Re: [BULK] Re: [caret-users] Map SPM volume
Thanks Donna, everything seems to work now, so Im happy :) About the surfaces, I saw something in the archive, is it a white brain, or deflated pial: http://sumsdb.wustl.edu:8081/sums/search.do?category_id=6 and then click the first option with a brain icon on it that is possible to view in the web browser. There are 12 versions of each hemisphere so I presume that it is an individual brain. Do you think is ok to use one of them, or do you happen to have an average surface? I think you are right, inflated brains may be best suited for visualizing purposes, however, just in case some stubborn SPM guy would like once in a while see hes activation the way he is used to . I think Freesurfer has a pial surface. Maybe it works to import that somehow? Also, it would be nice to have the option to see the whole brain at once (the non-split way) even inflated, but I guess thats not yet possible . Cheers, Julian > On 03/07/2007 10:27 AM, Julianm Macoveanu wrote: >> Yes, I use the CARET_TUTORIAL_SEPT06/MAPPNING_PROCEDURES files, and load >> the >> Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file. >> >> I think I got the hang of it. The break through was, after creating the >> metric file load one of the predefined scenes before trying to open my >> metric file. In this way it didn't complain anymore about different >> number >> of nodes. >> >> If I understand it right if I want now to see the activation on a pial >> surface I should just open the coord file and add it to my template spec >> file. Do you know where I could find this? I think it should also be >> something between pial and fiducial. >> > The PALS_B12 atlas (and the colin atlas before it) has no pial > surfaces. One can generate pseudo-pial surfaces by using Surface: > Geometry: Expand or Shrink surface to expand a fiducial surface, but > I've never tried this with an average fiducial surface, and I don't > really recommend it. We prefer the inflated surface for visualization, > unless you have activity in the operculum or insula that is difficult to > see; in such cases, we then use the Very Inflated surface. Activity in > buried sulci isn't visible when viewed on a pial or a regular fiducial > (less so with an average fiducial). > > I realize some people still prefer looking at a highly structured pial > surface, but considering this is group data you're mapping, the > structure of any one individual is not really representative of the > "group" structure of your subjects. We believe mapping to PALS_B12 and > viewing the results on the inflated surface is a more faithful > representation of your results than viewing them on, say, colin27's pial > surface. Slowly, we're hoping to win you over. ;-) > >> Also, L and R are overlaid wrong, what SPM reports as left, I see it on >> the >> right hemisphere in Caret. How can this be changed? >> > Use File: Open Data File: volume functional file and check the Volume is > an SPM2 Volume with Right on Left checkbox. >> Thanks, >> Julian >> >> -Original Message- >> From: [EMAIL PROTECTED] >> [mailto:[EMAIL PROTECTED] On Behalf Of Donna >> Dierker >> Sent: Wednesday, March 07, 2007 4:05 PM >> To: Caret, SureFit, and SuMS software users >> Subject: [BULK] Re: [caret-users] Map SPM volume >> Importance: Low >> >> Hi Julian, >> >> When mapping to atlas, are you selecting a spec file created from this >> dataset: >> >> CARET_TUTORIAL_SEPT-06 >> http://sumsdb.wustl.edu/sums/directory.do?id=6585200 >> >> ... using steps as described in Section 5.1 of this tutorial: >> >> Caret_Tutorial_Oct06.pdf >> http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379 >> >> It's tough to see how you could get this error under those >> circumstances, since the files in that spec file (or derivative thereof) >> all have the same 73730 standard mesh. >> >> While this spec won't have a pial surface, it will have left and right >> versions of the following configurations: >> >> PALS_B12 average fiducial >> inflated >> very inflated >> flat >> >> Since you're using SPM2, I'd suggest replacing the average fiducial >> coord files with these files: >> >> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord >> Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord >> >> To do so, after opening >> Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File: >> Open Data File: and select >> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord. Repeat >> for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord. >> Then, select Toolbar: Spec and use the X buttons to delete these >> versions, which are similar but not as optimal as the SPM2 versions in >> your case: >> >> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord >> Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord >> >> Both the SPM2 and FLIRT versions are in mni152 space, but the >> contributing PALS_B12 anatomicals were normalized using SPM2 for the >> SPM2 versions, while FS
Re: [caret-users] Map SPM volume
On 03/07/2007 10:27 AM, Julianm Macoveanu wrote: Yes, I use the CARET_TUTORIAL_SEPT06/MAPPNING_PROCEDURES files, and load the Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file. I think I got the hang of it. The break through was, after creating the metric file load one of the predefined scenes before trying to open my metric file. In this way it didn't complain anymore about different number of nodes. If I understand it right if I want now to see the activation on a pial surface I should just open the coord file and add it to my template spec file. Do you know where I could find this? I think it should also be something between pial and fiducial. The PALS_B12 atlas (and the colin atlas before it) has no pial surfaces. One can generate pseudo-pial surfaces by using Surface: Geometry: Expand or Shrink surface to expand a fiducial surface, but I've never tried this with an average fiducial surface, and I don't really recommend it. We prefer the inflated surface for visualization, unless you have activity in the operculum or insula that is difficult to see; in such cases, we then use the Very Inflated surface. Activity in buried sulci isn't visible when viewed on a pial or a regular fiducial (less so with an average fiducial). I realize some people still prefer looking at a highly structured pial surface, but considering this is group data you're mapping, the structure of any one individual is not really representative of the "group" structure of your subjects. We believe mapping to PALS_B12 and viewing the results on the inflated surface is a more faithful representation of your results than viewing them on, say, colin27's pial surface. Slowly, we're hoping to win you over. ;-) Also, L and R are overlaid wrong, what SPM reports as left, I see it on the right hemisphere in Caret. How can this be changed? Use File: Open Data File: volume functional file and check the Volume is an SPM2 Volume with Right on Left checkbox. Thanks, Julian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Wednesday, March 07, 2007 4:05 PM To: Caret, SureFit, and SuMS software users Subject: [BULK] Re: [caret-users] Map SPM volume Importance: Low Hi Julian, When mapping to atlas, are you selecting a spec file created from this dataset: CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu/sums/directory.do?id=6585200 ... using steps as described in Section 5.1 of this tutorial: Caret_Tutorial_Oct06.pdf http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379 It's tough to see how you could get this error under those circumstances, since the files in that spec file (or derivative thereof) all have the same 73730 standard mesh. While this spec won't have a pial surface, it will have left and right versions of the following configurations: PALS_B12 average fiducial inflated very inflated flat Since you're using SPM2, I'd suggest replacing the average fiducial coord files with these files: Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord To do so, after opening Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File: Open Data File: and select Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord. Repeat for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord. Then, select Toolbar: Spec and use the X buttons to delete these versions, which are similar but not as optimal as the SPM2 versions in your case: Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord Both the SPM2 and FLIRT versions are in mni152 space, but the contributing PALS_B12 anatomicals were normalized using SPM2 for the SPM2 versions, while FSL's flirt (affine only) was used to normalize the FLIRT versions. Donna On 03/07/2007 08:33 AM, Julianm Macoveanu wrote: Hi guys, I need some help with basic stuff. I just want to use Caret to visualize my SPM2 activations on inflated/Fiducial surfaces. So I have the normalized volume file to start with. I have opened a spec file from the Caret tutorial, use the map volume to surface function, choose my volume, then Map to spec file with atlas (and without). I have also tried not to open any spec file to begin with, and then just open the one I chose as output during the mapping procedure As space I tried the SPM2, as this is the kind of volume I have (but also 711-sc). After the metric file is generated, I just try to open it, but I get the error that my metric file contains different number of nodes. What I would like to have is a spec file that have all different surfaces (including pial and multi-fiducial which I could not find in any examples of spec files) and then just create metric files from my SPM volumes in order to visualize the activations. Cheers, Julian
RE: [BULK] Re: [caret-users] Map SPM volume
Yes, I use the CARET_TUTORIAL_SEPT06/MAPPNING_PROCEDURES files, and load the Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file. I think I got the hang of it. The break through was, after creating the metric file load one of the predefined scenes before trying to open my metric file. In this way it didn't complain anymore about different number of nodes. If I understand it right if I want now to see the activation on a pial surface I should just open the coord file and add it to my template spec file. Do you know where I could find this? I think it should also be something between pial and fiducial. Also, L and R are overlaid wrong, what SPM reports as left, I see it on the right hemisphere in Caret. How can this be changed? Thanks, Julian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Wednesday, March 07, 2007 4:05 PM To: Caret, SureFit, and SuMS software users Subject: [BULK] Re: [caret-users] Map SPM volume Importance: Low Hi Julian, When mapping to atlas, are you selecting a spec file created from this dataset: CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu/sums/directory.do?id=6585200 ... using steps as described in Section 5.1 of this tutorial: Caret_Tutorial_Oct06.pdf http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379 It's tough to see how you could get this error under those circumstances, since the files in that spec file (or derivative thereof) all have the same 73730 standard mesh. While this spec won't have a pial surface, it will have left and right versions of the following configurations: PALS_B12 average fiducial inflated very inflated flat Since you're using SPM2, I'd suggest replacing the average fiducial coord files with these files: Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord To do so, after opening Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File: Open Data File: and select Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord. Repeat for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord. Then, select Toolbar: Spec and use the X buttons to delete these versions, which are similar but not as optimal as the SPM2 versions in your case: Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord Both the SPM2 and FLIRT versions are in mni152 space, but the contributing PALS_B12 anatomicals were normalized using SPM2 for the SPM2 versions, while FSL's flirt (affine only) was used to normalize the FLIRT versions. Donna On 03/07/2007 08:33 AM, Julianm Macoveanu wrote: > > Hi guys, > > I need some help with basic stuff. I just want to use Caret to > visualize my SPM2 activations on inflated/Fiducial surfaces. So I have > the normalized volume file to start with. > > > > I have opened a spec file from the Caret tutorial, use the map volume > to surface function, choose my volume, then Map to spec file with > atlas (and without). I have also tried not to open any spec file to > begin with, and then just open the one I chose as output during the > mapping procedure > > > > As space I tried the SPM2, as this is the kind of volume I have (but > also 711-sc). > > > > After the metric file is generated, I just try to open it, but I get > the error that my metric file contains different number of nodes. > > > > What I would like to have is a spec file that have all different > surfaces (including pial and multi-fiducial which I could not find in > any examples of spec files) and then just create metric files from my > SPM volumes in order to visualize the activations. > > > > Cheers, > > Julian > > > ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Map SPM volume
Hi Julian, When mapping to atlas, are you selecting a spec file created from this dataset: CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu/sums/directory.do?id=6585200 ... using steps as described in Section 5.1 of this tutorial: Caret_Tutorial_Oct06.pdf http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379 It's tough to see how you could get this error under those circumstances, since the files in that spec file (or derivative thereof) all have the same 73730 standard mesh. While this spec won't have a pial surface, it will have left and right versions of the following configurations: PALS_B12 average fiducial inflated very inflated flat Since you're using SPM2, I'd suggest replacing the average fiducial coord files with these files: Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord To do so, after opening Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File: Open Data File: and select Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord. Repeat for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord. Then, select Toolbar: Spec and use the X buttons to delete these versions, which are similar but not as optimal as the SPM2 versions in your case: Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord Both the SPM2 and FLIRT versions are in mni152 space, but the contributing PALS_B12 anatomicals were normalized using SPM2 for the SPM2 versions, while FSL's flirt (affine only) was used to normalize the FLIRT versions. Donna On 03/07/2007 08:33 AM, Julianm Macoveanu wrote: Hi guys, I need some help with basic stuff. I just want to use Caret to visualize my SPM2 activations on inflated/Fiducial surfaces. So I have the normalized volume file to start with. I have opened a spec file from the Caret tutorial, use the map volume to surface function, choose my volume, then Map to spec file with atlas (and without). I have also tried not to open any spec file to begin with, and then just open the one I chose as output during the mapping procedure As space I tried the SPM2, as this is the kind of volume I have (but also 711-sc). After the metric file is generated, I just try to open it, but I get the error that my metric file contains different number of nodes. What I would like to have is a spec file that have all different surfaces (including pial and multi-fiducial which I could not find in any examples of spec files) and then just create metric files from my SPM volumes in order to visualize the activations. Cheers, Julian
[caret-users] Map SPM volume
Hi guys, I need some help with basic stuff. I just want to use Caret to visualize my SPM2 activations on inflated/Fiducial surfaces. So I have the normalized volume file to start with. I have opened a spec file from the Caret tutorial, use the map volume to surface function, choose my volume, then Map to spec file with atlas (and without). I have also tried not to open any spec file to begin with, and then just open the one I chose as output during the mapping procedure As space I tried the SPM2, as this is the kind of volume I have (but also 711-sc). After the metric file is generated, I just try to open it, but I get the error that my metric file contains different number of nodes. What I would like to have is a spec file that have all different surfaces (including pial and multi-fiducial which I could not find in any examples of spec files) and then just create metric files from my SPM volumes in order to visualize the activations. Cheers, Julian
