26 Jan
2009
26 Jan
'09
1:43 p.m.
Sid,
What is the field-of-view size? Use:
mri_info orig.mgz
and look for the 'fov' output. It should be 256. What is the fov of the input files in subj/mri/orig? If it is greater than 256, that might be the problem, but the cropping problem we have seen with that occurs during the original recons, not during make_average_subject. If it is
256, then the -cropsize256 flag should be added to recon-all.
Nick
On Sat, 2009-01-24 at 15:21 -0800, Siddharth Srivastava wrote:
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.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 <siddys@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 <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 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.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 < 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer