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 fischl@nmr.mgh.harvard.eduwrote:
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 analternative 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 <siddys@gmail.com
wrote:
Hi bruce,
I think the offending command ismri_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 < fischl@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 issimilar 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 fischl@nmr.mgh.harvard.eduwrote:
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 < > fischl@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 < >>> fischl@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 < >>>>> fischl@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 < >>>>>>> fischl@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. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>> >>>>> >>> >