fd:01 71696776  
/lib64/libdl-2.14.so
3cdfc02000-3cdfe02000 ---p 2000 fd:01 71696776  
/lib64/libdl-2.14.so
3cdfe02000-3cdfe03000 r-xp 2000 fd:01 71696776  
/lib64/libdl-2.14.so
3cdfe03000-3cdfe04000 rwxp 3000 fd:01 71696776  
/lib64/libdl-2.14.so
3ce000-3ce0015000 r-xp  fd:01 71696796  
/lib64/libgcc_s-4.6.0-20110603.so.1
3ce0015000-3ce0214000 ---p 00015000 fd:01 71696796  
/lib64/libgcc_s-4.6.0-20110603.so.1
3ce0214000-3ce0215000 rwxp 00014000 fd:01 71696796  
/lib64/libgcc_s-4.6.0-20110603.so.1
3ce040-3ce0416000 r-xp  fd:01 71696774  
/lib64/libz.so.1.2.5
3ce0416000-3ce0616000 ---p 00016000 fd:01 71696774  
/lib64/libz.so.1.2.5
3ce0616000-3ce0617000 rwxp 00016000 fd:01 71696774  
/lib64/libz.so.1.2.5
3ce200-3ce20e8000 r-xp  fd:01 891   
/usr/lib64/libstdc++.so.6.0.16
3ce20e8000-3ce22e8000 ---p 000e8000 fd:01 891   
/usr/lib64/libstdc++.so.6.0.16
3ce22e8000-3ce22f r-xp 000e8000 fd:01 891   
/usr/lib64/libstdc++.so.6.0.16
3ce22f-3ce22f2000 rwxp 000f fd:01 891   
/usr/lib64/libstdc++.so.6.0.16
3ce22f2000-3ce2307000 rwxp  00:00 0
3cea00-3cea05c000 r-xp  fd:01 71698673  
/lib64/libfreebl3.so
3cea05c000-3cea25b000 ---p 0005c000 fd:01 71698673  
/lib64/libfreebl3.so
3cea25b000-3cea25d000 rwxp 0005b000 fd:01 71698673  
/lib64/libfreebl3.so
3cea25d000-3cea261000 rwxp  00:00 0
3cea40-3cea408000 r-xp  fd:01 71698674  
/lib64/libcrypt-2.14.so
3cea408000-3cea607000 ---p 8000 fd:01 71698674  
/lib64/libcrypt-2.14.so
3cea607000-3cea608000 r-xp 7000 fd:01 71698674  
/lib64/libcrypt-2.14.so
3cea608000-3cea609000 rwxp 8000 fd:01 71698674

Re: [Freesurfer] tracula bvecs problem

If i flip4fsl my fake file the the numbers after the decimal point are missing 
in the output (bvecs_bvecs_onezero3decpoint1_western_out).

I have attached a fake bvecs fitting your tutorial data (70 lines). Would you 
be so kind, as to run this.

Thank you so much for your help,
Franz

bvecs_bvecs_onezero3decpoint1_western_out
Description: Binary data

bvecs_faketutorial
Description: Binary data

Am 06.07.2011 um 19:48 schrieb Anastasia Yendiki:

> 
> I'd need the nifti file to run flip4fsl. Can you try it on your data?
> 
> On Wed, 6 Jul 2011, Franz Liem wrote:
> 
>> does your flip4fsl convert this file correctly (with the numbers after the 
>> decimal point)?
>> 
>> Thank you,
>> Franz
>> 
>> Am 06.07.2011 um 18:06 schrieb Anastasia Yendiki:
>> 
>>> 
>>> Yes!
>>> 
>>> On Wed, 6 Jul 2011, Franz Liem wrote:
>>> 
 Hi Anastasia,
 thank you. I created this file from scratch with osx' TextEdit and saved 
 it as western european (Mac OS Roman).
 Are you able to read this?

 Thanks,
 Franz

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>> 
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Re: [Freesurfer] Hippocampal subfield segmentation

2011-07-06 Thread Wayne Su

Hi Koen,
Look like the outputs (posterior_*.mgz) are probability kind of images. How
can I transfer them back into 1x1x1 mm^3 FS space? Maybe merge them into one
image without overlapping?
Or maybe transfer my own image into this 0.5x0.5x0.5 mm^3 space. How can I
achieve this?
Thanks,
Wayne 


On 06/07/11 5:59 AM, "Koen Van Leemput"  wrote:

> Hi Tricia,
> 
> Yes, that summarizes it neatly. :-)
> 
> Koen
> 
> 
> On Mon, Jul 4, 2011 at 10:44 PM, Tricia Merkley  wrote:
>> Hi,
>> 
>> I understand that the models for the hippocampal subfield segmentation were
>> created using high resolution MRI scans.  But it sounds like this procedure
>> can be used for scans with 1mm ^3 resolution, right?  The resulting values
>> would just need to be divided by 8 in order to get the subfield volumes in
>> 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3. 
>> Is that correct?
>> 
>> Thanks,
>> Tricia Merkley
>> 
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>> 
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Re: [Freesurfer] tracula bvecs problem


I'd need the nifti file to run flip4fsl. Can you try it on your data?

On Wed, 6 Jul 2011, Franz Liem wrote:

> does your flip4fsl convert this file correctly (with the numbers after the 
> decimal point)?
>
> Thank you,
> Franz
>
> Am 06.07.2011 um 18:06 schrieb Anastasia Yendiki:
>
>>
>> Yes!
>>
>> On Wed, 6 Jul 2011, Franz Liem wrote:
>>
>>> Hi Anastasia,
>>> thank you. I created this file from scratch with osx' TextEdit and saved it 
>>> as western european (Mac OS Roman).
>>> Are you able to read this?
>>>
>>> Thanks,
>>> Franz
>>>
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>>
>>
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>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
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>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
>
>
>
>
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[Freesurfer] glibc detected *** mris_make_surfaces: double free or corruption (!prev): 0x000000003710cc10

2011-07-06 Thread Knut J Bjuland

The name of the subjects is 3. The command that was used were  recon-all
-autorecon2-pial -s 3. I then issued the bugr and got this output. I
have also included the error message. I belive that there were an double
free or an corruption detected by glibc. The recon-all files is available upon 
request.


Cheers
Knut J 




--
FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

RedHat release: Fedora release 15 (Lovelock)

Kernel info: Linux 2.6.38.8-32.fc15.x86_64 x86_64






*** glibc detected *** mris_make_surfaces: double free or corruption
(!prev): 0x3710cc10 ***
=== Backtrace: =
/lib64/libc.so.6[0x3cdf07703a]
mris_make_surfaces[0x518a39]
mris_make_surfaces[0x5a7e3c]
mris_make_surfaces[0x40f172]
/lib64/libc.so.6(__libc_start_main+0xed)[0x3cdf02139d]
mris_make_surfaces(__gxx_personality_v0+0x18a)[0x40bf5a]
=== Memory map: 
0040-00cf1000 r-xp  00:00 0
00cf1000-00df ---p  00:00 0
00df-26b79000 rwxp  00:00 0
26eb9000-383d5000 rwxp  00:00 0 
[heap]
3cdec0-3cdec1f000 r-xp  fd:01 71696709  
/lib64/ld-2.14.so
3cdec1f000-3cdee1e000 ---p  00:00 0
3cdee1e000-3cdee1f000 r-xp 0001e000 fd:01 71696709  
/lib64/ld-2.14.so
3cdee1f000-3cdee2 rwxp 0001f000 fd:01 71696709  
/lib64/ld-2.14.so
3cdee2-3cdee21000 rwxp  00:00 0
3cdf00-3cdf18f000 r-xp  fd:01 71696719  
/lib64/libc-2.14.so
3cdf18f000-3cdf38e000 ---p 0018f000 fd:01 71696719  
/lib64/libc-2.14.so
3cdf38e000-3cdf392000 r-xp 0018e000 fd:01 71696719  
/lib64/libc-2.14.so
3cdf392000-3cdf393000 rwxp 00192000 fd:01 71696719  
/lib64/libc-2.14.so
3cdf393000-3cdf399000 rwxp  00:00 0
3cdf40-3cdf483000 r-xp  fd:01 71696792  
/lib64/libm-2.14.so
3cdf483000-3cdf682000 ---p 00083000 fd:01 71696792  
/lib64/libm-2.14.so
3cdf682000-3cdf683000 r-xp 00082000 fd:01 71696792  
/lib64/libm-2.14.so
3cdf683000-3cdf684000 rwxp 00083000 fd:01 71696792  
/lib64/libm-2.14.so
3cdf80-3cdf816000 r-xp  fd:01 71696723  
/lib64/libpthread-2.14.so
3cdf816000-3cdfa15000 ---p 00016000 fd:01 71696723  
/lib64/libpthread-2.14.so
3cdfa15000-3cdfa16000 r-xp 00015000 fd:01 71696723  
/lib64/libpthread-2.14.so
3cdfa16000-3cdfa17000 rwxp 00016000 fd:01 71696723  
/lib64/libpthread-2.14.so
3cdfa17000-3cdfa1b000 rwxp  00:00 0
3cdfc0-3cdfc02000 r-xp  fd:01 71696776  
/lib64/libdl-2.14.so
3cdfc02000-3cdfe02000 ---p 2000 fd:01 71696776  
/lib64/libdl-2.14.so
3cdfe02000-3cdfe03000 r-xp 2000 fd:01 71696776  
/lib64/libdl-2.14.so
3cdfe03000-3cdfe04000 rwxp 3000 fd:01 71696776  
/lib64/libdl-2.14.so
3ce000-3ce0015000 r-xp  fd:01 71696796  
/lib64/libgcc_s-4.6.0-20110603.so.1
3ce0015000-3ce0214000 ---p 00015000 fd:01 71696796  
/lib64/libgcc_s-4.6.0-20110603.so.1
3ce0214000-3ce0215000 rwxp 00014000 fd:01 71696796  
/lib64/libgcc_s-4.6.0-20110603.so.1
3ce040-3ce0416000 r-xp  fd:01 71696774  
/lib64/libz.so.1.2.5
3ce0416000-3ce0616000 ---p 00016000 fd:01 71696774  
/lib64/libz.so.1.2.5
3ce0616000-3ce0617000 rwxp 00016000 fd:01 71696774  
/lib64/libz.so.1.2.5
3ce200-3ce20e8000 r-xp  fd:01 891   
/usr/lib64/libstdc++.so.6.0.16
3ce20e8000-3ce22e8000 ---p 000e8000 fd:01 891   
/usr/lib64/libstdc++.so.6.0.16
3ce22e8000-3ce22f r-xp 000e8000 fd:01 891   
/usr/lib64/libstdc++.so.6.0.16
3ce22f-3ce22f2000 rwxp 000f fd:01 891   
/usr/lib64/libstdc++.so.6.0.16
3ce22f2000-3ce2307000 rwxp  00:00 0
3cea00-3cea05c000 r-xp  fd:01 71698673  
/lib64/libfreebl3.so
3cea05c000-3cea25b000 ---p 0005c000 fd:01 71698673  
/lib64/libfreebl3.so
3cea25b000-3cea25d000 rwxp 0005b000 fd:01 71698673  
/lib64/libfreebl3.so
3cea25d000-3cea261000 rwxp  00:00 0
3cea40-3cea408000 r-xp  fd:01 71698674  
/lib64/libcrypt-2.14.so
3cea408000-3cea607000 ---p 8000 fd:01 71698674  
/lib64/libcrypt-2.14.so
3cea607000-3cea608000 r-xp 7000 fd:01 71698674  
/lib64/libcrypt-2.14.so
3cea608000-3cea609000 rwxp 8000 fd:01 71698674

Re: [Freesurfer] tracula bvecs problem

does your flip4fsl convert this file correctly (with the numbers after the 
decimal point)?

Thank you,
Franz

Am 06.07.2011 um 18:06 schrieb Anastasia Yendiki:

> 
> Yes!
> 
> On Wed, 6 Jul 2011, Franz Liem wrote:
> 
>> Hi Anastasia,
>> thank you. I created this file from scratch with osx' TextEdit and saved it 
>> as western european (Mac OS Roman).
>> Are you able to read this?
>> 
>> Thanks,
>> Franz
>> 
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Re: [Freesurfer] tracula bvecs problem

Yes!

On Wed, 6 Jul 2011, Franz Liem wrote:

> Hi Anastasia,
> thank you. I created this file from scratch with osx' TextEdit and saved it 
> as western european (Mac OS Roman).
> Are you able to read this?
>
> Thanks,
> Franz
>
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[Freesurfer] Subject information

2011-07-06 Thread leonardo kay

Hi all


Is there someway (command line) to get direct information on each  subject
acquisition parameters?

Best regards.
-- 
Leo Kay.
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Re: [Freesurfer] tracula bvecs problem

2011-07-06 Thread Pedro Paulo de Magalhães Oliveira Junior

Hi Anastasia,
thank you. I created this file from scratch with osx' TextEdit and saved it as 
western european (Mac OS Roman).
Are you able to read this?

Thanks,
Franz


bvecs_onezero3decpoint1_western
Description: Binary data

Am 06.07.2011 um 17:42 schrieb Anastasia Yendiki:
> 
> Hi Franz - Looks like it may be a windows vs. unix text file issue.
> 
> Looking at dwi_orig.mghdti.bvecs under unix, it seems that it has 
> windows-specific carriage returns (they look like "^M" in unix). Actually, 
> I could only see this on a darwin machine, on a centos machine I can only 
> read the first 3 lines of the file. This was probably courtesy of excel. 
> Can you try using dos2unix on the files or saving them in another program?
> 
> a.y
> 
> On Wed, 6 Jul 2011, Franz Liem wrote:
> 
>> Hi Priti and Anastasia.
>> 
>> Thank you very much for your replies.
>> 
>> Prit, I ran you modified_bvecs. This resulted in zeros (see bvecs_out). I 
>> also tried the modified_bvecs in a tab-deliniated version. same result.
>> 
>> Anastasia, the original bvecs file is attached as bvecs_orig. I imported 
>> this into excel and transposed it. Since (cp $bvecfile 
>> $dwidir/dwi_orig.mghdti.bvecs) the dwi_orig.mghdti.bvecs from my first 
>> post should be an exact copy of my original input.
>> 
>> 
>> 1) I then took the bvecs file provided in the tutorial data (and deleted the 
>> lines >33). This again resulted in zeros (see bvecs_tutorial_out).
>> 
>> 2) I then created a file with only ones and zeros (see 
>> bvecs_onezero_western):
>> 33 lines of
>> 0 0 0
>> 1 0 0
>> 
>> 
>> This resulted in correct bvecs after ecc (see bvecs_onezero_western_out).
>> 
>> 
>> 3) I then appended .000 (see bvecs_onezero3dec_western)
>> 0.000 0.000 0.000
>> 1.000 0.000 0.000
>> ...
>> 
>> this resulted in the exact same bvecs after ecc (with integers - see 
>> bvecs_onezero3dec_western_out).
>> 
>> 4) I then wrote 1.100 (instead of 1.000; see 
>> bvecs_onezero3decpoint1_western). This again led to the same output (see 
>> bvecs_bvecs_onezero3decpoint1_western_out).
>> 
>> So in conclusion, it seems as if the flip4fsl cannot read the digits after 
>> the decimal point. Can you reproduce this error? Might this be a problem 
>> with my german-language-settings computer (mac osx 10.6.4; although, since 
>> it is a swiss-german machine the system wide setting for decimal separator 
>> is the dot )?
>> 
>> Thank you,
>> Franz
>> 
>> 
>> 
>> 
>> 
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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

I usually can run one instance of FreeSurfer with 1GB if I use the -no-gut
flag

I have a benchmark of 4 recon-all running in a 4 Core AMD with 4GB RAM that
took only 10% more time than one recon-all alone.

2011/7/6 John Jan Drozd 

> Hi Bruce,
>
> Thanks for pointing this out to me about the RAM.
>
> I have 8 Gb of RAM. So I guess I can safely run 3 or 4 subjects
> simultaneously if each subject requires 2 to 3 Gb of RAM.
>
> Thanks,
> John
>
> Sent from my iPhone
>
> On 2011-07-05, at 6:08 PM, Bruce Fischl 
> wrote:
>
> > how much ram do you have? You'll need at least 2G/subject if not 3
> > On Tue, 5 Jul 2011, John Drozd wrote:
> >
> >> Hi Bruce,
> >> Thanks for the suggestion, Bruce. I'll run 8 different subjects at once.
> >> Take care,
> >> John
> >> 2011/7/5 Bruce Fischl 
> >> Sorry, that won't help a single subject much, although there are
> >> options to run the hemis in parallel. You can run multiple
> >> subjects at the same time, which is what we usually do. Or you
> >> can use cuss
> >> On Jul 5, 2011, at 5:11 PM, John Drozd  wrote:
> >>
> >> Hi Bruce,
> >>
> >> Okay, thank you. I understand and can see that to do an
> >> accurate job, the pipeline must be complicated.
> >> I have eight processors on my linux desktop computer.
> >> Maybe some parts of recon-all are multi-threaded which
> >> could speed things up for me :-)
> >>
> >> Thank you,
> >> John
> >>
> >> 2011/7/5 Bruce Fischl 
> >> sorry, but the majority of the time is
> >> required. We're working to speed things up,
> >> but it is complicated software with multiple
> >> nonlinear warps, segmentation procedures,
> >> etc
> >> Bruce
> >> On Tue, 5 Jul 2011, John Drozd wrote:
> >>
> >> Hi Bruce and Pedro,
> >>
> >> Thank you both for sending me your
> >> suggestions.
> >> Just to let you know, because my .dcm (dicom)
> >> files had a space and two dots
> >> in the filenames:
> >> (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
> >> (and using quotes around the file name or "\ "
> >> within the filename without
> >> the quotes did not work with recon-all),
> >> recon-all truncated the filename
> >> before the space as "2008_12_08.ek" feeding it
> >> to an mri_convert command and
> >> gave an error message.
> >>
> >> So I worked around this problem as follows: I
> >> converted the .dcm series to a
> >> nifti .nii volume using 3D Slicer, and then
> >> used mri_convert to convert the
> >> .nii format to .mgz format. Then I ran
> >> recon-all on the .mgz formatted file
> >> and it is now running successfully.
> >>
> >> I see on the online tutorials and slides, that
> >> this process takes about 20
> >> hours. Is there a way to only run partial
> >> steps pertaining only to the
> >> cortical thickness?
> >>
> >> Pedro also suggested that I go through the
> >> FreeSurferBeginnersGuide wiki
> >> which I am doing now.
> >>
> >> Also, reading some mailing lists emails, I
> >> noticed that matlab can be used
> >> to analyze the cortical thickness statistiics,
> >> and also freesurfer comes
> >> with matlab scripts. I will try these tools
> >> out as well.
> >>
> >> Thank you for your time,
> >> John
> >>
> >> On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl
> >> 
> >> wrote:
> >> recon-all \
> >> -i  >> dicom series> \
> >> -s  \
> >> -sd  >> folder in> \
> >> -all
> >>
> >> cheers
> >> Bruce
> >>
> >> On Tue, 5 Jul 2011, John Drozd wrote:
> >>
> >> Hi,
> >>
> >> I am running freesurfer on 64 bit Fedora
> >> 10 linux.
> >> I am using version:
> >>
> >> freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
> >> Can anyone point me to a reference web
> >> page listing what
> >> steps I need to
> >> type to process
> >> a series of MRI dicom slices and use
> >> FreeSurfer to measure
> >> cortical
> >> thickness for this dicom series?
> >>
> >> Thank you,
> >> John
> >>
> >> --
> >> John Drozd
> >> Post-Doctoral Fellow, Robarts Research
> >> Institute
> >> The University of Western Ontario
> >> London, ON, Canada
> >> http://publish.uwo.ca/~jdrozd2/index.htm
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >> The information in this e-mail is intended
> >> only for the person to whom
> >> it is
> >> addressed. If you believe this e-mail was sent
> >> to you in error and the
> >> e-mail
> >> contains patient information, please contact
> >> the Partners Compliance
> >> HelpLine at
> >> http://www.partners.org/complianceline . If
> >> the e-mail was sent to you
> >> in error
> >> but does not contain patient information,
> >> please contact the sender
> >> and properly
> >> dispose of the e-mail.
> >>
> >> --
> >> John Drozd
> >> Post-Doctoral Fellow, Robarts Research
> >> Institute
> >> The University of Western Ontario
> >> London, ON, Canada
> >> http://publish.uwo.ca/~jdrozd2/index.htm
> >>
> >> --
> >> John Drozd
> >> Post-Doctoral Fellow, Robarts Research Institute
> >> The University of Western Ontari

Re: [Freesurfer] tracula bvecs problem

Hi Franz - Looks like it may be a windows vs. unix text file issue.

Looking at dwi_orig.mghdti.bvecs under unix, it seems that it has 
windows-specific carriage returns (they look like "^M" in unix). Actually, 
I could only see this on a darwin machine, on a centos machine I can only 
read the first 3 lines of the file. This was probably courtesy of excel. 
Can you try using dos2unix on the files or saving them in another program?

a.y

On Wed, 6 Jul 2011, Franz Liem wrote:

> Hi Priti and Anastasia.
>
> Thank you very much for your replies.
>
> Prit, I ran you modified_bvecs. This resulted in zeros (see bvecs_out). I 
> also tried the modified_bvecs in a tab-deliniated version. same result.
>
> Anastasia, the original bvecs file is attached as bvecs_orig. I imported 
> this into excel and transposed it. Since (cp $bvecfile 
> $dwidir/dwi_orig.mghdti.bvecs) the dwi_orig.mghdti.bvecs from my first 
> post should be an exact copy of my original input.
>
>
> 1) I then took the bvecs file provided in the tutorial data (and deleted the 
> lines >33). This again resulted in zeros (see bvecs_tutorial_out).
>
> 2) I then created a file with only ones and zeros (see bvecs_onezero_western):
> 33 lines of
> 0 0 0
> 1 0 0
> 
>
> This resulted in correct bvecs after ecc (see bvecs_onezero_western_out).
>
>
> 3) I then appended .000 (see bvecs_onezero3dec_western)
> 0.000 0.000 0.000
> 1.000 0.000 0.000
> ...
>
> this resulted in the exact same bvecs after ecc (with integers - see 
> bvecs_onezero3dec_western_out).
>
> 4) I then wrote 1.100 (instead of 1.000; see 
> bvecs_onezero3decpoint1_western). This again led to the same output (see 
> bvecs_bvecs_onezero3decpoint1_western_out).
>
> So in conclusion, it seems as if the flip4fsl cannot read the digits after 
> the decimal point. Can you reproduce this error? Might this be a problem with 
> my german-language-settings computer (mac osx 10.6.4; although, since it is a 
> swiss-german machine the system wide setting for decimal separator is the dot 
> )?
>
> Thank you,
> Franz
>
>
>
>
>
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Re: [Freesurfer] tracula bvecs problem


Hi Franz - As long as you have a good aparc+aseg, the exact version of the 
recon should not matter.

a.y

On Wed, 6 Jul 2011, Franz Liem wrote:

> and another question.
> Is it OK to run tracula with recons done with an earlier version (5.0.0)?
>
> Thank you,
> Franz
>
> Am 06.07.2011 um 00:05 schrieb Anastasia Yendiki:
>
>>
>> Hi Franz - Which of the files that you sent us are the original files (the 
>> bvalfile and bvecfile from your dmrirc)? I could not find any files that had 
>> 33 lines among your attachments so I'm not sure what your input files look 
>> like.
>>
>> Thanks,
>> a.y
>>
>> On Tue, 5 Jul 2011, Franz Liem wrote:
>>
>>> Hello again.
>>>
>>> I dug into the code and could locate the problem (I don't have a solution, 
>>> though. My coding skills are quite amateurish.) I think the problem somehow 
>>> lies in the format of my bvecs file.
>>>
>>> flip4fsl is not able to read it correctly:
>>> ---
>>> if (-e $inbvecs) then
>>> echo "INFO: found $inbvecs, converting to FSL format"
>>> if $fslflipx then
>>>   set sign = `echo $inorient | sed "s/[RAS]/+\ /g; s/[LPI]/-\ /g"`
>>> endif
>>> cp /dev/null $outbvecs
>>> foreach j (1 2 3)
>>>   foreach k (1 2 3)
>>> if ($order[$k] == $j) then
>>>   printf '%s ' `cat $inbvecs | awk -v sgn=$sign[$k]1 -v n=$k '{print 
>>> sgn*$n}'` \
>>>  >> $outbvecs
>>>   printf '\n' >> $outbvecs
>>> endif
>>>   end
>>> end
>>> endif
>>> ---
>>>
>>> I tried
>>> awk '{ print $1 }' bvecs (with my original bvecs file)
>>> this printed:
>>> 0
>>>
>>> This has something to do with the file's carriage return. I then produced a 
>>> new bvecs file by manually typing values into a new text file. Now awk '{ 
>>> print $1 }' bvecs  delivers one column with 33 lines.
>>>
>>>
>>> Nevertheless, the bvecs output of flip4fsl is weird (full of zeros; 3 x 66; 
>>> see attachment).
>>> I don't really get how this printf  & awk command works.
>>>
>>> Any comments are very much appreciated.
>>> Franz
>>>
>>>
>>>
>>>
>>
>>
>> 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] mri_cvs_register version for CentOS4 and CentOS5

2011-07-06 Thread Lilla Zollei

Hi, Yes, you should. Lilla On Sat, 11 Jun 2011, t...@ms36.hinet.net wrote: >

Dear FS experts

I download CentOS5 x86-64 version (not CentOS4) of FS 5.1. should I > need to upgrade the mri_cvs_register and applyMorph for correction ?

best

JLH

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Re: [Freesurfer] Problems with automatic labelling of V1 using the Hinds method in 5.1.0


h, we'll take a look
On Wed, 6 Jul 2011, Krish Singh wrote:


Hi Bruce,
I have previously tried a completely clean recon-all and got the same
problem, but I did not use "-make all". I'll try that.

One thing I'm not sure if you noticed, though: 

If you look at the extract of the .out file I sent (between the  below),
you can see that the 5.1.0 version of mris_spherical_average crashes when
trying to load a file called lh.white from the surf subdirectory in the
V1_average (i.e. not from my data).

The 4.4.0 version of mris_spherical_average, when run on the same data as
part of the -label-v1 pipeline, does not throw this error.

It's odd that it tries to load this file because, from what I can see, the
V1_average subject provided in 5.1.0 (and 4.4.0) does not have any white
surface reconstructions?

Many thanks,

Krish

--
Prof. Krish Singh
CUBRIC
School of Psychology / Ysgol Seicoleg
Cardiff University /  Prifysgol Caerdydd
Park Place / Plas y Parc
Cardiff  / Caerdydd
CF10 3AT, UK
Tel / Ffôn: 02920 874690 / 870365 
Fax / Ffacs: 02920 870339
Email / Ebost : sing...@cardiff.ac.uk




On 6 Jul 2011, at 15:15, Bruce Fischl wrote:

  Hi Krish

  sounds like the processing of the subject was not finished. Can
  you run recon-all -s  -make all

  then rerun the hinds stuff?

  cheers
  Bruce



  On Wed, 6 Jul 2011, Krish Singh wrote:

Hi there,

I'm using Freesurfer version 5.1.0 to automatically
define labels for left

and right V1 using the method outlined in Hinds et
al.

To do this I add the -label-v1 flag to my recon-all
command line.

The problem is that this always fails with the
following error visible in

the .out file:

---

mris_spherical_average -osurf v1.invivo.reg -n -o
240211-50 label

lh.v1.invivo.label lh v1.invivo.reg V1_average

/cubric/scratch/CCGG/Freesurf/240211-50/label/lh.v1.prob.label

output surface = v1.invivo.reg

painting output onto subject 240211-50.

processing subject V1_average...

MRISreadVertexPosition(white): could not open file

/cubric/scratch/CCGG/Freesurf/V1_average/surf/lh.white

No such file or directory

MRISreadOriginalProperties: could not read surface
file white

No such file or directory

could not read surface positions from white

No such file or directory

---

The problem seems to be with the current version of
mris_spherical_average -

 if I modify the command line above to explicitly
execute the old (4.4.0)

version of mris_spherical_average then I do not get
this error and the

script completes without problems.

I'd be grateful of any advice/help on this.

Best Wishes,

Krish

--

Prof. Krish Singh

CUBRIC

School of Psychology / Ysgol Seicoleg

Cardiff University /  Prifysgol Caerdydd

Park Place / Plas y Parc

Cardiff  / Caerdydd

CF10 3AT, UK

Tel / Ffôn: 02920 874690 / 870365 

Fax / Ffacs: 02920 870339

Email / Ebost : sing...@cardiff.ac.uk




  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
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Re: [Freesurfer] Problems with automatic labelling of V1 using the Hinds method in 5.1.0

2011-07-06 Thread Krish Singh

Hi Bruce,

I have previously tried a completely clean recon-all and got the same problem, 
but I did not use "-make all". I'll try that.

One thing I'm not sure if you noticed, though: 

If you look at the extract of the .out file I sent (between the  below), 
you can see that the 5.1.0 version of mris_spherical_average crashes when 
trying to load a file called lh.white from the surf subdirectory in the 
V1_average (i.e. not from my data).

The 4.4.0 version of mris_spherical_average, when run on the same data as part 
of the -label-v1 pipeline, does not throw this error.

It's odd that it tries to load this file because, from what I can see, the 
V1_average subject provided in 5.1.0 (and 4.4.0) does not have any white 
surface reconstructions?

Many thanks,

Krish

--
Prof. Krish Singh
CUBRIC
School of Psychology / Ysgol Seicoleg
Cardiff University /  Prifysgol Caerdydd
Park Place / Plas y Parc
Cardiff  / Caerdydd
CF10 3AT, UK
Tel / Ffôn: 02920 874690 / 870365 
Fax / Ffacs: 02920 870339
Email / Ebost : sing...@cardiff.ac.uk




On 6 Jul 2011, at 15:15, Bruce Fischl wrote:

> Hi Krish
> 
> sounds like the processing of the subject was not finished. Can you run 
> recon-all -s  -make all
> 
> then rerun the hinds stuff?
> 
> cheers
> Bruce
> 
> 
> 
> On Wed, 6 Jul 2011, Krish Singh wrote:
> 
>> Hi there,
>> I'm using Freesurfer version 5.1.0 to automatically define labels for left
>> and right V1 using the method outlined in Hinds et al.
>> To do this I add the -label-v1 flag to my recon-all command line.
>> The problem is that this always fails with the following error visible in
>> the .out file:
>> ---
>> mris_spherical_average -osurf v1.invivo.reg -n -o 240211-50 label
>> lh.v1.invivo.label lh v1.invivo.reg V1_average
>> /cubric/scratch/CCGG/Freesurf/240211-50/label/lh.v1.prob.label
>> output surface = v1.invivo.reg
>> painting output onto subject 240211-50.
>> processing subject V1_average...
>> MRISreadVertexPosition(white): could not open file
>> /cubric/scratch/CCGG/Freesurf/V1_average/surf/lh.white
>> No such file or directory
>> MRISreadOriginalProperties: could not read surface file white
>> No such file or directory
>> could not read surface positions from white
>> No such file or directory
>> ---
>> The problem seems to be with the current version of mris_spherical_average -
>>  if I modify the command line above to explicitly execute the old (4.4.0)
>> version of mris_spherical_average then I do not get this error and the
>> script completes without problems.
>> I'd be grateful of any advice/help on this.
>> Best Wishes,
>> Krish
>> --
>> Prof. Krish Singh
>> CUBRIC
>> School of Psychology / Ysgol Seicoleg
>> Cardiff University /  Prifysgol Caerdydd
>> Park Place / Plas y Parc
>> Cardiff  / Caerdydd
>> CF10 3AT, UK
>> Tel / Ffôn: 02920 874690 / 870365 
>> Fax / Ffacs: 02920 870339
>> Email / Ebost : sing...@cardiff.ac.uk
>> 
> 
> 
> 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] calculating the surface area of each region on Desikan template


I believe this should be in the aparc*.stats files
cheers
Bruce

On Wed, 6 Jul 2011, 
Zhangyuanchao wrote:



hi, expert,
 
How could I obtain the surface area of each region on the Desikan template?
How can I obtain this area in both native space and the average template
space?
In the surf folder of each subjects, I noticed there is lh.area file, what
is meaning of this file? Do I need ?h.area for calculating the area of each
region?
 
yuanchao zhang

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Re: [Freesurfer] Problems with automatic labelling of V1 using the Hinds method in 5.1.0


Hi Krish

sounds like the processing of the subject was not finished. Can you run 
recon-all -s  -make all


then rerun the hinds stuff?

cheers
Bruce



On Wed, 6 Jul 2011, Krish Singh wrote:


Hi there,
I'm using Freesurfer version 5.1.0 to automatically define labels for left
and right V1 using the method outlined in Hinds et al.

To do this I add the -label-v1 flag to my recon-all command line.

The problem is that this always fails with the following error visible in
the .out file:

---
mris_spherical_average -osurf v1.invivo.reg -n -o 240211-50 label
lh.v1.invivo.label lh v1.invivo.reg V1_average
/cubric/scratch/CCGG/Freesurf/240211-50/label/lh.v1.prob.label

output surface = v1.invivo.reg
painting output onto subject 240211-50.
processing subject V1_average...
MRISreadVertexPosition(white): could not open file
/cubric/scratch/CCGG/Freesurf/V1_average/surf/lh.white
No such file or directory
MRISreadOriginalProperties: could not read surface file white
No such file or directory
could not read surface positions from white
No such file or directory
---

The problem seems to be with the current version of mris_spherical_average -
 if I modify the command line above to explicitly execute the old (4.4.0)
version of mris_spherical_average then I do not get this error and the
script completes without problems.

I'd be grateful of any advice/help on this.

Best Wishes,

Krish

--
Prof. Krish Singh
CUBRIC
School of Psychology / Ysgol Seicoleg
Cardiff University /  Prifysgol Caerdydd
Park Place / Plas y Parc
Cardiff  / Caerdydd
CF10 3AT, UK
Tel / Ffôn: 02920 874690 / 870365 
Fax / Ffacs: 02920 870339
Email / Ebost : sing...@cardiff.ac.uk





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[Freesurfer] Problems with automatic labelling of V1 using the Hinds method in 5.1.0

2011-07-06 Thread Krish Singh

Hi there,

I'm using Freesurfer version 5.1.0 to automatically define labels for left and 
right V1 using the method outlined in Hinds et al.

To do this I add the -label-v1 flag to my recon-all command line.

The problem is that this always fails with the following error visible in the 
.out file:

---
mris_spherical_average -osurf v1.invivo.reg -n -o 240211-50 label 
lh.v1.invivo.label lh v1.invivo.reg V1_average 
/cubric/scratch/CCGG/Freesurf/240211-50/label/lh.v1.prob.label

output surface = v1.invivo.reg
painting output onto subject 240211-50.
processing subject V1_average...
MRISreadVertexPosition(white): could not open file 
/cubric/scratch/CCGG/Freesurf/V1_average/surf/lh.white
No such file or directory
MRISreadOriginalProperties: could not read surface file white
No such file or directory
could not read surface positions from white
No such file or directory
---

The problem seems to be with the current version of mris_spherical_average -  
if I modify the command line above to explicitly execute the old (4.4.0) 
version of mris_spherical_average then I do not get this error and the script 
completes without problems.

I'd be grateful of any advice/help on this.

Best Wishes,

Krish

--
Prof. Krish Singh
CUBRIC
School of Psychology / Ysgol Seicoleg
Cardiff University /  Prifysgol Caerdydd
Park Place / Plas y Parc
Cardiff  / Caerdydd
CF10 3AT, UK
Tel / Ffôn: 02920 874690 / 870365 
Fax / Ffacs: 02920 870339
Email / Ebost : sing...@cardiff.ac.uk




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[Freesurfer] tkmedit error message even though tksurfer runs correctly

2011-07-06 Thread Sandy Goncalves

Hello!

I am brand new to this software (and command for that matter) and need some 
help. After installing all the software, when I enter tkmedit in the xterminal, 
I receive an error message that looks like this:
X Error of failed request: BadRequest (invalid request code or no such 
operation)
?? ? Major opcode of failed request: 128 (Apple-DRI)
?? ? Minor opcode of failed request: 1 ()
?? ? Serial number of failed request: 16
?? ? Current serial number in output stream: 16

Interestingly, when I type in tksurfer, this works. So I'm not sure what I 
should do in order to get tkmedit to work! Any help would be great!

Thanks,

Sandy
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[Freesurfer] Error while loading qdec project file

2011-07-06 Thread Tetiana Dadakova

Dear experts,

When I try to load a saved Project File, I get an error:

Loading data table /tmp/qdec_project_archive/qdec.table.dat...
ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat
Error loading the project file.

I do not have any /tmp subdirectory. Should it appear when I save the
Project File? Should it be in /qdec directory?

Thank you,
Tanja.
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Re: [Freesurfer] mri_cvs_register update

2011-07-06 Thread Lilla Zollei

Hi Peter,

The changes in the mri_cvs_register script do not affect the recon-all 
stream. All data that you analyzed with recon-all should be all set, the 
only changes that are indicated below are ones that affect 
mri)cvs_register.

Lilla

On Fri, 10 Jun 2011, Peter J. Molfese wrote:

> Is this significant enough that we should re-run data processed using the 
> standard recon-all stream in version 5.1?
>
> Thanks,
> Peter
>
> On Jun 10, 2011, at 3:28 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>
>> Message: 2
>> Date: Fri, 10 Jun 2011 12:59:34 -0400 (EDT)
>> From: Lilla Zollei 
>> Subject: [Freesurfer] mri_cvs_register update
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>>  
>> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>>
>>
>> Hi,
>>
>> We found a bug in the mri_cvs_register script after the
>> release. Please, download the new version of applyMorph and
>> mri_cvs_register from one of the below links for Linux Centos4,
>> Linux Centos4 x86 64 and Mac Leopard respectively:
>>
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/mac-leopard-intel
>>
>> --Lilla
>
>
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Re: [Freesurfer] having two freesurfer versions at one computer

Hi Tanja,

you can, but you'll want different FREESURFER_HOMEM dirs for each one. 
You can put them wherever you want.

cheers
Bruce
On Wed, 6 Jul 2011, Tetiana Dadakova 
wrote:

> Dear list,
>
> I would like to install both 5.0 and 5.1 versions on my computer. But
> I am not sure how exactly I should proceed after downloading the 5.1
> (5.0 is already installed).
> For example, how should I set FREESURFER_HOME, can it be the same for
> both versions? Also, can I have my 5.0 in /Applications/freesurfer and
> 5.1 in /Applications/freesurfer5.1/freesurfer ?
>
> Thank you,
> Tanja.
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Re: [Freesurfer] FreeSurfer use in dogs

Hi Marjorie,

I don't know of anyone who has used it in dogs, but you could try the 
monkey stream and see if it works for you (it will disable all the 
human-specific atlases and such). It will require more manual intervention 
though

cheers
Bruce
On Wed, 6 Jul 2011, Marjorie Milne wrote:

> Hello Freesurfers,
>
> I would like to use FreeSurfer to analyse brain morphology in dogs but do not 
> know if the techniques can be applied in this species.
>
> Does anyone have experience using FreeSurfer in dogs, and any tips to get the 
> techniques to work?
>
> Regards,
> Marjorie Milne
>
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Re: [Freesurfer] MRI registration

Hi Zeynep,

CVS is designed for this.

cheers
Bruce
On Tue, 5 Jul 2011, Zeynep Akalin Acar wrote:

> Hi all,
> 
> I'm trying to register two brain volumes using Freesurfer. I need to find a
> mapping for each voxel of the MR image to the reference image. I tried using
> mri_register with the option -vf as the wiki documentation suggests that it
> outputs a vector field. Instead it expects a variance volume. The surface
> registrations do not work for me either, because they don't include a
> mapping of inner points. I tried Talairach transformation, but, it is a
> rigid registration, and I need a non-rigid registration.
> 
> Is there a tool in Freesurfer that can register two brain volumes with a
> mapping of each voxel?
> 
> Thanks,
> 
> Zeynep.
> 
>
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Re: [Freesurfer] FreeSurfer use in dogs

my own experience with analyzing mri scans of dog brains have not been
fruitful from the brain morphometry perspective.  the reason is that the
scan parameters of the brains i worked with were not setup for
morphometry (rather, for clinical diagnostics) and so were lacking in
major areas, namely the contrast was not setup to discriminate gray
matter from white matter (mainly they were T2-like) and the resolution
was typically 2.5 to 4.5mm in one plane, which makes it hopeless to
reconstruct surfaces or resolve subcortical structures.

but my approach was attempting to use freesurfer tools.  it is possible
to conduct a morphometry analysis by manually segmenting slices, but
this would of course be very time consuming.  so if you could get images
that are T1-weighted, optimized for gm/wm contrast, and close to 1x1x1mm
resolution, then the freesurfer tools could be used.  manual work would
still be required (akin to work on primate brains).

there are others i know who have tried, so i can put you into contact
with them if you want.

n.

On Wed, 2011-07-06 at 09:49 +, Marjorie Milne wrote:
> Hello Freesurfers, 
> 
> I would like to use FreeSurfer to analyse brain morphology in dogs but do not 
> know if the techniques can be applied in this species.
> 
> Does anyone have experience using FreeSurfer in dogs, and any tips to get the 
> techniques to work?
> 
> Regards,
> Marjorie Milne
> 
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> 

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Re: [Freesurfer] Hippocampal subfield segmentation

2011-07-06 Thread Koen Van Leemput

Hi Tricia,

Yes, that summarizes it neatly. :-)

Koen

On Mon, Jul 4, 2011 at 10:44 PM, Tricia Merkley  wrote:

> Hi,
>
> I understand that the models for the hippocampal subfield segmentation were
> created using high resolution MRI scans.  But it sounds like this procedure
> can be used for scans with 1mm ^3 resolution, right?  The resulting values
> would just need to be divided by 8 in order to get the subfield volumes in
> 1mm^3 though, since the resulting volumes are reported as 0.5x0.5x0.5mm^3.
> Is that correct?
>
> Thanks,
> Tricia Merkley
>
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Re: [Freesurfer] MRI registration

2011-07-06 Thread lzollei

Hi Zeynep,

Could you give more details about your registration problem? What are the
modalities that you are registering? Are they of the same subject? What
kind of registration accuracy do you expect?

--Lilla

> Hi all,
>
> I'm trying to register two brain volumes using Freesurfer. I need to find
> a
> mapping for each voxel of the MR image to the reference image. I tried
> using
> mri_register with the option -vf as the wiki documentation suggests that
> it
> outputs a vector field. Instead it expects a variance volume. The surface
> registrations do not work for me either, because they don't include a
> mapping of inner points. I tried Talairach transformation, but, it is a
> rigid registration, and I need a non-rigid registration.
>
> Is there a tool in Freesurfer that can register two brain volumes with a
> mapping of each voxel?
>
> Thanks,
>
> Zeynep.
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[Freesurfer] having two freesurfer versions at one computer

2011-07-06 Thread Tetiana Dadakova

Dear list,

I would like to install both 5.0 and 5.1 versions on my computer. But
I am not sure how exactly I should proceed after downloading the 5.1
(5.0 is already installed).
For example, how should I set FREESURFER_HOME, can it be the same for
both versions? Also, can I have my 5.0 in /Applications/freesurfer and
5.1 in /Applications/freesurfer5.1/freesurfer ?

Thank you,
Tanja.
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[Freesurfer] FreeSurfer use in dogs

2011-07-06 Thread Marjorie Milne

Hello Freesurfers, 

I would like to use FreeSurfer to analyse brain morphology in dogs but do not 
know if the techniques can be applied in this species.

Does anyone have experience using FreeSurfer in dogs, and any tips to get the 
techniques to work?

Regards,
Marjorie Milne

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Re: [Freesurfer] tracula bvecs problem

and another question.
Is it OK to run tracula with recons done with an earlier version (5.0.0)?

Thank you,
Franz

Am 06.07.2011 um 00:05 schrieb Anastasia Yendiki:

> 
> Hi Franz - Which of the files that you sent us are the original files (the 
> bvalfile and bvecfile from your dmrirc)? I could not find any files that had 
> 33 lines among your attachments so I'm not sure what your input files look 
> like.
> 
> Thanks,
> a.y
> 
> On Tue, 5 Jul 2011, Franz Liem wrote:
> 
>> Hello again.
>> 
>> I dug into the code and could locate the problem (I don't have a solution, 
>> though. My coding skills are quite amateurish.) I think the problem somehow 
>> lies in the format of my bvecs file.
>> 
>> flip4fsl is not able to read it correctly:
>> ---
>> if (-e $inbvecs) then
>> echo "INFO: found $inbvecs, converting to FSL format"
>> if $fslflipx then
>>   set sign = `echo $inorient | sed "s/[RAS]/+\ /g; s/[LPI]/-\ /g"`
>> endif
>> cp /dev/null $outbvecs
>> foreach j (1 2 3)
>>   foreach k (1 2 3)
>> if ($order[$k] == $j) then
>>   printf '%s ' `cat $inbvecs | awk -v sgn=$sign[$k]1 -v n=$k '{print 
>> sgn*$n}'` \
>>   >> $outbvecs
>>   printf '\n' >> $outbvecs
>> endif
>>   end
>> end
>> endif
>> ---
>> 
>> I tried
>> awk '{ print $1 }' bvecs (with my original bvecs file)
>> this printed:
>> 0
>> 
>> This has something to do with the file's carriage return. I then produced a 
>> new bvecs file by manually typing values into a new text file. Now awk '{ 
>> print $1 }' bvecs  delivers one column with 33 lines.
>> 
>> 
>> Nevertheless, the bvecs output of flip4fsl is weird (full of zeros; 3 x 66; 
>> see attachment).
>> I don't really get how this printf  & awk command works.
>> 
>> Any comments are very much appreciated.
>> Franz
>> 
>> 
>> 
>> 
> 
> 
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Re: [Freesurfer] tracula bvecs problem