| T O P I C R E V I E W |
| tankersley |
Posted - Aug 25 2006 : 10:36:42 AM
Couldn't find any topics on FSL and wasnt sure where to post this, but here goes . . .
I have 4 exams in study Reward.01 (20060726_46003; 20060802_46027; 20060803_46030; 20060809_46050) where the functionals are not properly regsitering on the anatomicals.
I've looked at ORIENT.mat, FEAT_{run}.fsf, and bxh header files for these exams, and they all seem normal.
Any other ideas for whhat might cause registration problems?
Thanks :)
Dharol |
| 15 L A T E S T R E P L I E S (Newest First) |
| syam.gadde |
Posted - Nov 29 2006 : 12:01:21 PM
Dharol,
It looks like in your case the anatomical and functional brains do not match in the slice direction (I->S vs. S->I) and the orientation labels do correctly describe the data as they are. However, FSL doesn't do too well with this scenario without some help. Did the flipdim you introduced have something to do with this, or is that an independent issue?
In any case, you can start FSL in the right direction for this situation by specifying a functional-to-highres initial matrix. I will mail you separately on this. |
| tankersley |
Posted - Nov 28 2006 : 2:36:27 PM
I am continuing to have a problem registering the anatomicals for Exam 43044. The func registers fine to the normal brain, but the anat is inferior-superior flipped when registered to functionals as well as the normalized brain.
As far as I can tell, the headr file looks fine:
<?xml version="1.0"?>
<!-- This is a BXH (BIAC XML Header) file. -->
<bxh xmlns:bxh="http://www.biac.duke.edu/bxh" xmlns="http://www.biac.duke.edu/bxh" version="1.0">
<datarec type="image">
<!--AUTOGEN: Orientation is axial -->
<dimension type="x">
<units>mm</units>
<size>256</size>
<origin>119.53125</origin>
<gap>0</gap>
<spacing>0.9375</spacing>
<direction>-1 -0 0</direction>
</dimension>
<dimension type="y">
<units>mm</units>
<size>256</size>
<origin>119.53125</origin>
<gap>0</gap>
<spacing>0.9375</spacing>
<direction>-0 -1 -3.1e-05</direction>
</dimension>
<dimension type="z">
<units>mm</units>
<size>68</size>
<origin>-73.59635053125</origin>
<gap>0</gap>
<spacing>1.89999998507463</spacing>
<direction>0 0 1</direction>
</dimension>
<byteorder>lsbfirst</byteorder>
<elementtype>int16</elementtype>
<filename>mr5c_20040420_43044_002_00_00001.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00002.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00003.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00004.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00005.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00006.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00007.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00008.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00009.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00010.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00011.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00012.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00013.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00014.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00015.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00016.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00017.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00018.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00019.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00020.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00021.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00022.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00023.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00024.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00025.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00026.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00027.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00028.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00029.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00030.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00031.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00032.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00033.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00034.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00035.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00036.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00037.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00038.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00039.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00040.dcm</filename>
<fileoffset>9626</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00041.dcm</filename>
<fileoffset>9626</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00042.dcm</filename>
<fileoffset>9626</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00043.dcm</filename>
<fileoffset>9626</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00044.dcm</filename>
<fileoffset>9626</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00045.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00046.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00047.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00048.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00049.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00050.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00051.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00052.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00053.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00054.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00055.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00056.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00057.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00058.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00059.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00060.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00061.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00062.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00063.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00064.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00065.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00066.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00067.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
<filename>mr5c_20040420_43044_002_00_00068.dcm</filename>
<fileoffset>9630</fileoffset>
<filerecordsize>131072</filerecordsize>
</datarec>
<acquisitiondata>
<examnumber>43044</examnumber>
<studyid>ExecInfo04</studyid>
<seriesnumber>2</seriesnumber>
<runnumber>0</runnumber>
<institution>Duke University BIAC 4T</institution>
<scanningsequence>GR</scanningsequence>
<sequencevariant>SS/SP/SK</sequencevariant>
<magneticfield>4</magneticfield>
<description>Head,Obl,3D,SPGR,Fast</description>
<examdescription>ExecInfo04</examdescription>
<scandate>2004-04-20</scandate>
<scantime>16:21:55</scantime>
<scanner>mr5cmr5c</scanner>
<fieldofview>240 240</fieldofview>
<tr>12.300000</tr>
<ti>300.000000</ti>
<te>5.400000</te>
<operator>jt</operator>
<flipangle>20</flipangle>
<prescribedslicespacing>1.9</prescribedslicespacing>
<frequencydirection>1</frequencydirection>
<acquisitionmatrix>256 256</acquisitionmatrix>
<bandwidth>31.26</bandwidth>
<receivecoilname>HEAD</receivecoilname>
<transmitcoilname>HEAD</transmitcoilname>
<psdname>efgre3d</psdname>
<psdinternalname>EFGRE3D</psdinternalname>
<psddate>2002-05-16</psddate>
<psdtime>00:15:11</psdtime>
</acquisitiondata>
<subject>
<name>3820</name>
<age>0</age>
<sex>M</sex>
<weight>72.575000</weight>
</subject>
<history>
<entry>
<date>2004-04-20 17:01:56</date>
<description>
Generated on fourier.biac.duke.edu by '/usr/local/bin/dicom2bxh' from 68 input files (first is 'mr5c_20040420_43044_002_00_00001.dcm').
-VERSIONSTR-isf2b:1.8,x2b:1.14,bSI:1.36,p2b:1.48,d2b:1.32,bDI:1.47,m2b:1.7,bab:1.21,a2b:1.17,sf2b:1.14</description>
</entry>
</history>
</bxh>
In MATLAB I used flipdim and saved the brain, but had to save the structure as .img files instead of .dcm files. I can convert the new header file to nifti format, but when I try to run BET on the nifti, FSL tells me that it is not equipped for this kind of file.
Any other suggestions?
Thanks,
Dharol |
| syam.gadde |
Posted - Nov 20 2006 : 1:48:13 PM
I think (hope) this problem will be resolved by using the standard version of MkFlirtInitMtx.pl (rather than the one that was [but is no longer] in my home directory). I posted to a new thread about this. |
| syam.gadde |
Posted - Nov 20 2006 : 12:43:07 PM
Dharol,
Can you email me separately the location of this anatomical and I will see I can look at it. |
| tankersley |
Posted - Nov 20 2006 : 12:29:19 PM
We're trying to run FSL on this old data set and having registration problems. I think the ANAT header file is messed up, but am not sure how to fix it.
<?xml version="1.0"?>
<!-- This is a BXH (BIAC XML Header) file. -->
<bxh xmlns:bxh="http://www.biac.duke.edu/bxh" xmlns="http://www.biac.duke.edu/bxh" version="1.0">
<datarec type="image">
<!--AUTOGEN: Orientation is axial -->
<dimension type="x">
<units>mm</units>
<size>256</size>
<origin>119.53125</origin>
<gap>0</gap>
<spacing>0.9375</spacing>
<direction>-1 -0 0</direction>
</dimension>
<dimension type="y">
<units>mm</units>
<size>256</size>
<origin>119.53125</origin>
<gap>0</gap>
<spacing>0.9375</spacing>
<direction>-0 -1 -3.1e-05</direction>
</dimension>
<dimension type="z">
<units>mm</units>
<size>68</size>
<origin>-73.59635053125</origin>
<gap>0</gap>
<spacing>1.89999998507463</spacing>
<direction>0 0 1</direction>
</dimension>
Can I go in and manually put
1 0 0
0 1 0
0 0 1
for direction specifications for x y and z respetively, and maybe this fix it, or is something else going on?
Sorry if this is the second time I've posted this.
The registration is getting mixed up on the func to highres stage, but I've posted the highres to standard because it's easier to see.
Also, the registration is backwards from func to highres and from highres to standard, but then loooks good from func to standard. But FSL probably needs the correct func to highres for intermediate processing, right?
Thanks,
Dharol |
| syam.gadde |
Posted - Nov 15 2006 : 4:32:06 PM
quote:
Originally posted by Dichter
Thank you. How would we verify that it should indeed be LPS? I wouldn't want to guess with something like this.
Other evidence in the P-file indicates LPS (i.e. the
first coordinate is elsewhere labeled as
[ 120 124.27070617675 -53.4404602050781], so starting
on the right side of the brain). |
| Dichter |
Posted - Nov 15 2006 : 4:25:43 PM
Thank you. How would we verify that it should indeed be LPS? I wouldn't want to guess with something like this. |
| syam.gadde |
Posted - Nov 15 2006 : 4:23:07 PM
quote:
Originally posted by Dichter
20061115_46256 and 20061115_46258, both from today. Thanks.
The orientation labels are definitely wrong, and this
matches with data we've seen in the past. A temporary
solution until we figure out what is going on here is
to manually set the orientation in the .bxh file to what
you suspect it really is using bxhsetorient. The current
,bxh file says PRS, but I think it is either LPS or RPS
(probably LPS):
bxhsetorient LPS run005_01.bxh run005_01-new.bxh
And then use the new .bxh file.
|
| Dichter |
Posted - Nov 15 2006 : 4:03:09 PM
20061115_46256 and 20061115_46258, both from today. Thanks. |
| syam.gadde |
Posted - Nov 15 2006 : 4:00:34 PM
quote:
Originally posted by Dichter
My functional bxh header has this orientation information:
<direction>0 -0.982088208198547 0.188421785831451</direction>
<direction>1 0 0</direction>
<direction>0 0.188137769699097 0.982142627239227</direction>
That orientation info looks unusual (and perhaps wrong). I think we've had examples of this in the past. Can you let me know what exam number this is? |
| Dichter |
Posted - Nov 15 2006 : 3:53:59 PM
I am also having trouble with FSL registration:
This is the "example_func to standard " registration from data acquired this morning (i.e., with the most recent pfile to bxh conversion). I am using an ORIENT.mat file.
My functional bxh header has this orientation information:
<?xml version="1.0"?>
<!-- This is a BXH (BIAC XML Header) file. -->
<bxh xmlns:bxh="http://www.biac.duke.edu/bxh" xmlns="http://www.biac.duke.edu/bxh" version="1.0">
<datarec type="image">
<!--AUTOGEN: Orientation is oblique axial -->
<rasorigin>-118.125 104.508865371346 -83.8343312218785</rasorigin>
<dimension type="x">
<units>mm</units>
<size>64</size>
<origin>104.508865371346</origin>
<gap>0</gap>
<spacing>3.75</spacing>
<direction>0 -0.982088208198547 0.188421785831451</direction>
</dimension>
<dimension type="y">
<units>mm</units>
<size>64</size>
<origin>-118.125</origin>
<gap>0</gap>
<spacing>3.75</spacing>
<direction>1 0 0</direction>
</dimension>
<dimension type="z">
<units>mm</units>
<size>34</size>
<origin>-83.8343312218785</origin>
<gap>0</gap>
<spacing>3.80121279988374</spacing>
<direction>0 0.188137769699097 0.982142627239227</direction>
</dimension>
<dimension type="t">
<units>ms</units>
<size>340</size>
<origin>0</origin>
<gap>0</gap>
<spacing>1</spacing>
</dimension>
My anatomical bxh header has this orientation information:
<?xml version="1.0"?>
<!-- This is a BXH (BIAC XML Header) file. -->
<bxh xmlns:bxh="http://www.biac.duke.edu/bxh" xmlns="http://www.biac.duke.edu/bxh" version="1.0">
<datarec type="image">
<!--AUTOGEN: Orientation is oblique axial -->
<rasorigin>119.531254 105.8899244375 -61.81858225</rasorigin>
<dimension type="x">
<units>mm</units>
<size>256</size>
<origin>119.531254</origin>
<gap>0</gap>
<spacing>0.937492</spacing>
<direction>-1 -0 0</direction>
</dimension>
<dimension type="y">
<units>mm</units>
<size>256</size>
<origin>105.8899244375</origin>
<gap>0</gap>
<spacing>0.9375</spacing>
<direction>-0 -0.982094 0.188392</direction>
</dimension>
<dimension type="z">
<units>mm</units>
<size>68</size>
<origin>-61.81858225</origin>
<gap>0</gap>
<spacing>1.90121430638578</spacing>
<direction>0 0.188410614216783 0.982090342305867</direction>
</dimension>
Thanks for any help...
-Gabriel
|
| tankersley |
Posted - Nov 15 2006 : 3:43:59 PM
FYI:
The standard brain that FSL normalizes all your data to is
avg152T1_brain.hdr
and can be found in:
\\Gall\Programs\User_Scripts\fsl_standard |
| tankersley |
Posted - Nov 14 2006 : 5:52:32 PM
I have lost access to Nernst from Golgi and so can't look at the fslview;
in showsrs, the x-dimension values get larger as you go from right to left. I don't know if you can tell from this.
 |
| syam.gadde |
Posted - Nov 14 2006 : 5:27:42 PM
I would have to have access to the data to know for sure what is going on. It sounds like maybe the anatomical might be mislabeled (if the func2standard registration is correct). Does the anatomical come up with the correct labels if you open it in showsrs2? You can also try viewing it using fslview (one of the options in the FSL GUI). |
| tankersley |
Posted - Nov 14 2006 : 5:18:20 PM
Okay. We ran pfile2bxh and the problem wasn't fixed.
So the func to highres is flipped on the inferior-superior axis, as is the highres to standard. Below is highres to standard run without using the pfile fix.
Interstingly, the func to standard ends up looking right.
So is this a problem that FLIRT ends up fixing by the last step, or do we need to fix it, and any suggestions as to how?
Fyi, this data was collected April 2004 to March 2005 on 4T.
Thanks,
Dharol
|
