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 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 youthink 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. >>>> >>>> >>>> >>>> >>>> >>>> >>
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 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. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>> >
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 fischl@nmr.mgh.harvard.eduwrote:
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. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>
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 siddys@gmail.comwrote:
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 <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. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>> >>> >
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Siddharth Srivastava