[caret-users] simple user's guide for caret
Hy, I just downloaded caret this week..versions 5.51 I guess I'm looking for a SIMPLE user's guide to make the first approaches to caret... wich one is the one to start with? I started reading The basic's one but since it is a list of command is not useful if I cannot understand what is a spec file ecc ecc... thank you Sofia Crespi
Re: [caret-users] simple user's guide for caret
Thank you very much John.. I will have a look at that! Best Sofia - Original Message - From: John Harwell [EMAIL PROTECTED] To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Sent: Wednesday, January 16, 2008 3:50 PM Subject: Re: [caret-users] simple user's guide for caret Sofia, Go to http://brainmap.wustl.edu/resources/caretnew.html#Tutorials55; and try the Caret 5.504 Quick Start Tutorial. We have used it in workshops for a short (one hour or so) introduction to Caret. --- 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 16, 2008, at 8:32 AM, Sofia Crespi wrote: Hy, I just downloaded caret this week..versions 5.51 I guess I'm looking for a SIMPLE user's guide to make the first approaches to caret... wich one is the one to start with? I started reading The basic's one but since it is a list of command is not useful if I cannot understand what is a spec file ecc ecc... thank you Sofia Crespi ___ 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] data set
Hi, I just want to download the data set for the segmentation-flattening and registration tutorial. unfortunately the link below is not active why? http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6588227 thanks in advance Sofia Crespi
[caret-users] caret debug
HI, I've installed caret version 5.51 on windows XP. I've set the path Environment variable to start caret from the command window as suggested. Any time I start caret the warning set the envirnment variable CARET_DEBUG for debigging information appear. Does anyone has experienced the same problem? How can I fix it? thanks in advance Sofia
[caret-users] viewing fMRI data
Hello I'm trying to visualize my fMRI data on the flat map that I've already generated. 1) I opened my spec file ( the one relative to 1 hemispher only) loadding both the fiducial and the flat surface. 2) from File - Open Data File I've selected my .ifh file (generated with FIDL) containing my functional volume (data of both hemispheres together..is this a problem?) 3) I selected the page Overlay/underlay -Volume from the Display Control Window and I've set the Primary Overlay to Functional View. 4) I selected the page Metric from the Display Control Window and pressed the Setting tab to set the Display mode ecc ecc. Unfortunately I cannot see the activation plotted on the flat map but only when I selected the volume ffrom the Model of the main window... have a look at the attached JPEG, please. Does anyone has experienced the same problem? can you help me? Thanks in advance Sofia attachment: main window1.JPGattachment: main window2.JPGattachment: main window3.JPG
[caret-users] how to select a Region of interest on flat surface
hello.. i wanto to select a Region of Interest (RoI) on the falt surface previously genereated. I usually use the option: Layers- Border-Draw border I assign the name (plus the numeber of talairach coordinates) - type: closed boundary -2D -I select the option Assign voxels within closed border -thickness: +/-1. I design my RoI finally I save my file as: 1. border file-Surface 2. Border color file sometimes when I load my spec file later + the borders file I can see the selected borders without problems other times I see the saved files ma I cannot display my borders even if I've correctly selected tha border file... can you explain me why? where is my error??? thanks in advance Sofia Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Finanziamento agli enti della ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org
Re: [caret-users] how to select a Region of interest on flat surface
thank you Donna.. I'll try! sofia - Original Message - From: Donna Dierker [EMAIL PROTECTED] To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Sent: Thursday, April 24, 2008 3:07 PM Subject: Re: [caret-users] how to select a Region of interest on flat surface Hi Sofia, I confess this *Assign voxels within closed border feature is news to me. If you save both the border and border color files, and then open these files later with the flat surface loaded in the main window, then you should see the borders. But if any other surface is loaded in the main window, you won't see them. (Make sure D/C: Border menu has Show Borders toggled on; the default behavior depends on the caret version.) In order to see the borders on other surface configurations (fiducial, inflated, etc.), you need to either select auto-project when you draw the border (unavailable on older versions), or do Layers: Borders: Project borders. Then, save the resulting borderproj file. Border and borderproj files differ like so: * Borderproj attaches the border points to tiles, when facilitates viewing across configurations. * Border files are points in space/grid relative to some reference surface. This can be handy if you need to display multiple borders generated from different meshes (subjects or distinct timepoints). Also, my guess is that when you use this feature, your output is a volume paint file (voxels), and that you probably need to save File: Volume Paint file in order to save the voxel assignments. Donna * On 04/24/2008 06:10 AM, Sofia Crespi wrote: hello.. i wanto to select a Region of Interest (RoI) on the falt surface previously genereated. I usually use the option: Layers- Border-Draw border I assign the name (plus the numeber of talairach coordinates) - type: *closed boundary -2D* *-*I select the option *Assign voxels within closed border* -thickness: +/-1. I design my RoI finally I save my file as: *1. border file-Surface* *2. Border color file * ** *sometimes when I load my spec file later + the borders file I can see the selected borders without problems* *other times I see the saved files ma I cannot display my borders even if I've correctly selected tha border file...* *can you explain me why?* *where is my error???* ** thanks in advance Sofia ** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Finanziamento agli enti della ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Finanziamento agli enti della ricerca sanitaria) il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito www.5xmille.org
Re: [caret-users] problem with border file
Dear Donna unfortunately the borders checkbox is selected on the D/C: Overlay/Underlay - Surface menu . When I select the Border Page on the D/C I can see tha name of the new borders in the color section but not in the name section.. I guess this is the problem. the next time I'll try to design the border and save the resulting borderproj files but what you mean with we project borders after drawing them ? thank you Sofia - Original Message - From: Donna Dierker [EMAIL PROTECTED] To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Sent: Tuesday, June 10, 2008 2:55 PM Subject: Re: [caret-users] problem with border file Hi Sofia, See inline replies below. Donna On 06/10/2008 06:18 AM, Sofia Crespi wrote: Hi I have a question. I've designed some closed border on my flat surface in order to use them for surface region of interest operation. More precisely I've daone these operations: 1.LayersBordersdraw Borders 2. I've selected a new name, closed boundaries and 2D, in the closed border assignement frame- Voxels I've selected Assign voxels within closed borders and +/-1 for the thickness. 3. I've choosed a color and designed my border on the flat map. 4.Then I saved the file with a new name as: border file Surface, border file Volume, Border color file. Now I'm able to see the border and if I select the Border Page in the Dispaly control dialog I can find the name and the color of my new border. Now I close caret. If I open caret again and load my spec file, loading also the new border file already created I cannot display the new border on the flat map... why? If both the border file Surface and border color files that you saved in step 4 above were selected when you loaded the spec file, then the only other reason I can imagine that you don't see the border on your flat map is that borders are not selected on the D/C: Overlay/Underlay - Surface menu (scroll all the way to the bottom, until you see a borders checkbox); see attached capture, which shows the Borders checkbox toggled on at the bottom of the D/C: Overlay/Underlay - Surface page. Depending on which Caret version you have, this checkbox may or may not be on by default when you load a spec with borders selected. I opened the border file Surface just created all the other border file come out as *appended* (why since are different file) the last one is not appended and I cannot see that border This is not clear to me. Perhaps if you uploaded your dataset, I could decipher what you mean. http://pulvinar.wustl.edu/cgi-bin/upload.cgi It sounds like one or more of the following possibilities might contribute to the confusion: 1. You have multiple border files loaded, which may have borders that intersect/duplicate with one another. 2. When you couldn't see the border upon opening, you tried loading again, resulting in the same borders being loaded twice. I hope this is just a case of the borders not being turned on when you relaunch Caret. Please have a look to the doc fiel attached: No doc file was attached. in yellow I've underlined all the attached file...: *1* *why the same file V6 border color is appended more than 1 time?* Something similar to possibilities 1 and 2 occurred wth the bordercolor file. *2. the appended file LO-MST-MT is refereed to 3 border That I'm not able to disply any more..* I don't understand this question, but I hope the display problem is resolved by the D/C checkbox. *3 the new border V6NEW does not result as appended ??* Perhaps it was added after the last save? I can't think of another plausible explanation. where is my error? Let's hope the D/C checkbox resolves 90% of your issues. can you help me? Typically, we project borders after drawing them and save the resulting borderproj files. This allows you to view the borders on multiple surfaces (e.g., fiducial, inflated). There are definitely contexts in which border files have distinct advantages, however (e.g., when viewing on surfaces of different mesh / number of nodes than the drawing substrate; when using the 2D/3D coordinates for an outside application). But you clearly state above you are trying to view your borders on the flat map, which is the same surface used for the drawing substrate. Thus, I conclude that this is probably a D/C checkbox not selected issue. Thank you in advance Sofia Crespi ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi (Finanziamento agli enti della ricerca sanitaria) il codice fiscale della Fondazione
Re: [caret-users] problem with border file
Hi Donna I've just uploaded the directory with my data. The name of the zipped directory is SofiaCrespi_BorderProblem_forDonna.zip I'll wait fur further suggestions tomorrow thank you Sofia - Original Message - From: Donna Dierker [EMAIL PROTECTED] To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Sent: Wednesday, June 11, 2008 3:06 PM Subject: Re: [caret-users] problem with border file Hi Sofia, See inline replies below. Donna On 06/11/2008 06:45 AM, Sofia Crespi wrote: Dear Donna unfortunately the borders checkbox is selected on the D/C: Overlay/Underlay - Surface menu . So much for the quick fix When I select the Border Page on the D/C I can see tha name of the new borders in the color section but not in the name section.. I guess this is the problem. This is informative: It suggests that the border colors are fine (unless the color is transparent, which I doubt), but that the border didn't load or was empty. If you saved your border, relative to the FLAT map (i.e., with the FLAT map in the main window or the FLAT map selected in the Save Data File: Border surface file dialog), then this should not happen with you relaunch Caret and select this border file. Can you upload your data directory (if less than a Gigabyte zipped) here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi I want to look at the border file in particular, but other files might also offer clues. the next time I'll try to design the border and save the resulting borderproj files but what you mean with we project borders after drawing them ? More recent Caret versions have the radio button Auto Project (no by default); we usually change this to Yes, because then then the border will automatically project as soon as you draw it. If Auto Project is set to No, you can manually project by selecting Layers: Borders: Project Borders (or Project Fiducial Borders on older versions). The projection process takes each border point and attaches it to the closest surface tile. This is why you can view projected borders on multiple surface configurations (fiducial, flat, inflated). When you save a borderproj file, you're saving the border as attached to the nearest tile; when you save as border, there is no surface allegiance; the points are floating in 2D or 3D space -- perhaps close to the surface, perhaps not (kind of like foci in that respect). I don't think your trouble with the border saving/reloading is due to your not projecting; the cause remains elusive. thank you Sofia - Original Message - From: Donna Dierker [EMAIL PROTECTED] To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Sent: Tuesday, June 10, 2008 2:55 PM Subject: Re: [caret-users] problem with border file Hi Sofia, See inline replies below. Donna On 06/10/2008 06:18 AM, Sofia Crespi wrote: Hi I have a question. I've designed some closed border on my flat surface in order to use them for surface region of interest operation. More precisely I've daone these operations: 1.LayersBordersdraw Borders 2. I've selected a new name, closed boundaries and 2D, in the closed border assignement frame- Voxels I've selected Assign voxels within closed borders and +/-1 for the thickness. 3. I've choosed a color and designed my border on the flat map. 4.Then I saved the file with a new name as: border file Surface, border file Volume, Border color file. Now I'm able to see the border and if I select the Border Page in the Dispaly control dialog I can find the name and the color of my new border. Now I close caret. If I open caret again and load my spec file, loading also the new border file already created I cannot display the new border on the flat map... why? If both the border file Surface and border color files that you saved in step 4 above were selected when you loaded the spec file, then the only other reason I can imagine that you don't see the border on your flat map is that borders are not selected on the D/C: Overlay/Underlay - Surface menu (scroll all the way to the bottom, until you see a borders checkbox); see attached capture, which shows the Borders checkbox toggled on at the bottom of the D/C: Overlay/Underlay - Surface page. Depending on which Caret version you have, this checkbox may or may not be on by default when you load a spec with borders selected. I opened the border file Surface just created all the other border file come out as *appended* (why since are different file) the last one is not appended and I cannot see that border This is not clear to me. Perhaps if you uploaded your dataset, I could decipher what you mean. http://pulvinar.wustl.edu/cgi-bin/upload.cgi It sounds like one or more of the following possibilities might contribute to the confusion: 1. You have multiple border files loaded, which may have borders that intersect/duplicate with one another. 2. When you couldn't see the border upon opening
Re: [caret-users] problem with border file
Dear Donna Thank you very very much.. I've understand and fixed all the problems! Sofia - Original Message - From: Donna Dierker [EMAIL PROTECTED] To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Sent: Wednesday, June 11, 2008 5:46 PM Subject: Re: [caret-users] problem with border file Hi Sofia, I looked at your dataset, and all these flat border files show borders on my end: Human.intsac4.LR.border_file_33.2008-04-22_V1-V2-V3-V3a.border Human.intsac4.LR.border_file_33.2008-04-22_V6NEW.border Human.intsac4.L.border_file_102.2008-02-21_LO-MT-MST.border Human.intsac4.L.border_file_102.2008-02-21_LIP.border Human.intsac4.L.border_file_102.2008-02-21_VIP.border Human.intsac4.L.border_file_102.2008-02-21_V6.border Human.intsac4.L.border_file_102.2008-02-21_VHMer.border But this one does not: Human.intsac4.L.border_file_102.2008-02-21_V6NEW.border If you cat that file, it confirms there are no border points: BeginHeader caret-version 5.51 comment V6 left: -17,-83,35 V6 center: -5,-76,32V6 right: fuoco alto -3,-8,23, fuoco basso -4,-85,30selezionate su RGB, EmicampoIpsi-Contro, EmicampoUp-Down , Eyepos F2S0 ipsilaterale configuration_id VOLUME date mar 10. giu 12:42:40 2008 encoding ASCII pubmed_id EndHeader 0 The configuration_id VOLUME suggests you saved this as a VOLUME border file -- after first saving as a FLAT border file using the same filename. (The fact that the same filename is listed in the spec file under both FLAT and VOLUME border files is the clue.) Per John Harwell, this won't work: If you draw on the FLAT map, you have to first project the borders (in effect to convert flat 2D to 3D coordinates). Even then I'm not sure saving as a VOLUME border file would work, but it's worth a try. Either way, use distinct filenames for FLAT and VOLUME borders, since those coordinates won't match. Also, if you were not already aware of it, the Surface: ROI menu allows you to threshold anatomical (shape) and/or functional (metric) maps and have Cared automatically draw a border around the resulting cluster. Perhaps not useful now, but in the future Donna On 06/11/2008 10:11 AM, Sofia Crespi wrote: Hi Donna I've just uploaded the directory with my data. The name of the zipped directory is SofiaCrespi_BorderProblem_forDonna.zip I'll wait fur further suggestions tomorrow thank you Sofia - Original Message - From: Donna Dierker [EMAIL PROTECTED] To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Sent: Wednesday, June 11, 2008 3:06 PM Subject: Re: [caret-users] problem with border file Hi Sofia, See inline replies below. Donna On 06/11/2008 06:45 AM, Sofia Crespi wrote: Dear Donna unfortunately the borders checkbox is selected on the D/C: Overlay/Underlay - Surface menu . So much for the quick fix When I select the Border Page on the D/C I can see tha name of the new borders in the color section but not in the name section.. I guess this is the problem. This is informative: It suggests that the border colors are fine (unless the color is transparent, which I doubt), but that the border didn't load or was empty. If you saved your border, relative to the FLAT map (i.e., with the FLAT map in the main window or the FLAT map selected in the Save Data File: Border surface file dialog), then this should not happen with you relaunch Caret and select this border file. Can you upload your data directory (if less than a Gigabyte zipped) here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi I want to look at the border file in particular, but other files might also offer clues. the next time I'll try to design the border and save the resulting borderproj files but what you mean with we project borders after drawing them ? More recent Caret versions have the radio button Auto Project (no by default); we usually change this to Yes, because then then the border will automatically project as soon as you draw it. If Auto Project is set to No, you can manually project by selecting Layers: Borders: Project Borders (or Project Fiducial Borders on older versions). The projection process takes each border point and attaches it to the closest surface tile. This is why you can view projected borders on multiple surface configurations (fiducial, flat, inflated). When you save a borderproj file, you're saving the border as attached to the nearest tile; when you save as border, there is no surface allegiance; the points are floating in 2D or 3D space -- perhaps close to the surface, perhaps not (kind of like foci in that respect). I don't think your trouble with the border saving/reloading is due to your not projecting; the cause remains elusive. thank you Sofia - Original Message - From: Donna Dierker [EMAIL PROTECTED] To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Sent: Tuesday, June 10, 2008 2:55 PM Subject: Re: [caret-users] problem with border
Re: [caret-users] white matter point on flattened surface
thank you Donna I would think too! Sofia - Original Message - From: Donna Dierker do...@brainvis.wustl.edu To: Caret, SureFit, and SuMS software users caret-users@brainvis.wustl.edu Sent: Thursday, May 14, 2009 3:27 PM Subject: Re: [caret-users] white matter point on flattened surface Hi Sofia, Let's say you have an activation map (fMRI) in volumetric form for your subject, for whom you also have a fiducial surface. Provided that the fMRI has been volume-registered to the same anatomical used to generate the fiducial surface. When you map that fMRI volume onto the surface, you always map to the fiducial surface. (Note that the fiducial surface might be a white matter, pial, or midthickness representation. If the surface was generated using Caret, it's a midthickness surface. If it was generated using, say, Freesurfer, then a midthickness surface is easily generated by averaging the WM and pial surfaces.) Once the fMRI is mapped onto the fiducial surface, then you have a node-scalar mapping that can be rendered/overlaid on any surface configuration (flat, inflated, etc.). But one never maps to the inflated/flat surfaces directly. It's worth mentioning that the Caret surface, being a midthickness surface, won't necessarily intersect your white matter voxel. It depends on the fMRI resolution and how the fiducial surface intersects the fMRI volume there. There are various mapping algorithms that help you get around this problem (gaussian being the most helpful, probably). But if you have an actual white matter surface available, it is possible to map to that, as well. If the voxel is deep in the white matter, it will still not intersect the WM surface, but then it is of questionable validity, I would think. Hope this helps, Donna On 05/14/2009 04:45 AM, s.cres...@campus.unimib.it wrote: dear Donna I have a we question concerning the overlapping metrical data on the flat map. If I have some voxel belonging to the white matter how does caret manage them with respect to the flat? thank you! sofia ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users - La tua mano puo' lasciare un segno importante. Dona il tuo 5 per mille al San Raffaele di Milano. E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi Finanziamento della ricerca sanitaria il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Per saperne di piu': 5permi...@hsr.it o vai sul sito http://www.5xmille.org. ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
