[Freesurfer] R: Re: R: import FS-FAST results in FSL

[stdp82]

I'd like to open with FSLview the sig.nii.gz which is produced by 
selxavg3-sess.
If I use mri_surf2vol, which is the template to added in --template? 
It should be in Tailairach space? Where can I find the template that I 
should added?
Thanks,

Stefano

subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz 
data_type  FLOAT32
dim1   27307
dim2   1
dim3   6
dim4   1
datatype   16
pixdim11.00
pixdim21.00
pixdim31.00
pixdim41100.00
cal_max49.1815
cal_min-12.3855
file_type  NIFTI-1+







Thanks,

Stefano


>Messaggio originale
>Da: gr...@nmr.mgh.harvard.edu
>Data: 29-set-2015 22.09
>A: 
>Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL
>
>Do you mean surface-based analysis? You'd have to put them back into 
the 
>volume using mri_surf2vol, write them out as nifti and then run 
fslview 
>on them
>
>On 09/29/2015 11:17 AM, std...@virgilio.it wrote:
>>
>> Hi list,
>>
>> I would like to import FS-FAST results (conjunction maps) in 
FSL,
>> opening them by fslview.
>> Could you provide me any suggestion?
>>
>> Thank you very much
>> Best regards,
>>
>>
>> Stefano
>>
>>
>>
>>
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Re: [Freesurfer] mri_convert with --like and -rt options

[Seung-Goo KIM]

Hi Bruce,Thank you for response. This is the output message:$ mri_convert -rt nearest --like template.nii.gz label.nii.gz label_nn.nii.gzmri_convert -rt nearest --like template.nii.gz label.nii.gz label_nn.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $reading from label.nii.gz...TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 0, 0)j_ras = (0, 1, 0)k_ras = (0, 0, 1)INFO: transform src into the like-volume: template.nii.gzwriting to label_nn.nii.gz...It doesn’t print out interpolation method for reslicing, which I see when running mri_convert without “—like” switch. And the output (label_nn.nii.gz) has mixed labels due to linear interpolation.Just in case, please find the attached for the header information of the two image files.$ mri_info template.nii.gz 
Volume information for template.nii.gz
  type: nii
dimensions: 142 x 151 x 104
   voxel sizes: 1.7000, 1.7000, 1.7000
  type: FLOAT (3)
   fov: 241.400
   dof: 0
xstart: -120.7, xend: 120.7
ystart: -128.4, yend: 128.4
zstart: -88.4, zend: 88.4
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -0.0506, y_r =   0.0557, z_r =   0.9972, c_r =-1.2606
  : x_a =  -0.9987, y_a =  -0.0028, z_a =  -0.0505, c_a =14.0143
  : x_s =   0., y_s =   0.9984, z_s =  -0.0558, c_s =   -13.0322
Orientation   : PSR
Primary Slice Direction: sagittal

voxel to ras transform:
   -0.0860   0.0948   1.6952   -90.4587
   -1.6978  -0.0048  -0.0859   139.3876
0.   1.6973  -0.0949  -136.2474
0.   0.   0. 1.

voxel-to-ras determinant -4.913

ras to voxel transform:
   -0.0298  -0.5875  -0.79.1956
0.0328  -0.0017   0.587383.2187
0.5866  -0.0297  -0.032852.7279
0.   0.   0. 1.

$ mri_info label.nii.gz 
Volume information for label.nii.gz
  type: nii
dimensions: 182 x 218 x 182
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 182.000
   dof: 0
xstart: -91.0, xend: 91.0
ystart: -109.0, yend: 109.0
zstart: -91.0, zend: 91.0
TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =-1.
  : x_a =   0., y_a =   1., z_a =   0., c_a =   -17.
  : x_s =   0., y_s =   0., z_s =   1., c_s =19.
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
   -1.   0.   0.90.
0.   1.   0.  -126.
0.   0.   1.   -72.
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0.90.
   -0.   1.  -0.   126.
   -0.  -0.   1.72.
0.   0.   0. 1.Best,-SGHi Seung-GooI would have that that your command line would work as is. Can you send us the full screen output?cheersBruceOn Fri, 16 Oct 2015, Seung-Goo KIM wrote:Dear all,I wish to know whether mri_convert provide a nifty way to reslice and crop a NIFTIimage with labels (positive integers) with “—like” and “-rt” options. It seems like“—like” option overrides “-rt” option, thus the result from such a command: mri_convert -rt nearest —like ${referenceImage} ${inputImage} ${outputImage} is resampled with trilinear interpolation. I don’t know if I did something wrong(maybe file format?) or this is a bug in mri_convert.Of course, one can write a script that creates binary images for each label values,transforms it (using "mri_convert —like"), threshold it (like value>0.1), and finallyfinds the label with the highest value (probability) for each voxel in the referencespace. But I believe there should be a simpler and faster way to do this withmri_convert or any other program in freesurfer :)FIY, the version of freesurfer package I use is"Linux-centos6_x86_64-stable-pub-v5.3.0”.Best regards,-- Seung-Goo KIM
-- Seung-Goo KIM


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[Freesurfer] Using the cluster to speed up tractography

[Li, Baojuan]

Hi Freesurfer experts,

I am trying to use the clusters to run BedpostX on a Connectome
dataset.

Although the job is running now, it is running slowly. It has only got
though 18 slices over the last 10 hours:

pbsubmit -n 8 -m bl744 -c "bedpostx 
/space/iggy/5/users/baojuan/mgh_1007/diff/preproc/mri/"

As this is the first time I am using the Center's Clusters, I have a few
questions and hope someone can kindly help me or give me some suggestions.

1. How many CPUs and Vmem do you usually allocate when running BedpostX on
Connectom data?

2. Which queue do you usually use? Do I need to use the extended queue?

3. I checked the jobinfo and found the Walltime is larger than the CPUtime
which means the job did not use multiple processors. So could this be
the reason?


Thanks a lot!
Baojuan
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Re: [Freesurfer] Compiling dev version in ubuntu 15.10

[zkaufman]

Is is a warning or an error?

Passing the --disable-Werror flag to the configure script will prevent the
build from erroring out if it comes across a warning from the compiler. I
havent testing on Ubuntu 15 but I will give it a shot early early next
week.

-Zeke

> I'm preparing to migrate over to the new Ubuntu when it comes out.
>
> I'm having the following issues compiling it:
>
> The included VXL library doesnt compile, using the system version seems to
> fix this:
>
> /usr/pubsw/packages/vxl/current/include/vxl/core/vnl/algo/vnl_symmetric_eigensystem.h:82:1:
> warning: keyword 'export' not implemented, and will be ignored
> export template 
>
> The inline functions MRIgetVoxVal ... should be defined in the .h file,
> they are not, I have to comment out the inline versions
>
> ../include/mri.h:313:15: warning: inline function 'MRIgetVoxVal' declared
> but never defined
> inline float  MRIgetVoxVal(const MRI *mri, int c, int r, int s, int f);
>
> The included ITK library doesnt have the cxx11 ABI
> ../utils/libutils.a(mriio_nrrd_itk.o): In function
> `itk::MemoryAllocationError::MemoryAllocationError(std::__cxx11::basic_string std::char_traits, std::allocator > const&, unsigned int,
> std::__cxx11::basic_string,
> std::allocator > const&, std::__cxx11::basic_string std::char_traits, std::allocator > const&)':
> /usr/pubsw/packages/itk/current/include/InsightToolkit/Common/itkExceptionObject.h:174:
> undefined reference to
> `itk::ExceptionObject::ExceptionObject(std::__cxx11::basic_string std::char_traits, std::allocator > const&, unsigned int,
> std::__cxx11::basic_string,
> std::allocator > const&, std::__cxx11::basic_string std::char_traits, std::allocator > const&)'
> ../utils/libutils.a(mriio_nrrd_itk.o):(.rodata._ZTVN3itk24ImageFileReaderExceptionE[_ZTVN3itk24ImageFileReaderExceptionE]+0x40):
> undefined reference to
> `itk::ExceptionObject::SetLocation(std::__cxx11::basic_string std::char_traits, std::allocator > const&)'
> ../utils/libutils.a(mriio_nrrd_itk.o):(.rodata._ZTVN3itk24ImageFileReaderExceptionE[_ZTVN3itk24ImageFileReaderExceptionE]+0x48):
> undefined reference to
> `itk::ExceptionObject::SetDescription(std::__cxx11::basic_string std::char_traits, std::allocator > const&)'
> ../utils/libutils.a(mriio_nrrd_itk.o):(.rodata._ZTVN3itk21MemoryAllocationErrorE[_ZTVN3itk21MemoryAllocationErrorE]+0x40):
> undefined reference to
> `itk::ExceptionObject::SetLocation(std::__cxx11::basic_string std::char_traits, std::allocator > const&)'
> ../utils/libutils.a(mriio_nrrd_itk.o):(.rodata._ZTVN3itk21MemoryAllocationErrorE[_ZTVN3itk21MemoryAllocationErrorE]+0x48):
> undefined reference to
> `itk::ExceptionObject::SetDescription(std::__cxx11::basic_string std::char_traits, std::allocator > const&)'
> ../utils/libutils.a(mriio_nrrd_itk.o): In function
> `itk::ImageFileReader, 3u>,
> itk::DefaultConvertPixelTraits >
> >::GenerateOutputInformation()':
> /usr/pubsw/packages/itk/current/include/InsightToolkit/IO/itkImageFileReader.txx:136:
> undefined reference to
> `itk::ObjectFactoryBase::CreateAllInstance[abi:cxx11](char const*)'
> ../utils/libutils.a(mriio_nrrd_itk.o): In function
> `itk::ImageFileReader, 3u>,
> itk::DefaultConvertPixelTraits >
> >::DoConvertBuffer(void*, unsigned long)':
> /usr/pubsw/packages/itk/current/include/InsightToolkit/IO/itkImageFileReader.txx:545:
> undefined reference to
> `itk::ImageIOBase::GetComponentTypeAsString[abi:cxx11](itk::ImageIOBase::IOComponentType)
> const'
> ../utils/libutils.a(numerics.o):(.rodata._ZTV8fs_lbfgs[_ZTV8fs_lbfgs]+0x28):
> undefined reference to `vnl_nonlinear_minimizer::is_a[abi:cxx11]() const'
> ../utils/libutils.a(numerics.o):(.rodata._ZTV8fs_lbfgs[_ZTV8fs_lbfgs]+0x30):
> undefined reference to
> `vnl_nonlinear_minimizer::is_class(std::__cxx11::basic_string std::char_traits, std::allocator > const&) const'
> ../utils/libutils.a(numerics.o):(.rodata._ZTV9fs_powell[_ZTV9fs_powell]+0x28):
> undefined reference to `vnl_nonlinear_minimizer::is_a[abi:cxx11]() const'
> ../utils/libutils.a(numerics.o):(.rodata._ZTV9fs_powell[_ZTV9fs_powell]+0x30):
> undefined reference to
> `vnl_nonlinear_minimizer::is_class(std::__cxx11::basic_string std::char_traits, std::allocator > const&) const'
>
>
>
> Dr Chris Adamson
> Research Officer, Developmental Imaging, Murdoch Childrens Research
> Institute
> Murdoch Childrens Research Institute
> Royal Children's Hospital
> Flemington Road, Parkville, Victoria  3052, Australia
> www.mcri.edu.au
> E   chris.adam...@mcri.edu.au
> T   03 9936 6780
>
>
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[Freesurfer] Checking optseq efficiency of a custom par file.

[Sam Zorowitz]

Dear Freesurfer list,

Using the optseq2 program, is it possible to calculate the efficiency of a
custom par file? I have an fMRI task that will be split into three blocks.
I want to calculate the overall efficiency of my overall design
byconcatenating the best par file from optimizing each individual block. I
have already tried doing so by concatenating the three par files (updating
the onset times) and inputting this into optseq2 by:

>> optseq2 --in new_file.par --nosearch --tr 1.75 --ntp 1080 --psdwin 0 3.5
1.75 --o new_dir

If I do this, however, I get a "core dump" error. Does anyone know how I
might going about doing this? I've attached the new_par file for
convenience.

Best,
sam


new_file.par
Description: Binary data
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Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

[jorge luis]

Hi Pablo
Yes, too many locations at which the estimation algorithm didn't converge is 
problematic. That might mean that having two random effects is not appropriate 
for your data. You should try to run the command with just a single random 
effect for the intercept term:
lhstats = lme_mass_fit_vw(X, [1], lhY, ni, lhcortex, [], 4);
If the result still have too many non-convergence locations then something 
might be wrong with the ordering of the design matrix and its correspondence 
with the ordering of the ni vector or the ordering of the image data etc... You 
will need to check it thoroughly.
Cheers-Jorge





 
  De: pablo najt 
 Para: "freesurfer@nmr.mgh.harvard.edu"  
 Enviado: Viernes 16 de octubre de 2015 1:43
 Asunto: Re: [Freesurfer] A mixed effect model approach in within subject 
dataset {Disarmed}
   
#yiv7275178360 #yiv7275178360 --.yiv7275178360hmmessage 
P{margin:0px;padding:0px;}#yiv7275178360 
body.yiv7275178360hmmessage{font-size:12pt;font-family:Calibri;}#yiv7275178360 
Thanks you for the replies.Jorge and FS experts,I have run the analysis and 
first double checked that the sum of vectors of (ni) is equal to the number of 
rows in (X). Both are 140 which is the number of my subjects.The analysis gave 
the following 'error'(?) below:I looked up a previous thread coming across 
this. At that case you recommendedWould you recommend this afain>

Aproximate percentage of fitted locations: 100%Warning: matlabpool will be 
removed in a future release.To query the size of an already started parallel 
pool, query the 'NumWorkers'property of the pool.To check if a pool is already 
started use 'isempty(gcp('nocreate'))'. Warning: matlabpool will be removed in 
a future release.To shutdown a parallel pool use 'delete(gcp('nocreate'))' 
instead. Parallel pool using the 'local' profile is shutting down.  
Summary:Algorithm did not converge at 90.0637 percent of the total number of 
locations.Total elapsed time is 550.1023 minutes.

Also almost all the time the screen showed the following message:
144114: Algorithm did not converge. Initial and final likelihoods: 
-38.3408-1.5708i, -241.4153-1.570796i.Location 144113: Algorithm did not 
converge. Initial and final likelihoods: -5.5424-1.5708i, 
-133.8004-1.570796i.Location 144112: Algorithm did not converge. Initial and 
final likelihoods: -7.7571-1.5708i, -319.1378-1.570796i.Location 144111: 
Algorithm did not converge. Initial and final likelihoods: -16.8597-1.5708i, 
0.74448.Aproximate percentage of fitted locations: 100%

So my two questions are:1. Is this problematic?2. Are there any fixes to this 
issue?Thank you,Pablo
Date: Thu, 15 Oct 2015 13:38:22 +
From: jbernal0...@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
CC: pablon...@hotmail.com
Subject: Re: [Freesurfer] A mixed effect model approach in within subject 
dataset {Disarmed}



Hi Pablo
The error you are getting is because in your Matlab setup you can only request 
a maximum of 4 matlab parallel workers and by default lme requests 8. So you 
just need to modify your command like this: 
lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex, [], 4);
Please make sure that sum(ni) and length(X) give the same value before running 
the above command.
Cheers-Jorge


 
  De: pablo najt 
 Para: Freesurfer support list  
 Enviado: Jueves 15 de octubre de 2015 7:18
 Asunto: Re: [Freesurfer] A mixed effect model approach in within subject 
dataset {Disarmed}
   
#yiv7275178360 #yiv7275178360 --.yiv7275178360ExternalClass 
#yiv7275178360ecxyiv7790603773 body.yiv7275178360ecxyiv7790603773hmmessage 
{font-size:12pt;font-family:Calibri;}#yiv7275178360 Thank you Martin.I am 
trying to run the following command line and get the error below. Would you 
have a suggestion to overcome this issue?Just in case I am also including a 
snapshot of my loaded variables at the bottom.Many thanks,Pablo>> lhstats = 
lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);


Warning: matlabpool will be removed in a future release.

To query the size of an already started parallel pool, query the 'NumWorkers'

property of the pool.

To check if a pool is already started use 'isempty(gcp('nocreate'))'. 

Warning: matlabpool will be removed in a future release.

To query the size of an already started parallel pool, query the 'NumWorkers'

property of the pool.

To check if a pool is already started use 'isempty(gcp('nocreate'))'. 

Warning: matlabpool will be removed in a future release.

Use parpool instead. 

Starting matlabpool using the 'local' profile ... 

Error using matlabpool (line 148)

Failed to start a parallel pool. (For information in addition to the causing 
error,

validate the profile 'local' in the Cluster Profile Manager.)




Error in lme_mass_fit (line 128)

        matlabpool(prs);




Error in lme_mass_fit_vw (line 73)

[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);




Caused by:

    Error using parallel.internal.pool.InteractiveClient/start (line 330)

    Failed to start pool.

     

Re: [Freesurfer] Recon-all variations and 3T flag

[Lee Tirrell]

Hi Kaspar,

It doesn't matter where you place the flags in your command line, as long as 
all of them are there.  Also, -s and -subjid are equivalent, so the first two 
commands would be the same (although the path to your input data is different 
after the -i flag, and your subject name is different after the -s or -subjid 
flag).


Best,
Lee


On Sat, 10 Oct 2015, Kasper Jessen wrote:


Dear Freesurfer group,
 *  I have noticed different ways of writing the 'recon-all' commands (see 
below). What is the difference between these two ways of writing the command? 
Or is it the same?
 +  recon-all -all -s  -i path_to_tpN_dcm
 +  recon-all -i   -subjid  -all
 *  Does it matter where you place the 3T flag in the command line? fx
 +  recon-all -i   -subjid  -3T -all
Best regards,
Kasper Jessen
MD, PhD student


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[Freesurfer] recon-all stripped brains

[John Anderson]

Dear experts,

I want to run recon-all on a stripped brains ( T1 images after applying bet tool).

Do I need to add any flags to the command recon -all -all subjid 

 

 


 

Bests,
John

 
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Re: [Freesurfer] mri_convert with --like and -rt options

[Bruce Fischl]

Hi Seung-Goo

I would have that that your command line would work as is. Can you send 
us the full screen output?

cheers
Bruce
On Fri, 16 Oct 2015, Seung-Goo KIM wrote:


Dear all,
I wish to know whether mri_convert provide a nifty way to reslice and crop a 
NIFTI
image with labels (positive integers) with “—like” and “-rt” options. It seems 
like
“—like” option overrides “-rt” option, thus the result from such a command:

  mri_convert -rt nearest —like ${referenceImage} ${inputImage}
  ${outputImage}


 is resampled with trilinear interpolation. I don’t know if I did something 
wrong
(maybe file format?) or this is a bug in mri_convert.

Of course, one can write a script that creates binary images for each label 
values,
transforms it (using "mri_convert —like"), threshold it (like value>0.1), and 
finally
finds the label with the highest value (probability) for each voxel in the 
reference
space. But I believe there should be a simpler and faster way to do this with
mri_convert or any other program in freesurfer :)

FIY, the version of freesurfer package I use is
"Linux-centos6_x86_64-stable-pub-v5.3.0”.

Best regards,
-- 
Seung-Goo KIM


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Re: [Freesurfer] FreeSurfer and OpenMP

[Bruce Fischl]

Hi Linda

did you actually include the angle brackets?  If so, try without them. And 
don't you want 4 there instead of 8 (if you have 4 processors)?

On 
Fri, 16 Oct 2015, Linda BOUMGHAR wrote:

> I would like to use freesurfer with OpenMP, with 4 processors. I wrote this :
> recon-all -all -i
> /mnt/linuxwin/lboumgha/data/CENTER_TBI/tro/suj1/T1.nii.gz -subjid
> subj1 -openmp <8>
> and I got this error message :
>
> bash: syntax error near unexpected token `8'
>
> What is the good syntax if I want tu use OpenMP, please?
> Great regards,
> Linda Boumghar
>
> 
> This message was sent using IMP, the Internet Messaging Program.
>
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Re: [Freesurfer] pial surface encircling the optical chiasm

[Antonin Skoch]

Dear experts,

I am sending the example subject named chiasma_question.tar.gz to your FTP 
server.

The issue with encircling chiasma is located in slices ~134-140.

According to Aparc.a2009s+aseg the tissue is marked as optical chiasm, but also 
part of it is labeled as left cerebral white matter. I guess that for the 
whole-brain group analysis of cortical thickness this error probably will not 
have an effect since it seems that this region is masked by cortex.label, but 
in volumetric analyses there could be an effect, although probably very small. 
Or could this error cause some bias in cortical parcellation in adjacent 
cortical areas?...What do you think?

Regards,

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Re: [Freesurfer] FreeSurfer and OpenMP

[Chris Adamson]

It is -openmp 8
Delete the less than and greater than characters around the 8

> On 16 Oct 2015, at 3:25 PM, Linda BOUMGHAR  wrote:
> 
> I would like to use freesurfer with OpenMP, with 4 processors. I wrote this :
> recon-all -all -i  
> /mnt/linuxwin/lboumgha/data/CENTER_TBI/tro/suj1/T1.nii.gz -subjid  
> subj1 -openmp <8>
> and I got this error message :
> 
> bash: syntax error near unexpected token `8'
> 
> What is the good syntax if I want tu use OpenMP, please?
> Great regards,
> Linda Boumghar
> 
> 
> This message was sent using IMP, the Internet Messaging Program.
> 
> 
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[Freesurfer] SOLVED - mri_convert segmentation fault after tracula update on Linux/glibc-2.20 (Gentoo)

[Volkmar Glauche]

Dear all,

in reply to myself as a documentation for others: I tried a recent  
development version of mri_convert. Instead of crashing, this version  
instructed me to get a new license file for systems running GNU glibc  
version greater 2.15. The new license file (.license, not license.txt)  
seems to do the trick.

Best,

Volkmar

-- 
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http://fbi.uniklinik-freiburg.de/
Tel. +761 270-54110
Fax. +761 270-53100


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Re: [Freesurfer] mri_convert with --like and -rt options

[Seung-Goo KIM]

Dear freesurfer developers,

Following the previous e-mail, it seems like a variable handling bug.

 From the mri_convert.c, lines from 2588 to 2606 appear to be the part that 
handles “out_like” option. the variable “resample_type_val” in line 2605 should 
contain the user-specified value, but it seems it doesn’t (although I’m not 
very good at reading c codes..).

Please correct me if I’m wrong and just me using mri_convert in a wrong way.

Best,
-- 
Seung-Goo KIM

> On 2015-10-16, at 10:01, Seung-Goo KIM  wrote:
> 
> Dear all,
> 
> I wish to know whether mri_convert provide a nifty way to reslice and crop a 
> NIFTI image with labels (positive integers) with “—like” and “-rt” options. 
> It seems like “—like” option overrides “-rt” option, thus the result from 
> such a command:
> 
>> mri_convert -rt nearest —like ${referenceImage} ${inputImage} ${outputImage}
> 
> 
>  is resampled with trilinear interpolation. I don’t know if I did something 
> wrong (maybe file format?) or this is a bug in mri_convert.
> 
> Of course, one can write a script that creates binary images for each label 
> values, transforms it (using "mri_convert —like"), threshold it (like 
> value>0.1), and finally finds the label with the highest value (probability) 
> for each voxel in the reference space. But I believe there should be a 
> simpler and faster way to do this with mri_convert or any other program in 
> freesurfer :)
> 
> FIY, the version of freesurfer package I use is 
> "Linux-centos6_x86_64-stable-pub-v5.3.0”.
> 
> Best regards,
> -- 
> Seung-Goo KIM
> 

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[Freesurfer] mri_convert with --like and -rt options

[Seung-Goo KIM]

Dear all,

I wish to know whether mri_convert provide a nifty way to reslice and crop a 
NIFTI image with labels (positive integers) with “—like” and “-rt” options. It 
seems like “—like” option overrides “-rt” option, thus the result from such a 
command:

> mri_convert -rt nearest —like ${referenceImage} ${inputImage} ${outputImage}


 is resampled with trilinear interpolation. I don’t know if I did something 
wrong (maybe file format?) or this is a bug in mri_convert.

Of course, one can write a script that creates binary images for each label 
values, transforms it (using "mri_convert —like"), threshold it (like 
value>0.1), and finally finds the label with the highest value (probability) 
for each voxel in the reference space. But I believe there should be a simpler 
and faster way to do this with mri_convert or any other program in freesurfer :)

FIY, the version of freesurfer package I use is 
"Linux-centos6_x86_64-stable-pub-v5.3.0”.

Best regards,
-- 
Seung-Goo KIM

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[Freesurfer] mri_convert segmentation fault after tracula update on Linux/glibc-2.20 (Gentoo)

[Volkmar Glauche]

Dear List,

I am facing a similar problem as described by Knut Bjuland:

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg39745.html

I could not find a public reply in the mailing list archives.  
Therefore I would like to know whether it would be safe to either  
downgrade mri_convert to the version before the tracula update or use  
a newer development version of mri_convert with Freesurfer 5.3.

Best,

Volkmar

-- 
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http://fbi.uniklinik-freiburg.de/
Tel. +761 270-54110
Fax. +761 270-53100


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