Hi Tim,
the one run is okay, but the failure of the Talairach is probably an indication that the orientation information is incorrect. Because analyze doesn't specify the orientation, the info you get is just a guess. Bring the orig.mgz up in tkmedit and see if the anatomical views are correct (e.g. if when we say the view is coronal it in fact is). Even if you can orient it properly though you will never know left from right, which essentially makes the data useless.
sorry Bruce
On Wed, 23 Feb 2011, xiaotian yin wrote:
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 fischl@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 fischl@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 !
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