Hi All,
I was thinking that there was a freesurfer tool that performed simple math operations on volumetric labels (similar to those that mris_label_calc performs for surface labels) but I can't seem to find one. Is there such a tool that I am simply missing? I am hoping to easily create non-overlapping labels from a set of currently overlapping labels.
Thanks,
-kami
Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565
Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor.
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mris_calc should work for this purpose. Run mris_calc -h to see the options
On Thu, 6 Feb 2014, Kami Koldewyn wrote:
Hi All,
I was thinking that there was a freesurfer tool that performed simple math operations on volumetric labels (similar to those that mris_label_calc performs for surface labels) but I can't seem to find one. Is there such a tool that I am simply missing? I am hoping to easily create non-overlapping labels from a set of currently overlapping labels.
Thanks,
-kami
Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565
Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor.
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As far as I can tell - and I may very well be using incorrect syntax - mris_calc needs volumes as inputs and does not accept labels. Does mris_calc accept label files as inputs, for instance in a command like: "mris_calc roi2.label and roi3.label"? If so, could someone point me at the correct syntax to use?
Thanks,
-kami
On 06/02/2014 15:40, "Maritza Ebling" maritza@nmr.mgh.harvard.edu wrote:
mris_calc should work for this purpose. Run mris_calc -h to see the options
On Thu, 6 Feb 2014, Kami Koldewyn wrote:
Hi All,
I was thinking that there was a freesurfer tool that performed simple math operations on volumetric labels (similar to those that mris_label_calc performs for surface labels) but I can't seem to find one. Is there such a tool that I am simply missing? I am hoping to easily create non-overlapping labels from a set of currently overlapping labels.
Thanks,
-kami
Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565
Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor.
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Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565
Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor.
This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.
'mris_calc' accepts as inputs volumes or "curvature" files. Calculations on labels don't make sense in the context for which "mris_calc" was written -- what would an operation like "label1 multiply-by label2" even mean?
Having said that, 'mris_calc' does support labels in as much as using a label as a filter or ROI on which to do some calculation.
What you're looking to do, i.e. process labels and filter out non-overlapping from overlapping, isn't supported by 'mris_calc'.
On 2/6/14, 13:09 , Kami Koldewyn wrote:
As far as I can tell - and I may very well be using incorrect syntax - mris_calc needs volumes as inputs and does not accept labels. Does mris_calc accept label files as inputs, for instance in a command like: "mris_calc roi2.label and roi3.label"? If so, could someone point me at the correct syntax to use?
Thanks,
So in other words, there is not a tool in Freesurfer similar to mris_label_calc but that works with labels defined in the volume rather than on the surface, correct?
I am simply double checking that there is not a simple single step tool before I write a matlab script or start transforming labels to volumes.
-kami
On Feb 6, 2014, at 7:10 PM, "Rudolph Pienaar" rudolph.nmr@gmail.com wrote:
'mris_calc' accepts as inputs volumes or "curvature" files. Calculations on labels don't make sense in the context for which "mris_calc" was written -- what would an operation like "label1 multiply-by label2" even mean?
Having said that, 'mris_calc' does support labels in as much as using a label as a filter or ROI on which to do some calculation.
What you're looking to do, i.e. process labels and filter out non-overlapping from overlapping, isn't supported by 'mris_calc'.
On 2/6/14, 13:09 , Kami Koldewyn wrote: As far as I can tell - and I may very well be using incorrect syntax - mris_calc needs volumes as inputs and does not accept labels. Does mris_calc accept label files as inputs, for instance in a command like: "mris_calc roi2.label and roi3.label"? If so, could someone point me at the correct syntax to use?
Thanks,
-- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA
Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565
Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor.
This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.
freesurfer@nmr.mgh.harvard.edu
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Kami Koldewyn -
Maritza Ebling -
Rudolph Pienaar