from my research assistant -
On XXX the coordinates on the right side of the screen in tkmedit always start with a negative number.
So that part is correct.
Our problem is that the brain is not flipped - if freesurfer displays radiological and SPM8zero displays neurological, then when you compare the 2 side by side, the brains should be mirror images. Ours are not, they are the same.
Make sense?
On Tue, Sep 20, 2011 at 2:26 PM, Ilana Hairston hairstonster@gmail.comwrote:
could you check this? this a followup on my original email after looking at 110???yl with Barbara and Steve. thanks i.
On Tue, Sep 20, 2011 at 2:23 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
What are the talairach coords for the left hemi? The first coordinate (x) should always be negative. doug
Ilana Hairston wrote:
Hi Doug, No, we had the lh loaded in tksurfer, and when saving a point it showed up on the _left_ in tkmedit (i.e., the right side). thanks ilana
On Tue, Sep 20, 2011 at 11:34 AM, weiland, Barbara < bweiland@med.umich.edu mailto:bweiland@med.umich.edu**> wrote:
-----Original Message----- From: freesurfer-bounces@nmr.mgh.**harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@**nmr.mgh.harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu
[mailto:freesurfer-bounces@**nmr.mgh.harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@**nmr.mgh.harvard.edufreesurfer-bounces@nmr.mgh.harvard.edu>] On Behalf Of Douglas N Greve Sent: Wednesday, September 14, 2011 6:10 PM To: Ilana Hairston Cc: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] flipped orientation in tksurfer and tkmedit
When you say on the "right hemi in tkmedit" do you mean on the right side of the image (which is the left side of the brain)? doug
Ilana Hairston wrote:
Hi there, We recently had a problem that tksurfer and tkmedit were flipped relative to each other. Basically, when saving a point in the left hemisphere in tksurfer it it loaded in the right hemisphere in
tkmedit.
Any ideas how this could have happened? Thanks ilana
--
Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232 tel:734-232-0232; Mobile: 650-906-8449
Reminder: Women do 66% of the work worldwide, earn 10% of the
income,
and own 1% of the world's property
------------------------------**------------------------------**
--
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422
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FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu>
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
--
Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449
Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property
------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
--
Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449
Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property
Can you tar up that subject and drop it to me at our file drop (url at the end of this email). doug
Ilana Hairston wrote:
from my research assistant -
On XXX the coordinates on the right side of the screen in tkmedit always start with a negative number.
So that part is correct.
Our problem is that the brain is not flipped - if freesurfer displays radiological and SPM8zero displays neurological, then when you compare the 2 side by side, the brains should be mirror images. Ours are not, they are the same.
Make sense?
On Tue, Sep 20, 2011 at 2:26 PM, Ilana Hairston <hairstonster@gmail.com mailto:hairstonster@gmail.com> wrote:
could you check this? this a followup on my original email after looking at 110???yl with Barbara and Steve. thanks i. On Tue, Sep 20, 2011 at 2:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: What are the talairach coords for the left hemi? The first coordinate (x) should always be negative. doug Ilana Hairston wrote: Hi Doug, No, we had the lh loaded in tksurfer, and when saving a point it showed up on the _left_ in tkmedit (i.e., the right side). thanks ilana On Tue, Sep 20, 2011 at 11:34 AM, weiland, Barbara <bweiland@med.umich.edu <mailto:bweiland@med.umich.edu> <mailto:bweiland@med.umich.edu <mailto:bweiland@med.umich.edu>>> wrote: -----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] On Behalf Of Douglas N Greve Sent: Wednesday, September 14, 2011 6:10 PM To: Ilana Hairston Cc: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] flipped orientation in tksurfer and tkmedit When you say on the "right hemi in tkmedit" do you mean on the right side of the image (which is the left side of the brain)? doug Ilana Hairston wrote: > Hi there, > We recently had a problem that tksurfer and tkmedit were flipped > relative to each other. Basically, when saving a point in the left > hemisphere in tksurfer it it loaded in the right hemisphere in tkmedit. > Any ideas how this could have happened? > Thanks > ilana > > > > -- >> ****************************** >> Ilana Hairston ,PhD >> Research Assistant Professor >> 4250 Plymouth Rd. (rm 2439) >> Psychiatry Department, Addiction Research Center University of >> Michigan, Ann Arbor MI 48109-2700 >> Tel: 734-232-0232 <tel:734-232-0232> <tel:734-232-0232 <tel:734-232-0232>>; Mobile: 650-906-8449 <tel:650-906-8449> <tel:650-906-8449 <tel:650-906-8449>> >> >> ******************** >> Reminder: Women do 66% of the work worldwide, earn 10% of the income, >> and own 1% of the world's property > > > > ---------------------------------------------------------------------- > -- > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- ****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232 <tel:734-232-0232>; Mobile: 650-906-8449 <tel:650-906-8449> ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> --****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property--
Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449
Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, The the subject data is uploaded, however it seems that we have figured out the issue - so you may not need to look at it. Below is what we think the problem and its solution are. Let me know if it makes sense.
the reconstruction scripts at our campus imaging facility have two flaws: [1] there's is no orientation information in header of either Analyze or NIFTII outputs; [2] the Analyze format is non-standard (RAS instead of LAS). As a result the first mri_convert step which converts our file to .mgz format assumes that the orientation is neurological resulting in a flip of left to right (albeit with an error message saying that it did not have that info). this flipping can only be seen when comparing images in tkmedit and SPM, which should have been inveresed, but were not.
We think that in order to avoid this in future we should add a --in-orientation ras flag to mri_convert. Is that correct?
The other question is - now that we have processed some 50 subjects, is there a way of flipping the results so that we wont have to start from scratch (this is a longitudinal study and participants will be scanned again).?
Thanks Ilana
Ilana Hairston wrote:
Hi Doug, The the subject data is uploaded, however it seems that we have figured out the issue - so you may not need to look at it. Below is what we think the problem and its solution are. Let me know if it makes sense.
the reconstruction scripts at our campus imaging facility have two flaws: [1] there's is no orientation information in header of either Analyze or NIFTII outputs; [2] the Analyze format is non-standard (RAS instead of LAS). As a result the first mri_convert step which converts our file to .mgz format assumes that the orientation is neurological resulting in a flip of left to right (albeit with an error message saying that it did not have that info). this flipping can only be seen when comparing images in tkmedit and SPM, which should have been inveresed, but were not.
We think that in order to avoid this in future we should add a --in-orientation ras flag to mri_convert. Is that correct?
That might work. The orientation string is actually more specific than just "RAS". You data might in an RAS cooridnate system, but this means that the orientation string could be RAS, or it could be SAR, or ARS, or ARS, etc. See what I mean? If it shows up correctly in tkmedit, then you're got it right (assuming that you are sure that it is really in an RAS coordinate system).
The other question is - now that we have processed some 50 subjects, is there a way of flipping the results so that we wont have to start from scratch (this is a longitudinal study and participants will be scanned again).?
You can try using xhemireg --s reversedsubject --o newsubjectname --all-vol --noreg
This script was never intended for this purpose, so I don't know whether it will work fully or not. It should at least reverse all the volumes after which you can run recon-all on it. It should keep any edits you have made, but the control points won't be copied (and would be wrong in the reversed subject).
doug
Thanks Ilana
--
Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449
Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Ilana Hairston