Re: [Freesurfer] orientation problem when converting from SPM .nii format to bshort

[Doug Greve]

That is probably just the way they are oriented in the nii file. BTW, 
why are you using bshort? I'm trying to push people into using nii.


doug



Leila Reddy wrote:


Hi,

I am trying to convert SPM5 .nii files into bshort and I used the 
following command:


mri_concat fkoch-0007*.nii --o bold/007/fspm_000.bshort

The command seems to work in that I have a bunch of bshort files in my 
bold/007 directory but when I try to view the slices (using 
sliceview-sess for example) the slices are all upside-down (rotated by 
180 degrees). Is there an option I can use to get them the right side up?


I'm using FS v3 on an IntelMac and my version of mri_concat is 
stable3. Here is the output of bugr:

-

FREESURFER_HOME: /Applications/freesurfer

Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5

Kernel info: Darwin 8.11.1 i386

-

Thanks,
Leila



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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: Re: [Freesurfer] path error on cluster super-computer

[Pedro Paulo de Magalhães Oliveira Junior]

I think you can change

tmpdir in bin/mri_nu_correct.mni

But first check if you are setting the variables correctly: FREESURFER_HOME
and executing source SetUpFreeSurfer.sh

2008/7/7 Woo-Suk, Tae <[EMAIL PROTECTED]>:

> The super-user of super-computer did not give me the writing permission for
> /usr/tmp,
>
> so I should modify the source script of FreeSurfer.
>
> How can I do it?
>
>
> Woo-Suk, Tae
> Chuncheon, Korea
>
>
>   --- Original Message ---
> *From : *"Pedro Paulo de Magalh?es Oliveira Junior"<[EMAIL PROTECTED]>
> *To : *"Woo-Suk, Tae"<[EMAIL PROTECTED]>
> *Date : *2008/07/07 월요일 오전 9:28:29
> *Subject : *Re: [Freesurfer] path error on cluster super-computer
>
> I would try:
>
>  chmod -R 777 /usr/tmp
>
> 2008/7/6 Woo-Suk, Tae <[EMAIL PROTECTED]>:
>
>>
>> Dear FreeSurfer experts!
>>
>> I had a error message when I ran a subjects on cluter super-computer.
>> It seemed that the error was caused by permission on "/usr" directory.
>> How can I correct this problem?
>>
>> Woo-Suk, Tae
>> Chuncheon, Korea
>>
>>
>>
>>
>> ---
>> Iteration 1 Mon Jul  7 08:51:03 KST 2008
>> nu_correct -clobber ./tmp.mri_nu_correct.mni.25070/nu0.mnc
>> ./tmp.mri_nu_correct.mni.25070/nu1.mnc
>> couldn't create "/usr/tmp/nu_correct_25115/": Permission denied
>> [EMAIL PROTECTED]:/home01/a174tws/freesurfer/subjects/001/mri/]
>> [2008-07-07 08:51:04] running:
>>   /home01/a174tws/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log
>> -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify
>> -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir
>> /usr/tmp/nu_correct_25115/ ./tmp.mri_nu_correct..mni.25070/nu0.mnc
>> ./tmp.mri_nu_correct.mni.25070/nu1.imp
>>
>> nccreate: filename "/usr/tmp/nu_correct_25115/nu0.mnc": No such file or
>> directory
>> micreate: MINC package entry point
>> nu_estimate_np_and_em: crashed while running mincresample (termination
>> status=768)
>> nu_correct: crashed while running nu_estimate_np_and_em (termination
>> status=768)
>> ERROR: nu_correct
>> Linux tachyond 2.6.9-67.0.4.ELsmp #1 SMP Wed Mar 19 15:45:32 KST 2008
>> x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all exited with ERRORS at Mon Jul  7 08:51:05 KST 2008
>>
>> ---
>>
>>
>>
>> ___
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>
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>
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[Freesurfer] "Deflate compression support is not configured"

[Mark A. Pinsk]

Similar to a thread below, I'm having trouble running
mris_make_template.  First time I'm trying mris_make_template.  On a
Mac Pro, running 10.5.4, running FS 4.0.5, installed libtiff from
darwinports

mris_make_template rh sphere monk monk1.tif

.
monk1.tif: Deflate compression support is not configured.
TiffWrite: TIFFWriteScanline returned error
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Re: Re: Re: [Freesurfer] path error on cluster super-computer

[Woo-Suk, Tae]

.Bold { font-weight: bold; }
.Title { font-weight: bold; font-size: 18px; color: #cc3300; }
.Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: 
#66; font-family: 'Courier New' , Monospace;background-color: #ff9933; }
Thanks Pedro Paulo de Magalh?es Oliveira Junior!My error corrected after 
modifying 'tmpdir in bin/mri_nu_correct.mni'.Best regard!Woo-Suk, Tae 
Chuncheon, Korea--- Original Message ---From : "Pedro Paulo de Magalh?es 
Oliveira Junior"To : "Woo-Suk, Tae"Date : 2008/07/08 화요일 오전 
1:12:44Subject : Re: Re: [Freesurfer] path error on cluster super-computer
I think you can change 
 
tmpdir in bin/mri_nu_correct.mni
 
But first check if you are setting the variables correctly: FREESURFER_HOME and 
executing source SetUpFreeSurfer.sh
2008/7/7 Woo-Suk, Tae [EMAIL PROTECTED]:The super-user of super-computer did 
not give me the writing permission for /usr/tmp,so I should modify the source 
script of FreeSurfer.How can I do it?
Woo-Suk, TaeChuncheon, Korea


 
--- Original Message ---From : "Pedro Paulo de Magalh?es Oliveira 
Junior"[EMAIL PROTECTED] : "Woo-Suk, Tae"[EMAIL PROTECTED] : 
2008/07/07 월요일 오전 9:28:29Subject : Re: [Freesurfer] path error on cluster 
super-computer
I would try:
 
 chmod -R 777 /usr/tmp
2008/7/6 Woo-Suk, Tae [EMAIL PROTECTED]:
Dear FreeSurfer experts!I had a error message when I ran a subjects on cluter 
super-computer.It seemed that the error was caused by permission on 
"/usr" directory.How can I correct this problem?Woo-Suk, 
TaeChuncheon, 
Korea---Iteration
 1 Mon Jul  7 08:51:03 KST 2008nu_correct -clobber 
./tmp.mri_nu_correct.mni.25070/nu0.mnc 
./tmp.mri_nu_correct.mni.25070/nu1.mnccouldn't create 
"/usr/tmp/nu_correct_25115/": Permission [EMAIL 
PROTECTED]:/home01/a174tws/freesurfer/subjects/001/mri/] [2008-07-07 08:51:04] 
running:  /home01/a174tws/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log 
-sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify 
-b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir 
/usr/tmp/nu_correct_25115/ ./tmp.mri_nu_correct..mni.25070/nu0.mnc 
./tmp.mri_nu_correct.mni.25070/nu1.imp
nccreate: filename "/usr/tmp/nu_correct_25115/nu0.mnc": No such file 
or directorymicreate: MINC package entry pointnu_estimate_np_and_em: crashed 
while running mincresample (termination status=768)nu_correct: crashed while 
running nu_estimate_np_and_em (termination status=768)ERROR: nu_correctLinux 
tachyond 2.6.9-67.0.4.ELsmp #1 SMP Wed Mar 19 15:45:32 KST 2008 x86_64 x86_64 
x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Jul  7 08:51:05 KST 
2008---
 





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[Freesurfer] volume of Heschl's gyrus

[Woo-Suk, Tae]

.Bold { font-weight: bold; }
.Title { font-weight: bold; font-size: 18px; color: #cc3300; }
.Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: 
#66; font-family: 'Courier New' , Monospace;background-color: #ff9933; }
HiWhat is the exact term of heschl's gyrus in the lists of 
rh_lt.aparc.a2005s.stats?Woo-Suk, TaeChuncheon, Korea
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