Hi Bruce,
No, I was not able to successfully converting it to a different format using
mri_convert.
A similar error appeared.
When I read the tag information using MIPAV, it seems like it contains
plenty of information (listed in dicom tag format)
to know the orientation/positioning of the subject.
Attached is the tag information listed in a text file. (I've deleted
subject's personal info)
Thank you.
Best,
Lisa
______________________________
Lisa F. Akiyama
Research Study Assistant
Institute for Learning & Brain Sciences (I-LABS)
University of Washington
P Please consider the environment before printing this e-mail.
On Mon, Dec 13, 2010 at 3:12 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote:
> Hi Lisa,
>
> can you convert it to one of our supported formats? But even then, how will
> you know left from right?
>
> Bruce
>
> On Mon, 13 Dec 2010, Lisa F. Akiyama wrote:
>
> Hello FreeSurfer experts,
>>
>> I am trying to run recon-all on old (back from late 1990's) raw MRI data.
>> Each slice is in a raw format.
>> When I try to execute recon-all, I get the error shown below:
>>
>> todd:~$ recon-all -subjid A_H -i
>>
>>> $SUBJECTS_DIR/adults_jp/A_H/slices/HA970313a1997031316500756
>>>
>>
>> Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
>>
>> Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
>>
>> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
>>
>> Actual FREESURFER_HOME /usr/local/freesurfer
>>
>> Linux neptune-ubuntu 2.6.35-23-generic #41-Ubuntu SMP Wed Nov 24 11:55:36
>>
>>> UTC 2010 x86_64 GNU/Linux
>>>
>>
>> /usr/local/freesurfer/subjects/A_H
>>
>>
>> mri_convert
>>>
>>> /usr/local/freesurfer/subjects/adults_jp/A_H/slices/HA970313a1997031316500756
>>> /usr/local/freesurfer/subjects/A_H/mri/orig/001.mgz
>>>
>>
>>
>>
>> mri_convert
>>>
>>> /usr/local/freesurfer/subjects/adults_jp/A_H/slices/HA970313a1997031316500756
>>> /usr/local/freesurfer/subjects/A_H/mri/orig/001.mgz
>>>
>>
>> $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
>>
>> reading from
>>
>>>
>>> /usr/local/freesurfer/subjects/adults_jp/A_H/slices/HA970313a1997031316500756...
>>>
>>
>> Getting Series No
>>
>> INFO: Found 136 files in
>> /usr/local/freesurfer/subjects/adults_jp/A_H/slices
>>
>> INFO: Scanning for Series Number 32664
>>
>> Scanning Directory
>>
>> INFO: found 0 files in series
>>
>> ERROR: could not find any files (SeriesList==NULL)
>>
>> Linux neptune-ubuntu 2.6.35-23-generic #41-Ubuntu SMP Wed Nov 24 11:55:36
>>
>>> UTC 2010 x86_64 GNU/Linux
>>>
>>
>>
>> recon-all -s A_H exited with ERRORS at Mon Dec 13 14:34:21 PST 2010
>>>
>>
>>
>> Does anyone know how to resolve this issue?
>>
>>
>> Thank you.
>>
>>
>> Best,
>> Lisa
>> ______________________________
>> Lisa F. Akiyama
>> Research Study Assistant
>> Institute for Learning & Brain Sciences (I-LABS)
>> University of Washington
>> E-mail: lris...@uw.edu
>>
>> P Please consider the environment before printing this e-mail.
>>
>>
>
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> HelpLine at
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(0008,0000) Identifying Group Length 442
(0008,0001) Length to End 136898
(0008,0010) Recognition Code ACR-NEMA 2.0
(0008,0020) Study Date 1997.03.13
(0008,0022) Acquisition Date 1997.03.13
(0008,0023) Content (formerly Image) Date 1997.03.13
(0008,0030) Study Time 16:11:19.763
(0008,0032) Acquisition Time 16:11:20.950
(0008,0033) Content (formerly Image) Time 16:19:11.000
(0008,0040) Old Data Set Type 0
(0008,0041) Old Data Set Subtype IMA NONE
(0008,0060) Modality MAGNETIC_RESONANCE
(0008,0070) Manufacturer SIEMENS
(0008,0080) Institution Name C.R.L.
(0008,0090) Referring Physician's Name
(0008,1010) Station Name C.R.L.
(0008,1030) Study Description
(0008,1080) Admitting Diagnoses Description
(0008,1090) Manufacturer's Model Name MAGNETOM VISION
(0010,0000) Patient Group Length 142
(0018,0000) Acquisition Group Length 334
(0018,0010) Contrast/Bolus Agent NONE
(0018,0020) Scanning Sequence NONE
(0018,0050) Slice Thickness 001.500000E+00
(0018,0080) Repetition Time 001.140000E+01
(0018,0081) Echo Time 004.400000E+00
(0018,0082) Inversion Time 003.000000E+02
(0018,0083) Number of Averages 000001
(0018,0084) Imaging Frequency 006.365104E+01
(0018,0085) Imaged Nucleus 1H
(0018,0086) Echo Number(s) 000001
(0018,0090) Data Collection Diameter 000256
(0018,1000) Device Serial Number 7027
(0018,1020) Software Version(s) VB25A
(0018,1200) Date of Last Calibration 1996.06.10
(0018,1201) Time of Last Calibration 17:47:10.000
(0018,1250) Receive Coil Name CP Head
(0018,5100) Patient Position SUPINE
(0020,0000) Relationship Group Length 472
(0020,0010) Study ID 000002
(0020,0011) Series Number
(0020,0012) Acquisition Number 000001
(0020,0013) Instance (formerly Image) Number 000004
(0020,0020) Patient Orientation P , F
(0020,0030) Image Position -01.093063E+02, -1.248581E+02, 01.283806E+02
(0020,0035) Image Orientation 000.000000E+00, 01.000000E+00,
-0.000000E+00, 00.000000E+00, -0.000000E+00, -1.000000E+00
(0020,0050) Location -109.3
(0020,0060) Laterality NO
(0020,0070) Image Geometry Type PLANAR
(0020,0080) Masking Image
(0020,1001) Acquisitions in Series 000001
(0020,1020) Reference HA970313a , 000002
(0020,3100) Source Image IDs
(0020,3401) Modifying Device ID
(0020,3402) Modified Image ID
(0020,3403) Modified Image Date
(0020,3404) Modifying Device Manufacturer
(0020,3405) Modified Image Time
(0020,3406) Modified Image Description
(0020,5000) Original Image Identification 16, 0, 16, 0, 16, 0, 32, 0, 32,
0, 19, 0
(0020,5002) Original Image Identification Nomenclature Patient Name
(0010'H,0010'H), Patient ID (0010'H,0020'H) , Image (0020'H,0013'H)
(0028,0000) Image Presentation Group Length 216
(0028,0005) Image Dimensions 2
(0028,0010) Rows 256
(0028,0011) Columns 256
(0028,0030) Pixel Spacing 001.000000E+00, 01.000000E+00
(0028,0040) Image Format RECT
(0028,0050) Manipulated Image
(0028,0060) Compression Code NONE
(0028,0100) Bits Allocated 16
(0028,0101) Bits Stored 12
(0028,0102) High Bit 11
(0028,0103) Pixel Representation 0
(0028,0200) Image Location 32736
(0028,1050) Window Center 000042, 00042
(0028,1051) Window Width 000099, 00099
(0028,1052) Rescale Intercept 000000
(0028,1053) Rescale Slope 000001
(7FE0,0000) Pixel Data Group Length 131080
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