Dear Bruce,
Thank you so much for taking care of my stupid questions :)
I searched online regarding the ANALYZE vs Dicom, and I understand
your point now ... The problem is, for this scan, I am afraid the only
data format that I can play with is ANALYZE ... (although there might
be Dicom format available on later scans)
So ... I tried some other tools and got the orientation information
out of the ANALYZE data (not sure if it makes sense ...)
0.7000 0 0 0
0 0.7000 0 0
0 0 1.5000 0
0 0 0 1.0000
I save them in a *.mat file, and seems that mri_convert did the job
successfully, I got the *.mgz file. Then I setup the necessary
directories ( i.e. my_new_subjects_dir/subj001/mri/orig ), put the
*.mgz file there, and launched " recon-all -all -s subj001 ".
Then I got some warnings and errors (see below), and here comes my new
questions, if you do not mind ...
** Question-1 : After launching recon-all, got a warning immediately
(see below). Sorry for my stupid questions ... but what is a typical
input I should feed to recon-all ? Two scans of the same whole brain?
Or one scan for the left hemisphere scan and another one for the right
hemisphere? Or something else ?
"WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll copy the run to
rawavg and continue."
** Question-2 : The program seems running well after the warning,
until it terminates a couple of minutes later, throwing out some error
like below. I just have no idea what to do now ... Could you please
give me some hints?
"ERROR: talairach_afd: Talairach Transform:
transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 <
threshold=0.0050)"
The complete output from recon-all is attached, for your information.
If you need the data, is there any way I can send it to you without
bothering other members in the mailing list? Thank you !
Best Regards
Tim
On Sun, Feb 20, 2011 at 9:47 AM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
> Hi Tim,
>
> it doesn't help to convert from analyze to something else. Once you have
> gone through analyze all direction information is lost. Can you get access
> to the data before it was converted to analyze in whatever format the
> scanner produced?
> Bruce
>
> On Sun, 20 Feb 2011, xiaotian yin wrote:
>
>> Dear Bruce,
>>
>>
>> THanks for the quick response!
>>
>> I searched online for Analyze --> Dicom converter ... no luck ...
>>
>> Also tried to read the Analyze file (*.hdr) into Matlab, ending up
>> with the following info :
>>
>> Filename: 'IA_1_orig.hdr'
>> FileModDate: '04-ÿÿÿÿ-2010 01:08:20'
>> HdrFileSize: 348
>> ImgFileSize: 8126464
>> Format: 'Analyze'
>> FormatVersion: '7.5'
>> Width: 256
>> Height: 256
>> BitDepth: 8
>> ColorType: 'grayscale'
>> ByteOrder: 'ieee-le'
>> HdrDataType: 'volume '
>> DatabaseName: 'IA_1_%%%.pic.'
>> Extents: 16384
>> SessionError: -28067
>> Regular: 1
>> Dimensions: [256 256 124 1 1]
>> VoxelUnits: ''
>> CalibrationUnits: 'Y??·2w?·'
>> ImgDataType: 'DT_UNSIGNED_CHAR'
>> PixelDimensions: [1x5 single]
>> VoxelOffset: 0
>> CalibrationMax: 255
>> CalibrationMin: 0
>> Compressed: -2.7107e-005
>> Verified: -2.7172e-005
>> GlobalMax: 255
>> GlobalMin: 0
>> Descriptor: [1x80 char]
>> AuxFile: '?J?· ?ù·? ?oü·????°???'
>> Orientation: 'Orientation unavailable'
>> Originator: ' ·???'
>> Generated: ' p'
>> Scannumber: '??· '
>> PatientID: ''
>> ExposureDate: ''
>> ExposureTime: ''
>> Views: 0
>> VolumesAdded: 0
>> StartField: -1209816480
>> FieldSkip: -1208305456
>> OMax: -1208193036
>> OMin: -1208460092
>> SMax: -1208306728
>> SMin: -1077308224
>>
>>
>>
>> Did not see any "hist.orient" field or affine transformation field ...
>>
>> Do you have any recommendations ?
>>
>>
>> Best
>> Tim
>>
>>
>>
>>
>> On Sat, Feb 19, 2011 at 9:46 PM, Bruce Fischl
>> <fis...@nmr.mgh.harvard.edu> wrote:
>>>
>>> Hi Tim,
>>>
>>> the .hdr/.img format is called Analyze, and it doesn't come with
>>> orientation informaton. This means that it is easy for example to get a
>>> left/right swap that you will never know was in your data. Can you get it
>>> in any other format, like dicom, or whatever format it came off the
>>> scanner
>>> in?
>>>
>>> If not, you can send us one of the pairs of files that gives the segfault
>>> and we'll take a look
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>>
>>> On Sat, 19 Feb 2011, xiaotian yin wrote:
>>>
>>>> Hi,
>>>>
>>>> Thank you for reading this email !
>>>>
>>>> I am a newbie to Medical Imaging, and am learning to use FreeSurfer
>>>> for surface construction.
>>>>
>>>> Already installed FreeSurfer in Ubuntu, and the installation has been
>>>> verified to be 100% successful.
>>>>
>>>> I got a bunch of data (coming in pairs of *.hdr and *.img), and I am
>>>> trying to convert them to *.mgz files, so that I can use recon-all
>>>> then.
>>>>
>>>> but when I call mri_convert as follows:
>>>>
>>>> mri_convert Rcing.img Rcing.mgz
>>>>
>>>> I got the following error :
>>>>
>>>>
>>>> mri_convert Rcing.img Rcing.mgz
>>>> $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
>>>> reading from Rcing.img...
>>>> -----------------------------------------------------------------
>>>> INFO: could not find /mnt/Data/Rcing.mat file for direction cosine info.
>>>> INFO: use Analyze 7.5 hdr->hist.orient value: -40, .
>>>> INFO: if not valid, please provide the information in
>>>> /mnt/Data/Rcing.mat file
>>>> -----------------------------------------------------------------
>>>> Segmentation fault
>>>>
>>>>
>>>> I have searched the freesurfer website ... no luck ....
>>>> Would you mind to give me some advice or hints ? Thank you so much !
>>>>
>>>>
>>>> Best
>>>> Tim
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>> _______________________________________________
>>> 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.
>>>
>>>
>>
>>
>
glamor-virtual-machine:/mnt/hgfs/proj__Brain/Data_FS# recon-all -all -s
subj001Subject 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 /mnt/hgfs/proj__Brain/Data_FS
Actual FREESURFER_HOME /usr/local/freesurfer
Linux glamor-virtual-machine 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19
20:32:27 UTC 2010 x86_64 GNU/Linux
#--------------------------------------------
#@# MotionCor Sun Feb 20 00:51:20 EST 2011
Found 1 runs
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig/001.mgz
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
cp /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig/001.mgz
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/rawavg.mgz
/mnt/hgfs/proj__Brain/Data_FS/subj001
mri_convert /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/rawavg.mgz
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig.mgz --conform
mri_convert /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/rawavg.mgz
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
Original Data has (0.7, 0.7, 1.5) mm size and (256, 256, 124) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
Reslicing using trilinear interpolation
writing to /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig.mgz...
mri_add_xform_to_header -c
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/transforms/talairach.xfm
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig.mgz
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Nu Intensity Correction Sun Feb 20 00:51:32 EST 2011
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $
Linux glamor-virtual-machine 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19
20:32:27 UTC 2010 x86_64 GNU/Linux
Sun Feb 20 00:51:32 EST 2011
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
tmpdir is ./tmp.mri_nu_correct.mni.4982
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4982/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4982/nu0.mnc -odt float
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.4982/nu0.mnc...
--------------------------------------------------------
Iteration 1 Sun Feb 20 00:51:37 EST 2011
nu_correct -clobber ./tmp.mri_nu_correct.mni.4982/nu0.mnc
./tmp.mri_nu_correct.mni.4982/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4982/0/
[root@glamor-virtual-machine:/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/]
[2011-02-20 00:51:37] running:
/usr/local/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
./tmp.mri_nu_correct.mni.4982/0/ ./tmp.mri_nu_correct.mni.4982/nu0.mnc
./tmp.mri_nu_correct.mni.4982/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 22
CV of field change: 0.000991636
[root@glamor-virtual-machine:/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/]
[2011-02-20 00:52:06] running:
/usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3
./tmp.mri_nu_correct.mni.4982/nu0.mnc
./tmp.mri_nu_correct.mni.4982/0//template.mnc
Transforming
slices:......................................................................................Done
Transforming
slices:................................................................................................................................................................................................................................................................Done
--------------------------------------------------------
Iteration 2 Sun Feb 20 00:52:20 EST 2011
nu_correct -clobber ./tmp.mri_nu_correct.mni.4982/nu1.mnc
./tmp.mri_nu_correct.mni.4982/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.4982/1/
[root@glamor-virtual-machine:/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/]
[2011-02-20 00:52:21] running:
/usr/local/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
./tmp.mri_nu_correct.mni.4982/1/ ./tmp.mri_nu_correct.mni.4982/nu1.mnc
./tmp.mri_nu_correct.mni.4982/nu2.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 16
CV of field change: 0.00094021
[root@glamor-virtual-machine:/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/]
[2011-02-20 00:52:44] running:
/usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3
./tmp.mri_nu_correct.mni.4982/nu1.mnc
./tmp.mri_nu_correct.mni.4982/1//template.mnc
Transforming
slices:......................................................................................Done
Transforming
slices:................................................................................................................................................................................................................................................................Done
mri_binarize --i ./tmp.mri_nu_correct.mni.4982/nu2.mnc --min -1 --o
./tmp.mri_nu_correct.mni.4982/ones.mgz
$Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $
cwd /mnt/hgfs/proj__Brain/Data_FS/subj001/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.4982/nu2.mnc --min -1 --o
./tmp.mri_nu_correct.mni.4982/ones.mgz
sysname Linux
hostname glamor-virtual-machine
machine x86_64
user root
input ./tmp.mri_nu_correct.mni.4982/nu2.mnc
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.4982/ones.mgz
Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
Found 16777216 values in range
Counting number of voxels
Found 16777216 voxels in final mask
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4982/ones.mgz --i orig.mgz
--sum ./tmp.mri_nu_correct.mni.4982/sum.junk --avgwf
./tmp.mri_nu_correct.mni.4982/input.mean.dat
$Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4982/ones.mgz --i
orig.mgz --sum ./tmp.mri_nu_correct.mni.4982/sum.junk --avgwf
./tmp.mri_nu_correct.mni.4982/input.mean.dat
sysname Linux
hostname glamor-virtual-machine
machine x86_64
user root
Loading ./tmp.mri_nu_correct.mni.4982/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
0 1 16777216 1.67772e+07
Reporting on 1 segmentations
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.4982/input.mean.dat
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4982/ones.mgz --i
./tmp.mri_nu_correct.mni.4982/nu2.mnc --sum
./tmp.mri_nu_correct.mni.4982/sum.junk --avgwf
./tmp.mri_nu_correct.mni.4982/output.mean.dat
$Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4982/ones.mgz --i
./tmp.mri_nu_correct.mni.4982/nu2.mnc --sum
./tmp.mri_nu_correct.mni.4982/sum.junk --avgwf
./tmp.mri_nu_correct.mni.4982/output.mean.dat
sysname Linux
hostname glamor-virtual-machine
machine x86_64
user root
Loading ./tmp.mri_nu_correct.mni.4982/ones.mgz
Loading ./tmp.mri_nu_correct.mni.4982/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
0 1 16777216 1.67772e+07
Reporting on 1 segmentations
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.4982/output.mean.dat
mris_calc -o ./tmp.mri_nu_correct.mni.4982/nu2.mnc
./tmp.mri_nu_correct.mni.4982/nu2.mnc mul .92568628037958714125
Saving result to './tmp.mri_nu_correct.mni.4982/nu2.mnc' (type=3)
[ ok ]
mri_convert ./tmp.mri_nu_correct.mni.4982/nu2.mnc nu.mgz --like orig.mgz
--conform
mri_convert ./tmp.mri_nu_correct.mni.4982/nu2.mnc nu.mgz --like orig.mgz
--conform
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from ./tmp.mri_nu_correct.mni.4982/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
writing to nu.mgz...
Sun Feb 20 00:53:52 EST 2011
mri_nu_correct.mni done
#--------------------------------------------
#@# Talairach Sun Feb 20 00:53:52 EST 2011
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri
talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Sun Feb 20 00:55:00 EST 2011
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
INFO: Attempting MINC mritotal to perform Talairach align
#--------------------------------------------
#@# Talairach Sun Feb 20 00:55:00 EST 2011
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri
talairach --i nu.mgz --xfm transforms/talairach.auto.xfm
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri
/usr/local/freesurfer/bin/talairach
--i nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach,v 1.6 2007/03/15 23:23:11 greve Exp $
Linux glamor-virtual-machine 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19
20:32:27 UTC 2010 x86_64 GNU/Linux
Sun Feb 20 00:55:00 EST 2011
tmpdir is transforms/tmp.talairach.5742
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri
mri_convert nu.mgz transforms/tmp.talairach.5742/src.mnc
mri_convert nu.mgz transforms/tmp.talairach.5742/src.mnc
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from nu.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to transforms/tmp.talairach.5742/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir
/usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm
transforms/tmp.talairach.5742/src.mnc transforms/talairach.auto.xfm
Sun Feb 20 00:55:23 EST 2011
talairach done
INFO: transforms/talairach.xfm already exists!
The new transforms/talairach.auto.xfm will not be copied to
transforms/talairach.xfm
This is done to retain any edits made to transforms/talairach.xfm
Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Sun Feb 20 00:55:23 EST 2011
/mnt/hgfs/proj__Brain/Data_FS/subj001/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
Linux glamor-virtual-machine 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19
20:32:27 UTC 2010 x86_64 GNU/Linux
recon-all -s subj001 exited with ERRORS at Sun Feb 20 00:55:23 EST 2011
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The information in this e-mail is intended only for the person to whom it is
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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
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