[caret-users] Set current directory with Caret v5.512
Hi, I have downloaded the snapshot version of Caret v5.512 for windows and, when I try to Set current directory... and select a directory, the navigator always returns the error messagecaret5.exe has encountered a problem and needs to close.. Does anyone has experienced the same problem? Thanks, Mateus
Re: [caret-users] Set current directory with Caret v5.512
Hi John, Now, it is working. Thank you very much. Best, Mateus John Harwell wrote: Hi Mateus, I downloaded the windows snapshot and it also crashed when I tried to set the current directory. I have updated the windows snapshot version and the problem should be fixed so try downloading it again. --- John Harwell [EMAIL PROTECTED] Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave Box 8108 Saint Louis, MO 63110 On Jan 23, 2008, at 10:36 AM, Mateus Joffily wrote: Hi, I have downloaded the snapshot version of Caret v5.512 for windows and, when I try to Set current directory... and select a directory, the navigator always returns the error messagecaret5.exe has encountered a problem and needs to close.. Does anyone has experienced the same problem? Thanks, Mateus ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
[caret-users] Surface Shape Cluster Analysis
Hi, I was trying to explore the operation 'Surface Shape Cluster Analysis' in the 'Surface region of Interest' dialog, but I am not sure I understand the reported values. After selecting a ROI from my surface, the operation returns a long list of 'Threshold Column Num-Nodes Area AreaCorrected COG-X COG-Y COG-Z' values. Could someone explain me what does it means each line of the reported list? Thanks, Mateus
Re: [caret-users] Latitude/Longitude
Hi John, Thank you very much. Sorry for the large attachment. I just realized the message size, after sending it. My operating system is Linux. Thanks again, Mateus John Harwell wrote: Hi Mateus, The copy of the file you included does not have valid latitude longitude values. Latitude should range from -90 to +90 and Longitude should range -180 to +180. The problem is that Caret is not reading binary format latitude longitude files correctly and I have just fixed this problem. In addition, I have modified the Surface Region of Interest Dialog to allow node selection based upon a range of Lat/Long values. Let me know which operating system you are using and I will make an updated version of Caret available for you to download. Lastly, it is probably not a good idea to include caret data files in emails as they can make the messages very large. If needed, we do have a website where files can be uploaded. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Jun 14, 2007, at 3:45 AM, Mateus Joffily wrote: John, Thank you for the detailed explanation. I followed it, but I am not confident that I got the correct result. To be sure that there was not a problem with my lat/lon file, I decided to test it with CARET_TUTORIAL_SEPT06/PAL_B12.BOTH- HEMS.STANDARD-SCENES.73730.spec. I am attaching the images that I captured from the created metric columns LAT and LONG. The LONG column has only zeros and the LAT column has some strange values. Instead, I would expect a grading of values along the latitude- longitude isocontours. Is it correct? I am also attaching a copy of the latlon file (PALS_B12.LR.73730.latlon) converted to metric. Thanks, Mateus John Harwell wrote: Mateus, We will add ROI node selection with latitude/longitude to our to- do list. First, convert the LatLon file to a Metric file: * Write your latitude/longitude file and be sure that Data File Encoding at the bottom of the Save Data File Dialog is set to Ascii (Text). * Load the lat/lon file into a text editor. * Change tag-version 1 to tag-version 2 * Change tag-number-of-columns 1 to tag-number-of-columns 4 * Save the lat/lon file * Change then name of the lat-lon file so that it ends with .metric. * Select File Menu-Open Data File. Set the type to Metric, choose the file, and press the Open button. A Dialog will appear listing the columns for loading. Set the names of the first two columns to Long and Lat respectively. Second, to select the ROI * Use the Display Control to set the displayed metric to Lat. * On the Surface ROI Dialog, set the selection method to Nodes with Metric. * Set the Thresholds to the range of latitudes you want to select. * Press the Select Nodes button. * On the Display Control Dialog, change the selected metric to Long. * On the Surface ROI Dialog, change Normal Selection to And Selection (Intersection). * Set the thresholds to the range of longitudes you want to select. * Press the Select Nodes button. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Jun 13, 2007, at 11:13 AM, Mateus Joffily wrote: Hi, I would like to select every node that is inside a certain range of latitude/longitude coordinates. I thought to create a metric column with the nodes' longitude and latitude values and then use the 'Node with Metric' operation from 'Surface Region of Interest' dialog to select the nodes. But I am not sure it is the easiest way of doing it... Does anyone has any suggestion? Thank you very much. Mateus ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
[caret-users] Latitude/Longitude
Hi, I would like to select every node that is inside a certain range of latitude/longitude coordinates. I thought to create a metric column with the nodes' longitude and latitude values and then use the 'Node with Metric' operation from 'Surface Region of Interest' dialog to select the nodes. But I am not sure it is the easiest way of doing it... Does anyone has any suggestion? Thank you very much. Mateus
[caret-users] spm99 metrics projection
Hello, We have 18 subjects that have been analysed with spm99. Their structural images have been normalized into a template from Marseille (http://irmfmrs.free.fr/formation/traitement_des_donnees/GuideSPM.htm) in MNI space. Since, we didn't use spm99 standard template, I am not sure we can use Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM99_fMRI-MAPPER.B1-12.LEFT.73730.spec for projecting the metrics. What would be the correct way of projecting the metric files of those subjects into a Caret/PALS surface? Is there a Human.PALS_B12.LR.AVERAGE-FIDUCIAL_SPM96.RIGHT.73730.spec for spm99? Thank you for your help. Mateus
Re: [caret-users] spm99 metrics projection
Ok, I will try it. Thank you very much! Mateus Donna Dierker wrote: On 04/26/2007 08:29 AM, Mateus Joffily wrote: Hi Donna, Wasn't SPM96 the single subject colin target? I'm asking, because I really don't know the answer, but I think David may have told me this while working on his foci project. I don't know, but I will check it. It turns out my caret/data_files/fmri_mapping_files directory *does* have AVERAGE-FIDUCIAL_SPM95 and AVERAGE-FIDUCIAL_SPM96 spec files that almost certainly have to do with David's foci project. Your version may be older and not yet have these files. Yes. I also have an AVERAGE-FIDUCIAL_SPM95. But I was wondering if it exists an AVERAGE-FIDUCIAL_SPM99. But a worthwhile task might be to do this: cd /usr/local/caret/data_files/fmri_mapping_files caret5 Then, open whichever of these specs you think has the best chance of aligning: Human.PALS_B12.LR.AVERAGE-FIDUCIAL_SPM95.LEFT.73730.spec Human.PALS_B12.LR.AVERAGE-FIDUCIAL_SPM96.LEFT.73730.spec Human.colin.SPM2.LEFT.71785.spec Human.colin.SPM99.LEFT.71785.spec Human.PALS_B12.LR.MULTI-FIDUCIAL_FLIRT_fMRI-MAPPER.B1-12.LEFT.73730.spec Human.PALS_B12.LR.MULTI-FIDUCIAL_MRITOTAL_fMRI-MAPPER.B1-12.LEFT.73730.spec Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730.spec Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM99_fMRI-MAPPER.B1-12.LEFT.73730.spec Then File: Open Data File: Volume anatomy file: and open your Marseille template Switch to volume view ALL D/C: overlay/underlay volume: settings: Toggle on Show surface contour checkbox Scroll around and evaluate how well the fiducial contour intersects the surface Ok. I will try it. Finaly, if I choose to use a MULTI-FIDUCIAL spec, I will need to project each individual metric to each Buck_Case01:12 surface? After, how can I get an average fiducial map of the activations? No: If you decide MULTI-FIDUCIAL_SPM99 aligns nicely, then select SPM99 from the list of spaces in the Map to Atlas menu. Then you'll see the entries that correspond to this spec file, select them, and select either map to average fiducial only; map to each of the subjects; and/or generate the average of the individual mappings. In other words, the process is exactly the same; the only issue is first determining whether any of the existing surfaces intersects your template well enough, and if so, which intersects best. Thank you very much. Mateus Perhaps even get a capture, if the alignment is excellent, and use this as your reason for using this target. If none align well, then I don't have a good plan B for you. Donna On 04/26/2007 05:15 AM, Mateus Joffily wrote: Hello, We have 18 subjects that have been analysed with spm99. Their structural images have been normalized into a template from Marseille (http://irmfmrs.free.fr/formation/traitement_des_donnees/GuideSPM.htm) in MNI space. Since, we didn't use spm99 standard template, I am not sure we can use Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM99_fMRI-MAPPER.B1-12.LEFT.73730.spec for projecting the metrics. What would be the correct way of projecting the metric files of those subjects into a Caret/PALS surface? Is there a Human.PALS_B12.LR.AVERAGE-FIDUCIAL_SPM96.RIGHT.73730.spec for spm99? Thank you for your help. Mateus ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] ROI center of gravity
Hi Donald, Thanks for your comments. I would like to propose a 'new' method for calculating the surface's COG. To avoid the nodes density problem, I think it would be reasonable to calculate the COG of every tile on the surface and, after, to calculate the COG of the whole surface summing the COG of each tile multiplied by its own area and divided by the total surface area. I have done some tests using this method and compared the results with Caret's method. On the attached capture (cog_m1.jpg), you can see a flat map of the primary motor cortex. Depending on the method used (caret vs. 'new' method) the COG can be shifted of up to 10mm. The 'new' method shows a COG more superior, consistent with the lower concentration of nodes at this region of the surface. Capture 'cog_m1_zoom.jpg' is just a zoom in on the tiles' CoG (green points). I would appreciate any comment on this method. I couldn't find the paper you cited. I guess it hasn't been published yet. Do you know when it will be available for download? Best regards, Mateus DG MCLAREN wrote: Mateus, You raise a good point. In practice, it seems that you should keep the uneven distribution of nodes. The reason is as follows: If you resample the nodes to a more sparse uniform distribution, then you will distort the surface to some degree. The surface distortion will inevitable shift the center of gravity. I had thought about using the border points of a cluster to calculate the region; however, it seems that approach may unequally weight some parts of the cluster if there is an odd shape. It might be interesting to do a comparison between these methods. In the end, it probably doesn't matter how you do the calculation for COG, as they should be similar, as long as the method is reported. I should also note, a recently accepted article: Cortical network for vibrotactile attention: A fMRI study in Human Brain Mapping describes the method and uses the traditional method; so there is an established standard that one could rely on and cite in future work. Best Regards, Donald McLaren = D.G. McLaren University of Wisconsin - Madison Neuroscience Training Program Tel: (773) 406 2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406 2464 or email. - Original Message - From: Mateus Joffily [EMAIL PROTECTED] Date: Friday, January 26, 2007 12:12 pm Subject: [caret-users] ROI center of gravity To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Hi, I would like to calculate the center of gravity (COG) of a surface ROI. I see that 'Surface Region of Interest':'Statistical Report' gives me that information. However, if the nodes distribution over the surface is not uniform, the COG is biased toward the more dense regions. I understand that, if someone wants to calculate the COG, taking into account the nodes-density, this is the right calculation. But, if I suppose that the surface density is uniform, is there a way of calculating the COG avoiding the nodes distribution effect? Thanks, Mateus ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users inline: cog_m1.jpginline: cog_m1_zoom.jpg
Re: [caret-users] ROI - borders around clusters
Hi Donna,
I replicated your probelm exactly with the roi.zip archive you
uploaded. It contained only the flat coord and cut topo; have you
tried using the fiducial coord with closed topo? It may not help, but
it's worth a try.
Yes, the problem persists.
Although the clusters using metric2 appear smaller in area than the
metric1 clusters, the nodes within the metric2 clusters are denser,
which probably is a factor. See the attached captures, shows the
dense metric 2 clusters and the sparser metric 1 clusters, using
drawing mode: Links (No Backside) on the D/C surface misc menu. The
top two clusters are only a single tile wide, so I'm not surprised
Caret would have trouble drawing a border around them. The two bottom
ones also have places where they're only a tile wide, so maybe that's
the problem. If so, and switching coord/topo combos fails, then Im
not sure what else to suggest.
Yes, probably the number of tiles is a limitation for drawing the
borders. I see that borders are usualy not drawn around single tile
metrics. However, I have other metrics with denser clusters that it
doesn't draw the border neither (compare the top cluster (no border)
with the bottom cluster (cyan border) in the attached capture). May be
there is some other reason too... I will think a bit more about the
problem and, if I find something new, I will let you know.
Thanks a lot for your help,
Mateus
Doing a very small amount of metric smoothing (Average neighbors, 1
iteration, strength 1.0) and reducing the threshold a tad would
probably help (primarily just making the clusters larger), but I'm
guessing this is something you'd be very hesitant to do.
On 01/25/2007 08:33 AM, Mateus Joffily wrote:
Hi Donna,
I restarted Caret and I created a new Spec file, including only the
topology, flat coordinates, metric and surface shape files, and the
problem persists. I did the following tests until now:
1) I tried the same operation, selecting only one of the clusters for
which the program didn't draw borders before, but the program
complains No clusters were found.
2) I tried the same operation with another metric that has even
smaller cluster, and the program draws the borders correctly.
3) I tried some other operations on the selected nodes (e.g. Assign
metric column to selected nodes, and Statistical report), and the
program works fine for every cluster. Only 'Create Borders Around
Clusters' doesn't work.
I uploaded my new Spec file (roi.zip) with the two metrics included
('metric1': problematic one; and 'metric2': with smaller clusters
that works fine). If you have any other idea about what can be the
problem...
Thank you very much,
Mateus
Donna Dierker wrote:
The only thing I can think to try is to restart Caret and repeat
your selection of all nodes within threshold 1.0 to 5.0. I can
see from your capture that you did this and your green nodes include
clusters for which it didn't draw borders. My only guess is that
perhaps somehow the create borders is still acting on a previous
nodes connected to node number 33651 selection, even though this
radio button isn't selected (and the green nodes show select nodes
was pressed with All nodes within threshold selected). Restarting
simply removes any previous selections, if there is a bug lurking here.
Otherwise, my only other guess is that Caret has a minimum area for
clusters, before it will generate a border around it, and the
smaller ones fall below that threshold. I'm not aware of such a limit.
If you upload your spec file (including coord, topo, and metric), I
can see if my luck is any better than yours:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
On 01/24/2007 10:55 AM, Mateus Joffily wrote:
Hi,
I am trying to use 'Surface Region of Interest' to create borders
around metric clusters. The nodes on the surface are correctly
selected, but when I select 'Create Borders Around Clusters' only
one of the clusters is surrounded by a border. I have tried the
same operation with other metric columns and the program seems to
work fine. I don't know why, for this specific metric, some
clusters are left out.
I am attaching an image of caret windows. Any suggestion is well
appreciated.
Thanks,
Mateus
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___
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Re: [caret-users] ROI - borders around clusters
Hi Donna,
Thanks. I will look at the code and I let you know if I find something.
Mateus
Donna Dierker wrote:
Hi Mateus,
It's true the top cluster is mostly dense, but look at the node I've
highlighed in red in the attached capture. I wonder whether nodes
like this that cinch the cluster cause the algorithm to give up.
Attached is some code I dug out of the source that might be what Caret
is actually using. (John would know for sure.) Maybe it will prove
helpful in deciphering what is the bottleneck, so to speak.
On 01/26/2007 07:14 AM, Mateus Joffily wrote:
Hi Donna,
I replicated your probelm exactly with the roi.zip archive you
uploaded. It contained only the flat coord and cut topo; have you
tried using the fiducial coord with closed topo? It may not help,
but it's worth a try.
Yes, the problem persists.
Although the clusters using metric2 appear smaller in area than the
metric1 clusters, the nodes within the metric2 clusters are denser,
which probably is a factor. See the attached captures, shows the
dense metric 2 clusters and the sparser metric 1 clusters, using
drawing mode: Links (No Backside) on the D/C surface misc menu. The
top two clusters are only a single tile wide, so I'm not surprised
Caret would have trouble drawing a border around them. The two
bottom ones also have places where they're only a tile wide, so
maybe that's the problem. If so, and switching coord/topo combos
fails, then Im not sure what else to suggest.
Yes, probably the number of tiles is a limitation for drawing the
borders. I see that borders are usualy not drawn around single tile
metrics. However, I have other metrics with denser clusters that it
doesn't draw the border neither (compare the top cluster (no border)
with the bottom cluster (cyan border) in the attached capture). May
be there is some other reason too... I will think a bit more about
the problem and, if I find something new, I will let you know.
Thanks a lot for your help,
Mateus
Doing a very small amount of metric smoothing (Average neighbors, 1
iteration, strength 1.0) and reducing the threshold a tad would
probably help (primarily just making the clusters larger), but I'm
guessing this is something you'd be very hesitant to do.
On 01/25/2007 08:33 AM, Mateus Joffily wrote:
Hi Donna,
I restarted Caret and I created a new Spec file, including only the
topology, flat coordinates, metric and surface shape files, and the
problem persists. I did the following tests until now:
1) I tried the same operation, selecting only one of the clusters
for which the program didn't draw borders before, but the program
complains No clusters were found.
2) I tried the same operation with another metric that has even
smaller cluster, and the program draws the borders correctly.
3) I tried some other operations on the selected nodes (e.g. Assign
metric column to selected nodes, and Statistical report), and the
program works fine for every cluster. Only 'Create Borders Around
Clusters' doesn't work.
I uploaded my new Spec file (roi.zip) with the two metrics
included ('metric1': problematic one; and 'metric2': with smaller
clusters that works fine). If you have any other idea about what
can be the problem...
Thank you very much,
Mateus
Donna Dierker wrote:
The only thing I can think to try is to restart Caret and repeat
your selection of all nodes within threshold 1.0 to 5.0. I
can see from your capture that you did this and your green nodes
include clusters for which it didn't draw borders. My only guess
is that perhaps somehow the create borders is still acting on a
previous nodes connected to node number 33651 selection, even
though this radio button isn't selected (and the green nodes show
select nodes was pressed with All nodes within threshold
selected). Restarting simply removes any previous selections, if
there is a bug lurking here.
Otherwise, my only other guess is that Caret has a minimum area
for clusters, before it will generate a border around it, and the
smaller ones fall below that threshold. I'm not aware of such a
limit.
If you upload your spec file (including coord, topo, and metric),
I can see if my luck is any better than yours:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
On 01/24/2007 10:55 AM, Mateus Joffily wrote:
Hi,
I am trying to use 'Surface Region of Interest' to create borders
around metric clusters. The nodes on the surface are correctly
selected, but when I select 'Create Borders Around Clusters'
only one of the clusters is surrounded by a border. I have tried
the same operation with other metric columns and the program
seems to work fine. I don't know why, for this specific metric,
some clusters are left out.
I am attaching an image of caret windows. Any suggestion is well
appreciated.
Thanks,
Mateus
Re: [caret-users] ROI - borders around clusters
Hi Donna,
I restarted Caret and I created a new Spec file, including only the
topology, flat coordinates, metric and surface shape files, and the
problem persists. I did the following tests until now:
1) I tried the same operation, selecting only one of the clusters for
which the program didn't draw borders before, but the program complains
No clusters were found.
2) I tried the same operation with another metric that has even smaller
cluster, and the program draws the borders correctly.
3) I tried some other operations on the selected nodes (e.g. Assign
metric column to selected nodes, and Statistical report), and the
program works fine for every cluster. Only 'Create Borders Around
Clusters' doesn't work.
I uploaded my new Spec file (roi.zip) with the two metrics included
('metric1': problematic one; and 'metric2': with smaller clusters that
works fine). If you have any other idea about what can be the problem...
Thank you very much,
Mateus
Donna Dierker wrote:
The only thing I can think to try is to restart Caret and repeat your
selection of all nodes within threshold 1.0 to 5.0. I can see
from your capture that you did this and your green nodes include
clusters for which it didn't draw borders. My only guess is that
perhaps somehow the create borders is still acting on a previous nodes
connected to node number 33651 selection, even though this radio
button isn't selected (and the green nodes show select nodes was
pressed with All nodes within threshold selected). Restarting simply
removes any previous selections, if there is a bug lurking here.
Otherwise, my only other guess is that Caret has a minimum area for
clusters, before it will generate a border around it, and the smaller
ones fall below that threshold. I'm not aware of such a limit.
If you upload your spec file (including coord, topo, and metric), I
can see if my luck is any better than yours:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
On 01/24/2007 10:55 AM, Mateus Joffily wrote:
Hi,
I am trying to use 'Surface Region of Interest' to create borders
around metric clusters. The nodes on the surface are correctly
selected, but when I select 'Create Borders Around Clusters' only
one of the clusters is surrounded by a border. I have tried the same
operation with other metric columns and the program seems to work
fine. I don't know why, for this specific metric, some clusters are
left out.
I am attaching an image of caret windows. Any suggestion is well
appreciated.
Thanks,
Mateus
___
caret-users mailing list
caret-users@brainvis.wustl.edu
http://pulvinar.wustl.edu/mailman/listinfo/caret-users
[caret-users] ROI - borders around clusters
Hi, I am trying to use 'Surface Region of Interest' to create borders around metric clusters. The nodes on the surface are correctly selected, but when I select 'Create Borders Around Clusters' only one of the clusters is surrounded by a border. I have tried the same operation with other metric columns and the program seems to work fine. I don't know why, for this specific metric, some clusters are left out. I am attaching an image of caret windows. Any suggestion is well appreciated. Thanks, Mateus inline: roi_border.jpg
[caret-users] Create volume ROI from surface nodes
Hi, I am trying to create a volume ROI from selected nodes. I have selected the nodes inside a border, using the 'Surface Region of Interest' Query tab. Then I selected the 'Create Volume From Displayed Query Nodes' button and, after, I pressed OK in the 'Surface to Voulme Dialog'. The 'Converting Surface' wait bar appears, but, when it is done, I can't find where the volume ROI is saved. I see that a 'Segmention Volume' file is created, but I don't know how should I use it. What should I do next to create a volume ROI? Thanks for your help. Mateus
[caret-users] Flat surface crossovers
Dear experts, I am trying to flatten a surface. After medial wall and calcarine cut corrections, I obtain the attached flat surface with some crossovers. The 'initial Flattening Dialog' informs that cuts used to excise errors should begin and end outside the map perimeter. I am not really sure about what it means. Should I draw the new cuts inside or outside the borders (perimeter?) of the initial flat map. Could someone clarify it to me? Thanks for your help, Mateus inline: initial_flat_surface.jpg
[caret-users] tailarach coordinate
Hi, I have registred one individual surface into PALS-B12 (using Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec). I would like to know the talairach coordinate of a voxel in the registered surface. Is it possible? Thanks for your help, Mateus
Re: [caret-users] distance from a node
Hi David, Thanks for your reply. I asked for this capability because I am trying to perform a spherical registration. Many landmarks are defined as starting and terminating at a certain distance from an anatomical reference point. I thought that a tool, which allows the user to enter a reference point coordinate in the surface and, after, displays every node that is at a given geodesic distance from it, would be helpful This capability is not essential for me. I was wondering if it was already implemented in Caret. Best regards, Mateus David Vanessen wrote: Mateus, First, it is important to clarify whether your request pertains to nodes (as stated) or to foci. In Caret terminology, nodes refers specifically to the points that make up a surface and have locations specified within a coordinate file. Foci refers to stereotaxically identified locations (typically fMRI activation centers) that are specified within a foci file or foci projection file. I'm guessing you are referring to foci, but let us know. At present, I don't think that the capability you are asking about exists for either nodes or foci. If you can let us know what you will be using this for and whether this is a pressing need, it will help us to prioritize the request. Also, if other Caret users would like to see this functionality, let us know. Best regards, David On Nov 29, 2006, at 11:28 AM, Donna Dierker wrote: If you were talking about geodesic distance (i.e., running along the contour of the fiducial surface -- not as the crow flies through the CSF/WM), then you could use the Surface: ROI feature for this purpose. (First operation Geodesic Distance, and then threshold the resulting metric at the desired distance.) I'm not aware of something like that for 3D distances, but there's a Make Sphere feature in Window: Script Builder. Worst case, you could generate a sphere around the enclosing voxel and map that ROI volume to the surface. On 11/29/2006 11:18 AM, Mateus Joffily wrote: Hi, In Caret5.5, is there a way of selecting a node and finding all (or some) nodes that are at a given distance from it? I think I am looking for something similar to what is described in section 2.17.2 (Foci Data Searches) of the 'Caret Tutorial – the Basics'. But Section 2.17.2 regards only WebCaret. Does it exist something similar to Caret5.5? Thanks, Mateus ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http:// home.att.net/~donna.hanlon for details.) ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
[caret-users] projecting PALS-B12 atlas into individual brain
Hi, I have concluded the spherical registration of one individual surface into PALS-B12. Three spec files have been created: (1) Human.Isa.R.spec (original spec file); (2) deformed_Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec; (3) deformed_Human.Isa.R.spec; Could you, please, precise me differences among those three specs and for what purpose should I use each one? Although the names seem to be informative, when I compare the surfaces linked to each one, they look very similar, if not the same. In the next step, I would like to project PALS_B12 atlas (borders and paints) into the non-deformed individual surface. Could you, please, point me the documentation that explains how to do that, and how do I use the deformation map files? Thanks again for your help. Mateus
Re: [caret-users] Spherical registration
Hi, In the 'Caret5 Tutorial', during the spherical registration procedure, it is instructed to use the 'Human to Human' standard parameters (in Surface: Deformation: Run Spherical Surface Deformation: Spherical Parameters: Set Parameters). However, in Erin's cheat sheet, it is instructed to read params from: Def Map File: 'TEMPLATE_REG-with-POP-AVG_4k_NoFid.deform_map'. If I am using 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730' atlas, which procedure should I follow? Thanks, Mateus Donna Dierker wrote: I did remove the port numbers from the list, which seemed to have no ill effect on my end. Perhaps it resolved the problem on your end. On 11/29/2006 03:15 AM, Mateus Joffily wrote: Hi Donna, I don't know what happened, but now all the links work. Thanks, Mateus Donna Dierker wrote: Mateus, Yes -- that's the right archive. I don't understand why you're getting the time out errors; I can't replicate the problem on my end. What happens when you try this link (i.e., same, except port number omitted): http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499 On 11/28/2006 01:03 PM, Mateus Joffily wrote: Hi Donna, I don't know if I am the only one experiencing this problem, but I am also unable to access the location: http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499. I still get a 'time out error'. However, I can access the SuMS database from http://sumsdb.wustl.edu/. Could you, please, confirm me if this is the atlas that I need to download: 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730'? Thanks, Mateus Donna Dierker wrote: On 11/28/2006 11:48 AM, Mateus Joffily wrote: Hi, I am a little bit confused on how to proceed to register an individual surface into an Atlas. The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' explains how to perform a spherical registration using the 'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My questions are: 1) What spec file should I use to register into the right hemisphere? 2) If I choose to register into PALS-B12 atlas, what files should I use? The answer to both 1) and 2) is use the PALS_B12 LR combo registration target dataset: http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499 And use the template deform_map included in that dataset to preset your registration parameters. See this page and Erin's cheat sheet (linked from the page below) for more details: http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html This is what we do. There are separate landmark datasets for the left and right, but they differ very little, and using the LR combo enables you to do cross-hem or inter-hem analyses. The way we look at it, there's very little down side to using the combo dataset, but a lot of up side to doing so. So we routinely use the LR combo now. We stopped using colin as a registration target a couple of years ago, but some documentation may still refer to it. Thanks, Mateus ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] distance from a node
Hi Donna, That's exactly what I did (although, there are some details in your example that I didn't understand well, see below). But, instead of keep going forth and back selecting nodes and subtracting their coordinates values (I had to do it quite often), I was wondering if there was not an utility that would automatically highlight all the nodes that are at a given distance from my reference point. I am not saying that it is a necessary utility, but, if it was already implemented, I could benefit from it... Thanks, Mateus For example, there's a pretty big x and z offset between this occipital pole (first) and candidate most-posterior calcarine border point: In this example, I though that the biggest offset was for Y (dX: 15-28=-13; dY: -110 --78=32; dZ: -22 --6=-16). That's why you first chose to adjust the Y distance, no? Node 20734 Main Window Inflated XYZ: 15.015987396, -110.156700134, -22.251829147 Shape: -2.904558420 -2.124466896 Node 32819 Main Window Inflated XYZ: 27.664737701, -77.988800049, -6.281192303 Distance: 38.076580048 Shape: -10.455765724 -8.209010124 So I compute -110 - -78 = 32 -- so this point is 32mm from the occipital pole, so we need to find one whose y component of the inflated coordinate is closer to like -110 + 24 = -86. Hope this helps! On 11/30/2006 06:53 AM, Mateus Joffily wrote: Hi David, Thanks for your reply. I asked for this capability because I am trying to perform a spherical registration. Many landmarks are defined as starting and terminating at a certain distance from an anatomical reference point. I thought that a tool, which allows the user to enter a reference point coordinate in the surface and, after, displays every node that is at a given geodesic distance from it, would be helpful This capability is not essential for me. I was wondering if it was already implemented in Caret. Best regards, Mateus David Vanessen wrote: Mateus, First, it is important to clarify whether your request pertains to nodes (as stated) or to foci. In Caret terminology, nodes refers specifically to the points that make up a surface and have locations specified within a coordinate file. Foci refers to stereotaxically identified locations (typically fMRI activation centers) that are specified within a foci file or foci projection file. I'm guessing you are referring to foci, but let us know. At present, I don't think that the capability you are asking about exists for either nodes or foci. If you can let us know what you will be using this for and whether this is a pressing need, it will help us to prioritize the request. Also, if other Caret users would like to see this functionality, let us know. Best regards, David On Nov 29, 2006, at 11:28 AM, Donna Dierker wrote: If you were talking about geodesic distance (i.e., running along the contour of the fiducial surface -- not as the crow flies through the CSF/WM), then you could use the Surface: ROI feature for this purpose. (First operation Geodesic Distance, and then threshold the resulting metric at the desired distance.) I'm not aware of something like that for 3D distances, but there's a Make Sphere feature in Window: Script Builder. Worst case, you could generate a sphere around the enclosing voxel and map that ROI volume to the surface. On 11/29/2006 11:18 AM, Mateus Joffily wrote: Hi, In Caret5.5, is there a way of selecting a node and finding all (or some) nodes that are at a given distance from it? I think I am looking for something similar to what is described in section 2.17.2 (Foci Data Searches) of the 'Caret Tutorial – the Basics'. But Section 2.17.2 regards only WebCaret. Does it exist something similar to Caret5.5? Thanks, Mateus ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http:// home.att.net/~donna.hanlon for details.) ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] distance from a node
I already started having fun with Caret! ;-) Thank you very much Donna Dierker wrote: Come to think of it, I would benefit from that utility, too.;-) Even better would be an accurate, automated border drawing utility. Kidding aside, we recognize this is a highly desirable enhancement, but pretty tough to deliver right now. John Harwell has added some caret_command features that can trim some of the easy ones (e.g., calcarine posterior, central dorsal/medial): SURFACE BORDER EXTREMA caret_command -surface-border-extrema \ input-topo-file input-coord-file input-border-file border-name List the extrema for the surface, the extrema for the border, and the difference between the extrema. -- SURFACE BORDER NIBBLER (remove border points within a distance to surface ext rema) caret_command -surface-border-nibbler \ input-topo-file input-coord-file input-border-file border-name output-border-file surface-extrema-name-or-node-indicator surface-extrema-offset-or-node-number pos-neg Remove points from the named border that are within that are on a . specified side of a surface extrema or node number. But your idea is kind of interesting. Meanwhile, if you choose reference points which differ primarily along the axis of interest, then the distance is a good proxy for the component difference, so no math required. In either case, you'll be surprised how fast you get good at guessing. Before long, you'll need only a few tries, and it's always fun when your first guess is right. ;-) On 11/30/2006 12:52 PM, Mateus Joffily wrote: Hi Donna, That's exactly what I did (although, there are some details in your example that I didn't understand well, see below). But, instead of keep going forth and back selecting nodes and subtracting their coordinates values (I had to do it quite often), I was wondering if there was not an utility that would automatically highlight all the nodes that are at a given distance from my reference point. I am not saying that it is a necessary utility, but, if it was already implemented, I could benefit from it... Thanks, Mateus For example, there's a pretty big x and z offset between this occipital pole (first) and candidate most-posterior calcarine border point: In this example, I though that the biggest offset was for Y (dX: 15-28=-13; dY: -110 --78=32; dZ: -22 --6=-16). That's why you first chose to adjust the Y distance, no? Node 20734 Main Window Inflated XYZ: 15.015987396, -110.156700134, -22.251829147 Shape: -2.904558420 -2.124466896 Node 32819 Main Window Inflated XYZ: 27.664737701, -77.988800049, -6.281192303 Distance: 38.076580048 Shape: -10.455765724 -8.209010124 So I compute -110 - -78 = 32 -- so this point is 32mm from the occipital pole, so we need to find one whose y component of the inflated coordinate is closer to like -110 + 24 = -86. Hope this helps! On 11/30/2006 06:53 AM, Mateus Joffily wrote: Hi David, Thanks for your reply. I asked for this capability because I am trying to perform a spherical registration. Many landmarks are defined as starting and terminating at a certain distance from an anatomical reference point. I thought that a tool, which allows the user to enter a reference point coordinate in the surface and, after, displays every node that is at a given geodesic distance from it, would be helpful This capability is not essential for me. I was wondering if it was already implemented in Caret. Best regards, Mateus David Vanessen wrote: Mateus, First, it is important to clarify whether your request pertains to nodes (as stated) or to foci. In Caret terminology, nodes refers specifically to the points that make up a surface and have locations specified within a coordinate file. Foci refers to stereotaxically identified locations (typically fMRI activation centers) that are specified within a foci file or foci projection file. I'm guessing you are referring to foci, but let us know. At present, I don't think that the capability you are asking about exists for either nodes or foci. If you can let us know what you will be using this for and whether this is a pressing need, it will help us to prioritize the request. Also, if other Caret users would like to see this functionality, let us know. Best regards, David On Nov 29, 2006, at 11:28 AM, Donna Dierker wrote: If you were talking about geodesic distance (i.e., running along the contour of the fiducial surface -- not as the crow flies through the CSF/WM), then you could use the Surface: ROI feature for this purpose. (First operation Geodesic Distance, and then threshold the resulting metric at the desired distance.) I'm not aware of something like that for 3D distances, but there's a Make Sphere feature in Window: Script Builder. Worst
Re: [caret-users] Spherical registration
Hi Donna, I don't know what happened, but now all the links work. Thanks, Mateus Donna Dierker wrote: Mateus, Yes -- that's the right archive. I don't understand why you're getting the time out errors; I can't replicate the problem on my end. What happens when you try this link (i.e., same, except port number omitted): http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499 On 11/28/2006 01:03 PM, Mateus Joffily wrote: Hi Donna, I don't know if I am the only one experiencing this problem, but I am also unable to access the location: http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499. I still get a 'time out error'. However, I can access the SuMS database from http://sumsdb.wustl.edu/. Could you, please, confirm me if this is the atlas that I need to download: 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730'? Thanks, Mateus Donna Dierker wrote: On 11/28/2006 11:48 AM, Mateus Joffily wrote: Hi, I am a little bit confused on how to proceed to register an individual surface into an Atlas. The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' explains how to perform a spherical registration using the 'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My questions are: 1) What spec file should I use to register into the right hemisphere? 2) If I choose to register into PALS-B12 atlas, what files should I use? The answer to both 1) and 2) is use the PALS_B12 LR combo registration target dataset: http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6057499 And use the template deform_map included in that dataset to preset your registration parameters. See this page and Erin's cheat sheet (linked from the page below) for more details: http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html This is what we do. There are separate landmark datasets for the left and right, but they differ very little, and using the LR combo enables you to do cross-hem or inter-hem analyses. The way we look at it, there's very little down side to using the combo dataset, but a lot of up side to doing so. So we routinely use the LR combo now. We stopped using colin as a registration target a couple of years ago, but some documentation may still refer to it. Thanks, Mateus ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
[caret-users] border color file
Hi Donna, When I try to load the border files, after the surface alignement, I get the warning message: 'You have selected border files that require a border color file but no border color file is selected'. In Erin's document, it is said to: File : Open Data File : File Type = Border Color Files - Find ‘ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor’ - Yes – Copy to current directory But, I can't find this file anywhere. Do you know where it is saved? Is it 'Human.TEMPLATE-CUTS_STANDARD.03-05.bordercolor'? Thanks again for your help. Mateus
[caret-users] Spherical registration
Hi, I am a little bit confused on how to proceed to register an individual surface into an Atlas. The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' explains how to perform a spherical registration using the 'Human.colin.L.REGISTER-to-INDIVIDUAL.03-05.71785.spec' file. My questions are: 1) What spec file should I use to register into the right hemisphere? 2) If I choose to register into PALS-B12 atlas, what files should I use? Thanks, Mateus
[caret-users] SuMS
Hi, Since last week, I am trying to connect to SumsDB homepage (http://brainmap.wustl.edu/sums), but I always get a time out connection. Could you, please, confirm me if it is online? I need to download: * Colin ref-for-landmarks left: Human.colin.LEFT.REG-with-PALS-B12.71785.spec http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6387328 * Colin ref-for-landmarks right: Human.colin.RIGHT.REG-with-PALS-B12.71723.spec http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6387082 to help me drawing the registration borders. Thanks, Mateus
Re: [caret-users] nifti images
Hi John,
Thanks. Now, I understand. I thought that the reported dimensions and
voxel sizes refered to the volume (I,J,K) dimensions (voxel
coordinates), and not to the (X,Y,Z) dimensions (real world
coordinates). Please, correct me if I am still wrong?
I have another question: Does Caret take into account any rotation
specified in the nifti-1 header? Or is there any incompatibility with
transformations done by SPM5?
To better explain my question, let me describe the following test that I
did:
1) I rotated my 3D_original.nii image of 45degrees around the X-axis
(see 3D_original_rotated_spm5.pdf).
2) I saved this rotation in the image header, but I didn't reslice the
image.
3) When I loaded the rotated image with Caret, I couldn't see anything
in the P(YZ) and C(XZ) planes. However the H(XY) plane was displayed as
if the image was not rotated. When I used the 'x', 'y' and 'z' control
buttons to navigate through the image, the H(XY) slices were displayed
as if it was the non-rotated 3D_original.nii. The reported dimensions
and voxel sizes were 124x201x151 and 1.3x1.326x0.00, respectively.
Is it right?
Thanks,
Mateus
John Harwell wrote:
Mateus,
A volume has three-dimensions which are commonly indexed with I, J,
and K.
When Caret loads a volume it always stores the voxels such that the
voxels run left-to-right in the first dimension (I), posterior-to-
anterior in the second dimension (J), and inferior-to-superior
(K) in the third dimension. This is commonly referred to as an
LPI orientation and negative X points to the left side of the head,
negative Y points to the back of the head, and negative Z points down
into the neck. This is the same orientation used by the Talairach
atlas which places the origin at the anterior commissure.
Your volume has the voxels running anterior-to-posterior in the first
dimension (I), inferior-to-superior in the second dimension (J),
and left-to-right in the third dimension(K). This is an AIL
orientation.
Since Caret wants the volume in an LPI orientation and your volume is
in an AIL orientation, Caret will reorganize the voxels in memory so
that the volume is in an LPI orientation. It is this reorientation
operation that results in the voxel sizes and dimensions being permuted.
Output of 3DInfo for your volume and your volume saved by Caret with
an LPI orientation:
Dataset File:3D_original.nii
Identifier Code: NII_Oo8IAJJUzJFWVH2nBnBIQA Creation Date: Thu Nov
16 13:44:28 2006
Dataset Type:Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = MSB_FIRST]
Storage Mode:NIFTI file
Data Axes Orientation:
first (x) = Anterior-to-Posterior
second (y) = Inferior-to-Superior
third (z) = Left-to-Right [-orient AIL]
R-to-L extent: -80.652 [R] -to-79.248 [L] -step- 1.300 mm
[124 voxels]
A-to-P extent: -73.912 [A] -to- 113.588 [P] -step- 0.938 mm
[201 voxels]
I-to-S extent: -70.210 [I] -to-70.415 [S] -step- 0.938 mm
[151 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is float
-
Dataset File:3D_original_saved_with_caret.nii
Identifier Code: NII_Ffg_VXBk3o4b2q-dpSG84g Creation Date: Thu Nov
16 13:44:41 2006
Dataset Type:Anat Bucket (-abuc)
Byte Order: MSB_FIRST {assumed} [this CPU native = MSB_FIRST]
Storage Mode:NIFTI file
Data Axes Orientation:
first (x) = Left-to-Right
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient LPI]
R-to-L extent: -80.653 [R] -to-79.248 [L] -step- 1.300 mm
[124 voxels]
A-to-P extent: -73.912 [A] -to- 113.588 [P] -step- 0.938 mm
[201 voxels]
I-to-S extent: -70.210 [I] -to-70.415 [S] -step- 0.938 mm
[151 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is float
--
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.Box 8108
St. Louis, MO 63110 USA
On Nov 16, 2006, at 11:39 AM, Mateus Joffily wrote:
Hi John,
Although the image orientation is fine and the origin is correctly
localized at the AC, it still seems to have some problem with the
image dimension and voxel size.
The correct image dimension and voxel size are 201 x 151 x 124 and
-0.938 x 0.938 x 1.3 (X x Y x Z), respectively (see the
3D_original_spm5.pdf file that I uploaded). However, the values
reported by Caret are 124 x 201 x 151 and 1.3 x 0.938 x 0.938.
Thanks for your help,
Mateus
John Harwell wrote:
Mateus,
To download updated versions of Caret:
1) Go to the website http://brainmap.wustl.edu/pub/john/;. Use
the username pub and the password download to access the web
site.
2) Download the file caret5_exe_linux.zip or
caret5_exe_windows.zip which contain the linux and windows
Re: [caret-users] nifti images
Hi John, Although the image orientation is fine and the origin is correctly localized at the AC, it still seems to have some problem with the image dimension and voxel size. The correct image dimension and voxel size are 201 x 151 x 124 and -0.938 x 0.938 x 1.3 (X x Y x Z), respectively (see the 3D_original_spm5.pdf file that I uploaded). However, the values reported by Caret are 124 x 201 x 151 and 1.3 x 0.938 x 0.938. Thanks for your help, Mateus John Harwell wrote: Mateus, To download updated versions of Caret: 1) Go to the website http://brainmap.wustl.edu/pub/john/;. Use the username pub and the password download to access the web site. 2) Download the file caret5_exe_linux.zip or caret5_exe_windows.zip which contain the linux and windows versions of the caret5 executable. To install: 1) Go into your Caret installation's bin directory and backup (rename) your current caret5 executable. 2) Place the downloaded file in the Caret installation's bin directory and unzip the downloaded file which will produce either caret5 or caret5.exe. You might have to change the permissions on linux using the command chmod a+rx caret5. As for the negative x voxel size, this usually means the the origin is specified on the right side of the volume and that the voxels are ordered right-to-left. When Caret reads a volume and the volume contains valid orientation information, Caret flips the volume in memory to place the volume in an LPI (-x=left, -y=posterior, - z=inferior) orientation. Visit the website http:// www.grahamwideman.com/gw/brain/orientation/orientterms.htm for more information. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Nov 15, 2006, at 4:08 AM, Mateus Joffily wrote: Hi John, Thank you very much. The image looks good to me. I use Linux and Windows (preference for Linux). Just one more question: How does Caret deals with the negative 'x' voxel size set by SPM5? Does it affect the way Caret displays the image? In the 'Volume Attributes Editor' dialog - 'Resample' tab, the voxel size is always positive. thanks, Mateus John Harwell wrote: Hi Mateus, I think I have the problem corrected and here is how 3D_original.nii appears in Caret. If the images look good to you let me know which operating system you are using and I will make an update available for you to download. This problem only occurred if the X-axis was not left/right, the Y-axis was not posterior/anterior, or the Z-axis not inferior/superior. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Nov 13, 2006, at 3:33 AM, Mateus Joffily wrote: Hi John, I uploaded four files in Caret, their names are: 1) 3D_original.nii : original volume that doesn't display correctly in Caret (case 1 described in my previous message) 2) 3D_original_spm5.pdf : capture of 3D_original.nii display in spm5 1) 3D_resliced.nii : same original volume but resliced (case 2 described in my previous message) 1) 3D_resliced_spm5.pdf : capture of 3D_resliced.nii display in spm5 Thank you very much. Mateus John Harwell wrote: Hi Mateus, Can you upload the nifti volume that is not displayed correctly in Caret at http://pulvinar.wustl.edu/cgi-bin/upload.cgi;. Also, can you capture and upload an image of the volume displayed correctly in SPM5 so that I know how it should appear. After uploading the files, please email me the names of the files. It may be a few days before I can look into this problem. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Nov 10, 2006, at 9:42 AM, Mateus Joffily wrote: Hi, I am having some trouble to load nifti images with caret5. The problem is the following: 1) When I try to load an image that has a rotation specified in the header, Caret seems not to apply it properly. The displayed image shows a strange orientation and the voxels size is wrong. 2) However, when the same image is resliced and no rotation is specified in its header, Caret displays the image correctly, the voxels size are correct and the image origin is also correctly located. Those same images, (1) and (2), are both correctly displayed with SPM5. The images extension is .nii, so I don't think this should be a problem related to image format interpretation (like interpreting nifti images as analyze and ignoring part of the header
Re: [caret-users] nifti images
Hi John, Thank you very much. The image looks good to me. I use Linux and Windows (preference for Linux). Just one more question: How does Caret deals with the negative 'x' voxel size set by SPM5? Does it affect the way Caret displays the image? In the 'Volume Attributes Editor' dialog - 'Resample' tab, the voxel size is always positive. thanks, Mateus John Harwell wrote: Hi Mateus, I think I have the problem corrected and here is how 3D_original.nii appears in Caret. If the images look good to you let me know which operating system you are using and I will make an update available for you to download. This problem only occurred if the X-axis was not left/right, the Y-axis was not posterior/anterior, or the Z-axis not inferior/superior. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Nov 13, 2006, at 3:33 AM, Mateus Joffily wrote: Hi John, I uploaded four files in Caret, their names are: 1) 3D_original.nii : original volume that doesn't display correctly in Caret (case 1 described in my previous message) 2) 3D_original_spm5.pdf : capture of 3D_original.nii display in spm5 1) 3D_resliced.nii : same original volume but resliced (case 2 described in my previous message) 1) 3D_resliced_spm5.pdf : capture of 3D_resliced.nii display in spm5 Thank you very much. Mateus John Harwell wrote: Hi Mateus, Can you upload the nifti volume that is not displayed correctly in Caret at http://pulvinar.wustl.edu/cgi-bin/upload.cgi;. Also, can you capture and upload an image of the volume displayed correctly in SPM5 so that I know how it should appear. After uploading the files, please email me the names of the files. It may be a few days before I can look into this problem. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Nov 10, 2006, at 9:42 AM, Mateus Joffily wrote: Hi, I am having some trouble to load nifti images with caret5. The problem is the following: 1) When I try to load an image that has a rotation specified in the header, Caret seems not to apply it properly. The displayed image shows a strange orientation and the voxels size is wrong. 2) However, when the same image is resliced and no rotation is specified in its header, Caret displays the image correctly, the voxels size are correct and the image origin is also correctly located. Those same images, (1) and (2), are both correctly displayed with SPM5. The images extension is .nii, so I don't think this should be a problem related to image format interpretation (like interpreting nifti images as analyze and ignoring part of the header information). Does anyone else has experienced this problem? Thanks for your help. Mateus ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] nifti images
Hi Donna, Thanks for your help. I am sending you two histograms of 3D_resliced.nii: (1) histogram_resliced_1.jpg is the same histogram you already sent to me; (2) histogram_resliced_2.jpg is the histogram of 3D_resliced.nii after resampling at 1x1x1mm with Caret. We can see that the spikes disapear in (2). It looks like much closer to the histograms described in your 'Peak Tweaking' document. As I don't have much experience with image segmentation, I was wondering if there was any problem with my images. I am glad to know that they look fine for you. May be the problem is the one pointed by Simon. If this is the case, adjusting the histogram bins could minimize the effect. Do we have control over the histogram bins with Caret interface? Thanks, Mateus Dierker wrote: Hi Mateus, I can't address your original problem with the NIfTI orientation/rotation, but I did have a look at your volumes, and this statement confuses me: The histogram of my images (3D_original.nii and 3D_resliced.nii) shows several noisy sharp peaks. The attached captures show the histograms of 3D_original.nii (histogram_orig.jpg) and 3D_resliced.nii (histogram_resliced.jpg). The original has smoother looking peaks, but both have discernible gray and white matter peaks. Neither look particularly bothersome. Could you be more clear about what concerns you? On 11/13/2006 05:43 AM, Mateus Joffily wrote: John, May I profit from the fact that I have already uploaded my images to ask you one more question about them? The histogram of my images (3D_original.nii and 3D_resliced.nii) shows several noisy sharp peaks. Do you know what do they mean? I know that, if I reslice the 3D_resliced.nii to 1x1x1mm voxels size with Caret, they disappear. Thanks. Mateus John Harwell wrote: Hi Mateus, Can you upload the nifti volume that is not displayed correctly in Caret at http://pulvinar.wustl.edu/cgi-bin/upload.cgi;. Also, can you capture and upload an image of the volume displayed correctly in SPM5 so that I know how it should appear. After uploading the files, please email me the names of the files. It may be a few days before I can look into this problem. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Nov 10, 2006, at 9:42 AM, Mateus Joffily wrote: Hi, I am having some trouble to load nifti images with caret5. The problem is the following: 1) When I try to load an image that has a rotation specified in the header, Caret seems not to apply it properly. The displayed image shows a strange orientation and the voxels size is wrong. 2) However, when the same image is resliced and no rotation is specified in its header, Caret displays the image correctly, the voxels size are correct and the image origin is also correctly located. Those same images, (1) and (2), are both correctly displayed with SPM5. The images extension is .nii, so I don't think this should be a problem related to image format interpretation (like interpreting nifti images as analyze and ignoring part of the header information). Does anyone else has experienced this problem? Thanks for your help. Mateus ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users inline: histogram_resliced_1.jpginline: histogram_resliced_2.jpg
