Hi bruce,
This happens for every orig.mgz that passes through
mri_convert at the start of
make_average_volumes. The files are 9M each, is there a drop-area where i
can upload
them? I just made some checks: my orig/001.mgz files are LPS
(primary->axial), while
the converted files are LIA (coronal). Can this effect the result? In any
case, if you send
me the link to the drop area, i will put an example mgz.
thanks,
sid.
On Sat, Jan 24, 2009 at 12:40 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu>wrote:
> Hi Sid,
>
> can you send us the volume that has this happen? I think it's just a
> display problem and won't affect anything else, but if you give us the
> example we'll fix it.
>
> Bruce
>
> On Sat, 24 Jan 2009, Siddharth Srivastava wrote:
>
> Hi everyone,
>> Has anyone faced this problem before? Is there an
>> alternative
>> to mri_convert than i can try to get the transformation, and then run the
>> subsequent steps? Why are k_ras components approaching zero, and not
>> exactly zero. make_average_surface works fine, no clipping, i have spent
>> the
>>
>> last 20 or so odd hours checking each surf directory. This happens only
>> for
>> the
>> structurals that pass through mri_convert. Tried changing the -oc
>> values, there is a shift, as expected, but the clipping remains fixed at
>> this level (hence more brain gets cropped if the -oc values shift the
>> brain posteriorly.
>> sid.
>>
>>
>>
>> On Fri, Jan 23, 2009 at 11:37 AM, Siddharth Srivastava <sid...@gmail.com
>> >wrote:
>>
>> Hi bruce,
>>> I think the offending command is
>>> mri_convert /../../orig.mgz /../../orig-subject.mgh --apply_transform
>>> /../../mri/transforms/talairach.xfm -oc 0 0 0
>>> I am attaching the pre- and post mri_convert as tiffs. I have also
>>> attached
>>> the pial_avg surface in the
>>> posterior view, for you comments.
>>> The folowing is the screen dump (patient name deleted):
>>>
>>>
>>> ----------------------------------------------------------------------------------------------------
>>> $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $
>>> reading from /../subject/mri/orig.mgz...
>>> TR=1820.00, TE=2.93, TI=1100.00, flip angle=12.00
>>> i_ras = (-1, 0, 0)
>>> j_ras = (0, 0, -1)
>>> k_ras = (-9.31323e-10, 1, -1.49012e-08)
>>> INFO: Applying transformation from file
>>> /../subject/mri/transforms/talairach.xfm...
>>> Reading transform with LTAreadEx()
>>> ---------------------------------
>>> INFO: Transform Matrix (linear_ras_to_ras)
>>> 1.026 0.084 0.079 -9.471;
>>> -0.105 1.048 0.228 -84.640;
>>> -0.106 -0.174 1.165 -38.874;
>>> 0.000 0.000 0.000 1.000;
>>> ---------------------------------
>>> Applying LTAtransformInterp (resample_type 1)
>>> INFO: Transform dst volume info is not used (valid flag = 0).
>>> applying the vox to vox linear transform
>>> 1.026 0.079 -0.084 -1.205;
>>> -0.106 1.165 0.174 9.576;
>>> 0.105 -0.228 1.048 -61.401;
>>> 0.000 0.000 0.000 1.000;
>>> writing to /../../orig-subject.mgh...
>>> ----------------------------------------------------------------------
>>> does this help in any way?
>>>
>>> thanks,
>>> sid.
>>>
>>>
>>>
>>> On Fri, Jan 23, 2009 at 11:01 AM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu
>>>
>>>> wrote:
>>>>
>>>
>>> Hi Sid,
>>>>
>>>> have you looked through the individual datasets? That's where the
>>>> cropping
>>>> would be, which would have caused big errors in your surfaces. I assume
>>>> that
>>>> is not the case.
>>>> Bruce
>>>>
>>>>
>>>> On Fri, 23 Jan 2009, Siddharth Srivastava wrote:
>>>>
>>>> Hi Bruce,
>>>>
>>>>> I just realised that the cropping at the posterior aspect is
>>>>> similar to the
>>>>> cropping usually done for the inferior aspect in a saggital view (to
>>>>> get
>>>>> rid
>>>>> of the
>>>>> neck etc..) . Could it be (remotely) possible that the cropping was
>>>>> done
>>>>> in
>>>>> a different
>>>>> orientation (nose pointing up in the sagittal view), and then oriented
>>>>> to
>>>>> the views
>>>>> that we see now? I have only used the basic commands
>>>>> "make_average_subject"
>>>>> with no special flags except --force
>>>>> sid.
>>>>>
>>>>>
>>>>> On Fri, Jan 23, 2009 at 10:33 AM, Bruce Fischl
>>>>> <fis...@nmr.mgh.harvard.edu>wrote:
>>>>>
>>>>> I'm not really sure. Doug or Nick: any ideas?
>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, 23 Jan 2009, Siddharth Srivastava wrote:
>>>>>>
>>>>>> Hi Bruce,
>>>>>>
>>>>>> please find attached a tiff file generated by mri_concat
>>>>>>> --mean on the original mprages.
>>>>>>> Here i can see the full view, and i think no registration has been
>>>>>>> performed
>>>>>>> as yet on these
>>>>>>> images... Regarding exploring the dataset for 1 image, is it
>>>>>>> possible
>>>>>>> that
>>>>>>> just 1 rouge image
>>>>>>> can cause this problem? The clipping has a sharp border, almost as if
>>>>>>> the
>>>>>>> bounding box
>>>>>>> itself has been cropped at that level. the intensity in these
>>>>>>> posterior
>>>>>>> slices is zero.
>>>>>>> thanks,
>>>>>>> sid.
>>>>>>>
>>>>>>> On Fri, Jan 23, 2009 at 9:51 AM, Bruce Fischl <
>>>>>>> fis...@nmr.mgh.harvard.edu
>>>>>>>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>> if you can find a small set (1?) of subjects that generate the same
>>>>>>>
>>>>>>> image,
>>>>>>>> then maybe you can just send us that subject and your commandline
>>>>>>>>
>>>>>>>> On Fri, 23 Jan 2009, Siddharth Srivastava wrote:
>>>>>>>>
>>>>>>>> ok.. i will try that and let you know... what other image/logs can
>>>>>>>> i
>>>>>>>>
>>>>>>>> provide
>>>>>>>>
>>>>>>>>> for
>>>>>>>>> localizing the source of the error?
>>>>>>>>> sid.
>>>>>>>>>
>>>>>>>>> On Fri, Jan 23, 2009 at 9:04 AM, Bruce Fischl <
>>>>>>>>> fis...@nmr.mgh.harvard.edu
>>>>>>>>>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> not really, it seems like there is a bug. If you can localize it
>>>>>>>>> to
>>>>>>>>> just
>>>>>>>>>
>>>>>>>>> one or a few subjects it would a lot easier to track down
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Fri, 23 Jan 2009, Siddharth Srivastava wrote:
>>>>>>>>>>
>>>>>>>>>> Hi Bruce,
>>>>>>>>>>
>>>>>>>>>> These are about 28 images. I have not tried fewer...do you
>>>>>>>>>>
>>>>>>>>>> think there
>>>>>>>>>>> are some images with incorrect orientation in the cohort? That
>>>>>>>>>>> would
>>>>>>>>>>> show
>>>>>>>>>>> up
>>>>>>>>>>> in the other location in the average i think...
>>>>>>>>>>> sid.
>>>>>>>>>>> On Fri, Jan 23, 2009 at 8:46 AM, Bruce Fischl <
>>>>>>>>>>> fis...@nmr.mgh.harvard.edu
>>>>>>>>>>>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> I don't think so. How many subjects? Have you tried fewer?
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Fri, 23 Jan 2009, Siddharth Srivastava wrote:
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> The surfaces look all right. It happens only to T1. It cant be
>>>>>>>>>>>> a
>>>>>>>>>>>> display
>>>>>>>>>>>>
>>>>>>>>>>>> problem, can it??
>>>>>>>>>>>>
>>>>>>>>>>>> sid.
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Fri, Jan 23, 2009 at 5:58 AM, Bruce Fischl <
>>>>>>>>>>>>> fis...@nmr.mgh.harvard.edu
>>>>>>>>>>>>>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> that is strange. Do the surfaces look ok? How many subjects
>>>>>>>>>>>>>> are
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> you
>>>>>>>>>>>>>
>>>>>>>>>>>>> averaging? Does this happen if you only average one or a few?
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Thu, 22 Jan 2009, Siddharth Srivastava wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi everyone,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I am attaching a tiff file showing the tkmedit
>>>>>>>>>>>>>> view
>>>>>>>>>>>>>> of
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> the average
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> T1 that freesurfer created during make_average_subject. I am
>>>>>>>>>>>>>>> a
>>>>>>>>>>>>>>> bit
>>>>>>>>>>>>>>> concerned
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> about the cropping that is evident at the posterior aspect of
>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>> brain.
>>>>>>>>>>>>>>> The
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> individual T1's are complete and ok, so i am guessing that
>>>>>>>>>>>>>>> something
>>>>>>>>>>>>>>> went
>>>>>>>>>>>>>>> wrong during the transform of the individual brain during the
>>>>>>>>>>>>>>> process.
>>>>>>>>>>>>>>> Can
>>>>>>>>>>>>>>> anyone help me find out the problem ? The average surfaces
>>>>>>>>>>>>>>> also
>>>>>>>>>>>>>>> look
>>>>>>>>>>>>>>> all
>>>>>>>>>>>>>>> right.
>>>>>>>>>>>>>>> thanks,
>>>>>>>>>>>>>>> sid.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>>>
>>
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