[Freesurfer] New UserContributions page on the wiki
Noticing that many FreeSurfer users have developed their own scripts for automating various tasks, somebody had the idea of adding a user contributions section to our documentation. I've added this page to the Wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions Please use it to add your scripts and check out what other people are doing. If you have anything else you'd like to add, such as tips or techniques, that might be useful to others, please feel free to do so. To edit a Wiki page, you'll need to create an account; instructions on how to do this can be found on the front page, or here: http://surfer.nmr.mgh.harvard.edu/fswiki/GettingAccess -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] multiple surface overlays
Yes, you can do it with scripting. Start by checking out this page: http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide_2fTkSurferScripting_2fTkSurferIntroToScripting In your case, if your overlay files are volumes, you should use the function sclv_read_from_volume instead of sclv_read_from_dotw. Reference for scripting commands is here: http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide_2fTkSurferScripting_2fTkSurferScriptingReference On Fri, 2007-10-05 at 13:52 -0400, Cameron Ellis wrote: Hi all, Sourcing stable3, using tksurfer, does anyone know how to load more than one overlay at a time from the command line? (something like: tksurfer subject hemi surface -overlay1 ??? -overlay2 ??? overlay3 ???) Does this require scripting w/ tksurfer? Cameron -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: Error: Cannot allocate memory
There is a bug in today's stable4 build that affects reading mgh/mgz volumes. I've checked in a fix. It should be fine by tomorrow. On Thu, 2007-10-04 at 16:27 -0400, Help Desk -- Paul Raines wrote: Okay, so it is not just CentOS5. But the timestamp on the build is TODAY. So I guess we wait for someone from the freesurfer development team to say something about what changed. On Thu, 4 Oct 2007, Pratap Kunwar wrote: Yes, here is the info below - FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20071004 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18_recon/ PWD: /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18VvI - Pratap Kunwar [EMAIL PROTECTED] What computer are you getting the error on, is it running CentOS5 ? Pratap Kunwar wrote: I am also getting the same error as below. Hi Chris, Can you forward me to the person I could ask about this issue? I've been running jobs the same way using freesurfer for months and today I keep gettting this error message: Cannot allocate memory i.e. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29819/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29819/nu0.mnc TAGskip: failed to calloc 808464384 bytes! $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from orig.mgz... Cannot allocate memory ERROR: converting to minc Linux madrc 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:39:17 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Oct 4 13:35:24 EDT 2007 i.e. reading '/usr/local/freesurfer/stable4/average/RB_all_2007-08-08.gca'... average std = 6.7 using min determinant for regularization = 4.5 0 singular and 1985 ill-conditioned covariance matrices regularized reading 'nu.mgz'... TAGskip: failed to calloc 842542592 bytes! Cannot allocate memory Linux madrc 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:39:17 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Oct 4 13:40:14 EDT 2007 Is there something I can do to fix this problem? Thanks! ~Amy -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error: no gl window open
Does it work with other subjects? Was this working before, and did it just suddenly stop working? Have you done anything recently to the software coinciding with it not working, like upgrading to version 4, or is this a new install of version 4? Does tkmedit work? Have you tried updating your graphics drivers? On Sat, 2007-09-15 at 04:29 -0400, Xiangchuan Chen wrote: Hi all, I have got the following error message when running tksurfer to load inflated surface: surfer: ### redraw failed: no gl window open The result is that no surface appears. Any suggestions for solving this issue? My system: HP NC8430 laptop (ATI X1600 video card) Fedora 6 (X86_64) Freesurfer V4.0 Thanks in advance, Xiangchuan Chen -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] using tkmedit
Use the menu command View-Configure-Functional Overlay... to open the Configure Functional Overlay dialog box. At the top of this are two spinboxes to control the time point and condition (if available) for your functional data. Don't forget to click the Apply button at the button of the dialog after changing the time point. On Fri, 2007-09-14 at 14:25 -0400, Robert Levy wrote: Hi, I am attempting to work with volume data for the first time and trying to figure out how to control what temporal offset is shown in the functional overlay. I checked the options, the wiki, etc, but didn't find anything yet. That is most like because I'm looking at old data that was generated in a way that is incompatible (it seems) with newer versions, so I am sourcing stable2. The command that originally generated the group comparison I am viewing is intergroupavg-sess -analysis EMerror -contrast ASevASc -group1 BwGroupNormalsError5 -group2 BwGroupAspError5 -intergroup BwGroupError5 -space tal -spacedir tal This is the path to the resulting group comparison /space/balagula/8/users/EMexec/fMRI/GROUP_ANALYSIS/BwGroupError5/bold/EMerror/tal-rfx/ASevASc/ To view it I am running: tkmedit-sess -analysis EMerror -contrast ASevASc -space tal -map minsig -s BwGroupError5 -isxavg random -fthresh 1.3 My environment looks like: FREESURFER_HOME /usr/local/freesurfer/stable2 FSFAST_HOME /usr/local/freesurfer/stable2/fsfast SUBJECTS_DIR/space/ventzl/1/users/SUBJECTS_DIR FUNCTIONALS_DIR /usr/local/freesurfer/stable2/sessions MINC_BIN_DIR/usr/pubsw/packages/mni/current/bin MINC_LIB_DIR/usr/pubsw/packages/mni/current/lib PERL5LIB/usr/pubsw/packages/mni/current/lib/perl5/5.8.5 GSL_DIR /usr/pubsw/packages/gsl/current QTDIR /usr/pubsw/packages/qt/current TCLLIBPATH /usr/local/freesurfer/stable2/lib/tcltktixblt/lib FSL_DIR /usr/pubsw/packages/fsl/current Thanks for any advice, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] xform avesurf- subject
In tksurfer, use Tools-Send to Subject. In this dialog box, enter the subject name, then hit Apply. Load up another tksurfer with the individual subject, and then use Goto Saved Point to go to that point. On Wed, 2007-08-29 at 18:27 -0400, Kirk, Gregory wrote: Hi All, I want to click on a point on my average surface for my group and ' save point' load a T1 or orig subject in the group with tkmedit and 'goto saved point' i.e. map by the inverse of the transform that embeded the subject surface into the average surface and see the point on the structural that mapped to it. Seems I remember this can be done, I have to load a transform I think. looked through the docs and mail archive but perhaps I was not thinking of the best key to search the archive. thankx -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] editing labels
Hi Sarah, When you save the label, is there any output on the shell? Can you load and edit a single label, save it out, exit tksurfer, restart it, and load the label in again, with the changes you made present in the label? On Mon, 2007-08-06 at 14:09 -0400, Sarah J Greene wrote: Hi all, I just wanted to ask about editing labels in tksurfer. I have converted my annot files to labels using mri_annotation2label, and now have all of the labels in the label directory. However when I edit the labels, and then save them using save selected label (highlighting the label and choosing the correct label in the correct hemisphere), nothing is saved when I pull up the image again. I have tried to convert the labels to annot files using mris_label2annot, but this isn't working either. I'm not sure what I am doing incorrectly. Thanks, sarah -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem to save images
The RGB format is an old Irix format, I think. The UNIX/Linux program 'convert' should be able to convert it to a jpeg for you. On Wed, Jun 27, 2007 at 12:34:44PM -0400, Wang, Xin wrote: Hello, group I have problems to save the display in TKsurfer. I tried 'Save RGB as', but I could not open the file with photoshop in windows, and it was total black when I opened it with adobe illustrator in windows or GIMP in Linux. Please tell me how to save the images so that I can open them with photoshop. Thank you in advance, XIn -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] linear opaque threshold
This is one of those ugly, not officially supported things: set gaHistogramData(threshMode) linear-opaque set gaLinedVars(fopaqueflag) 1 SendLinkedVarGroup overlay On Tue, Jun 26, 2007 at 11:27:39AM -0400, Robert Levy wrote: Hello, Does anyone know if it is possible to set the overlay threshold to linear opaque mode in tksurfer using TCL commands? I looked at the documentation, and I didn't see a method explicitly for that purpose, but maybe there is some way to specify that option. Thanks, Rob -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] long delay before tksurfer launches
strace shows you the system calls being made by the program. When it's hanging for a long time, note the last few lines of output from strace and let us know what those are. The last one will be the call that is taking so long to finish. On Mon, Jun 25, 2007 at 11:56:00AM -0400, Robert Levy wrote: Hello, Apologies for cross-posting (this list and martinos-tech), but I think that by posting here I might be able to reach a few more people who may have had the problem before and solved it. I have been experiencing very long load-up times, when running tksurfer. It can take up to 6 or 7 minutes to load. As far as I can tell, the application does not have any unusual or slow behaviors once it finally launches. The problem was not present until Friday, but has persisted since, and I run it the same now as I did before. Paul Raines mentioned on martinos-tech that there used to be a problem where the SUBJECTS_DIR was searched recursively and it would slow down the loading times for a comparable length of time. Can anyone confirm that this is still what tksurfer does? When I run it, I source the latest development version. If the problem is not the long search and file checks, then what could be the source of the delay? The command is: tksurfer average7 lh inflated The output is normal and I'm running it from /space/ventzl/1/users/SUBJECTS_DIR/ This is the tksurfer /usr/local/freesurfer/dev/bin/tksurfer The initial output is: surfer: current subjects dir: /space/ventzl/1/users/SUBJECTS_DIR surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/space/ventzl_001/users/SUBJECTS_DIR Then it hangs for 6 minutes or longer, and launches the tk gui. When I strace it, there is trace information to show initially, and then there is the text output I mentioned above, but during the waiting period there is no output from strace at all. Thanks in advance, Rob -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to import private color scales
Sorry, there's no way to do that for overlay data. On Mon, 2007-06-04 at 13:23 -0400, Istvan Akos Morocz wrote: dear freesurfers, how do i import my own 'private' colorscales, i.e., colormaps for the overlay data ? something richer in colors than 'heat' ? what's the format and size for such a file? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Changing the color in Edit Segmentation tool
Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT? On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote: I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the Main Toolbar, by choosing *Tools-Edit Segmentation*, or by pressing the 'g' key. By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools-Configure Segmentation Brush* However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas? Jared -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Changing the color in Edit Segmentation tool
Sorry, I was thinking you were talking about Scuba. Do you see the segmentation properly, in colors? If not, there was probably an error in loading the segmentation; do you see any errors in the shell window? If you do see the segmentation volume displayed properly as a translucent color overlay on the anatomical, are you sure you are using the Edit Segmentation tool? It's a paintbrush over a volume divided into quarters. Does clicking and dragging with the tool actually change the segmentation volume, that is, can you mouse over the edited voxels and verify that the values in the Sgmtn label line in the tools window matches the value you selected in the Segmentation Brush Info dialog? On Thu, May 17, 2007 at 02:56:57PM -0400, Jared Conley wrote: Yes, I believe so. The layer's color map is set to FreeSurferColorLUT.txt when loading the segmentation. The Segmentation Brush source is set at Segmentation (under Configure Segmentation Brush)--I imagine that's what you are referring to when you say target layer. Kevin Teich wrote: Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT? On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote: I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the Main Toolbar, by choosing *Tools-Edit Segmentation*, or by pressing the 'g' key. By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools-Configure Segmentation Brush* However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] quick scatterplot label question
This is the MeasurementName in the .fsgdf file. On Sun, 2007-05-13 at 23:03 +0100, Morgan Hough wrote: Once I have defined a label in tksurfer and I select *Tools - *Group* - Graph Marked Vertices Avg to open a scatterplot window, how do I change the y axis label from the default external label. I assume that I need to set this beforehand in the fsgd file but I wasn't sure how. Thanks in advance. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] can't load sig.mgh in dev tksurfer
This suggests that the number of values in the .mgh file is different than the number of vertices in the surface. Did you regenerate the surface after generating the .mgh file? On Sun, 2007-05-13 at 15:29 -0400, Catherine Hartley wrote: Hi, I'm having a problem with the development version of tksurfer. When I try to load a sig.mgh file as an overlay, I get the following error: % surfer: couldn't load /Applications/freesurfer/subjects/reruns/ glmleft/ReappCSplusContrast/sig.mgh sclv_read_from_volume: error in FunD_New Thanks, Cate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer - list overlay values inside a label
If you have an overlay loaded, and you save a label, the label file that is created will have the current overlay values in the last column. Does this do what you want? On Wed, 2007-04-18 at 17:01 -0400, [EMAIL PROTECTED] wrote: Hi Doug Kevin, I am trying to save a text list from tksurfer that contains all the overlay values (one value per each vertex point) inside in a functionally defined label. The labels were originally defined from a different data set than the overlays where I need the values. The overlay where I want the values picked from is in the format of a series of spherical surface files (ico7): *_time005-tau-lh_000.bfloat *_time005-tau-lh_001.bfloat *_time005-tau-lh_002.bfloat *_time005-tau-lh_003.bfloat *_time005-tau-lh_004.bfloat *_time005-tau-lh_005.bfloat *_time005-tau-lh_006.bfloat Notice that our overlay does not have the usual h-lh.bhdr files that would collect all the time frames and contrast conditions (this is after some custom post-processing) so we have to access the *000.bfloat - *006.bfloat files directly. Not sure that matters though. Any suggestions how to come about this? I tried to look at the tcl scripting reference but did not quite see what I needed there (or then I just did not understand what I read :). Thanks!!! -Tommi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] label ID in tksurfer
I was wondering if there is any way to have it automatically identify the labels in the image, say by printing the label-id next to the actual label outline. Sorry, no. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit question
On Tue, 2007-04-17 at 12:36 +0200, Sebastian Moeller wrote: Aloha FreeSurfers, I have a small question regarding tkmedit and the line tool. Is it possible to specify start and end point for a line on the tcl prompt? Sorry, no. My goal is to create a line in a volume that is not parallel to one of the main axes. ATM I resort to turning the volume in question into a plane parallel to the line, but my overlays are not rotated accordingly so that is not as comfortable as I want it to be, and since it is somewhat exploratory pre-rotating volume and overlay is a bit unwieldy ;). For completeness, I am using 3.0.5 centos4-x86_64 under suse linux 10.1, but I guess that does not really matter. I'm sorry but I don't understand what you're trying to do here. Why do you need to create a line parallel to the main axes? What does this have to do with specifying a line on the shell? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Scripting: Feeding arguments and variables to script?
1. When you launch FS from command line and provide a -tcl command to invoke a tcl script, how do you supply arguments to that script (or is that even possible)? There's no way to pass arguments along on the command line, so Bruce's suggestion works best. 3. What assumptions, if any, can a script rely on as to current directory? It will be the same directory from which you started tksurfer. There is a tcl command 'pwd' that will return this. I see most people use an environment variable as the base for paths, unless they want to script to specifically act on something that is in a relative path (like writing a log to the current directory). -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Manuals and Scuba
1.Where can I find more information regarding SCUBA? https://surfer.nmr.mgh.harvard.edu/fswiki/Scuba 3. What is the newest version of the FreeSurfer Manual and where can I find it The freesurfer wiki at that address is our current live documentation. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Complex value color scales.
There color wheel only works for complex, and there's currently no way to pass an arbitrary color map. We realize how annoying this is, though, and a future version of our surface viewer won't have this limitation. On Fri, 2007-03-23 at 16:38 -0500, Greg Appelbaum wrote: Thanks for the info Kevin. The angle function is quite revealing. As it happens I am looking at EEG data, which likely wasn't in mind in the functional development of FreeSurfer. Might I also ask if you (the general FreeSurfer 'you') know if it's possible to pass a 'wheel' scale bar to non-complex data? Or generally how to pass in an arbitrary color map? Thanks again Greg On 3/22/07 4:27 PM, Kevin Teich [EMAIL PROTECTED] wrote: I am trying to display phase information on the cortical surface using tksurfer, but am running into problems with the scale bar. Specifically when plotting scalar values using a complex color scale (e.g. RYGB Wheel), I am getting nice looking (continulus) cortical maps, with the correct scale values, but the color bar is showing up inconsistent (two colors). Is there any way to correct this problem, or access the actual color values being projected to the cortical mesh? Unfortunately, the scale bar isn't really meant to be used with the complex color wheel. There is no way to get a nice legend for the color wheel. However, if you select View-Information-Angle, you can see the actual value that is being passed into the color function, so you can mouseover a color on the surface and see what value is mapped to it. I know it's not great, but maybe it will help a bit. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Complex value color scales.
I am trying to display phase information on the cortical surface using tksurfer, but am running into problems with the scale bar. Specifically when plotting scalar values using a complex color scale (e.g. RYGB Wheel), I am getting nice looking (continulus) cortical maps, with the correct scale values, but the color bar is showing up inconsistent (two colors). Is there any way to correct this problem, or access the actual color values being projected to the cortical mesh? Unfortunately, the scale bar isn't really meant to be used with the complex color wheel. There is no way to get a nice legend for the color wheel. However, if you select View-Information-Angle, you can see the actual value that is being passed into the color function, so you can mouseover a color on the surface and see what value is mapped to it. I know it's not great, but maybe it will help a bit. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] min and max voxel values in tkmedit?
You can use the -mm-main option: -mm-main min max : color scale min and max for main volume -mm-aux min max : color scale min and max for aux volume e.g. $ tkmedit bert T1.mgz -mm-main 0 255 On Mon, Nov 27, 2006 at 07:35:18AM -0500, Bruce Fischl wrote: Hi Glenn, I think it just depends on whether things like the orbital fat got stripped by the skull stripping. Nothing really to do with the intrinsic tissue contrast. Kevin: maybe you can put something in to allow the user to specify the max? Bruce On Mon, 27 Nov 2006, Glenn Lawyer wrote: Hi, Ran into an odd problem with some of our scans. After processing the dicoms with recon-all autorecon2, we open the brain.mgz and T1.mgz images in tkmedit. The brain.mgz image tends to have terrible contrast. The problem seems to be the 'colorscale' for the image. The max values are around 185 (as compared to 244-254 for images acquired using a different scan protocol). Resetting the max to 254 fixes the problem. I am wondering if this indicates something went wrong in the automatic generation of the brain image? How would you go about forcing tkmedit to have the max value be 254 at startup (so the lab tech doesn't have to manually reset this each time she loads the image)? Include a tcl script on the command-line with SetVolumeMinMax 0 254 in it? Tkmedit reads the min and max values for the volumes when it loads them, correct? Note we only see this problem on some scans, not all. Also, we have scans from several projects/magnets/protocols. It is only one magnet/protocol where we see the problem. Thanks! details: FreeSurfer v3.0.3 on FC4. The scans in question are from a Siemens machine with the following specs (output of mri_convert): Identification NumarisVersyngo MR 2004A 4VA25A ScannerModel SonataVision Date and time StudyDate 20060429 StudyTime 093246.125000 SeriesTime110508.984000 AcqTime 105807.800018 Acquisition parameters PulseSeq *tfl3d1_ns Protocol unknown PhEncDir ROW EchoNo0 FlipAngle 7 EchoTime 3.93 InversionTime 1000 RepetitionTime2730 PhEncFOV 256 ReadoutFOV256 Image information RunNo 12 SeriesNo 13 ImageNo 1 NImageRows256 NImageCols256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 75.4460 179.1284 108.3390 VolRes 1. 1. 1. VolDim256 256 160 Vc 0.0209 -0.9998 0. Vr -0. -0. -1. Vs -0.9998 -0.0209 0. VolCenter -1.8558 49.4811 -19.6610 TransferSyntaxUID 1.2.840.10008.1.2.1 -- I'm only in it for the glory. Glenn Lawyer +352 661 967 244 Instituttgruppe for psykiatri Postboks 1130 Blindern 0318 Oslo http://folk.uio.no/davidgl :) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Head Points data files
The head points file (.hpts) is just a file of lines containing a label, an index, and an xyz coordinate: cardinal 2 0.00 0.112500 0.00 cardinal 3 0.071534 0.00 0.00 hpi 1 0.068430 0.020674 0.088621 hpi 2 0.040329 -0.083517 0.094487 hpi 3 -0.041193 -0.079972 0.100122 hpi 4 -0.054395 0.032501 0.102959 extra 1 0.72 0.111427 0.58 extra 2 0.070781 0.000371 0.000230 extra 3 -0.072046 -0.000394 -0.000207 extra 4 0.067647 0.020419 0.088373 ... The transform file (.trans) is a 4x4 float matrix: 9.999452e-01 -1.047178e-02 0.00e+00 -4.73e+00 1.044092e-02 9.969981e-01 7.671904e-02 -1.033253e+01 -8.033852e-04 -7.671483e-02 9.970528e-01 -6.399206e+01 0.00e+00 0.00e+00 0.00e+00 1.00e+00 I don't know of anybody who actively uses the head point stuff, so I'm not sure if it's up to date with how you generated the data. On Fri, Oct 27, 2006 at 11:16:04AM -0500, Juranek, Jenifer wrote: Hi, What are the file format requirements for the 2 files called to load head points - *.hpts and *.trans into tkmedit or tksurfer? We have a whole-head neuromagnetometer (4-D Neuroimaging 3600 Magnes MEG system) with 248 sensor channels. I'd like to co-register my dipole locations with FreeSurfer's aseg+aparc.mgz to efficiently localize dipoles x ROIs. I have already co-registered index points and headshape files to each subject's aMRI within 4D's software. Any advice is greatly appreciated! Jenifer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] functional overlay onto the occiptal patch with fieldsign
Are you sure the viewing threshold is set correctly for that data? Check out the View-Configure-Overlay dialog box and try changing the values. On Wed, Oct 04, 2006 at 03:22:54PM +0200, [EMAIL PROTECTED] wrote: Hi Dear FreeSurfers, I'm using the new version of FreeSurfer to process retinotopic data. I can view the finial results of eccen, polar and fieldsign on the occiptal patch. Now I want to overlay another block designed activations onto the fieldsign patch with file---load overlay--select the corresponding fsig_000.bfloat---select register.dat---OK, but actually no activations appeared on the patch altough the fsig_000.bfloat can be shown on the overlay layer. Would smeone let me know how to overlay the functional activations onto the retinotopic patch? Thanks in advance! Lei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer time course script help
1. Save the time course window in /path/filename-timecourse.ps Graph_SaveToPS fileName e.g. Graph_SaveToPS /tmp/graph.ps 2. Select only some of the contrasts for display (e.g., we have contrasts 0-7 and only want to display 1, 2, and 3) set gGraphSetting(color,visible) 0|1 Where color is one of: Red Green Blue Purple Brown Pink Gray LightBlue Yellow Orange Red is condition one, Green is condition two, etc. e.g. set gGraphSetting(Green,visible) 0 3. Setting subtract pre-stim average on, i.e. forcing the pre-stimulus time window mean values to zero on the y-axis (baseline correction). set gbPreStimOffset 0|1 e.g. set gbPreStimOffset 1 -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer marking nodes on opposite side of brain
I think the version that you have supports individual deslecting. Try middle-clicking a selected vertex. You may need to redraw the surface to see if it was deselected. On Fri, Sep 15, 2006 at 04:37:01PM +0100, Johannes Klein wrote: Hi everyone, I'm currently hand-drawing some labels using tksurfer. Unfortunately, quite often a node that I try to click will not be selected. Instead, the mark is placed on the surface behind the one I'm viewing, e.g. when trying to outline calcarine structures, the node mark will appear somewhere on the lateral surface. I wonder if anyone else has run into this? Is it possible to constrain tksurfer's node selection to the currently visible part of the cortex only? Alternatively, an undo feature to de-select the last point clicked would save me re-drawing the whole outline, but in my Edit menu, tksurfer consistently says Nothing to Undo. Do I need to enalbe the Undo feature somewhere? I'm running FS 3.0.3 centos4. Thank you very much, Johannes -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit crashes/freezes
Hm, I can't reproduce this. So, you load up a volume, and repeatedly press an arrow key to scroll through the slices? Or hold the button down? On Mon, Aug 28, 2006 at 11:16:49AM -0500, Derin Cobia wrote: I've been experiencing some crashes/freezing using tkmedit lately, and have been able to reproduce it pretty reliably. It occurs when I scroll through the slices of the subject either using the arrows keys or clicking through on the toolbar. It happens when viewing a variety of volumes (brainmask, T1, etc), and from a variety of perspectives (coronal, sagittal, etc); it also happens on different subjects as well. This occurs no matter what workstation I use in the lab (networked environment). My X freezes up as well as the keyboard, but the mouse doesn't. I used to be able to restart my X remotely, but now tkmedit locks up so bad I have to reboot. Any ideas? Dell Precision 670 Workstations CentOS 4.1 (32-bit) freesurfer-Linux-centos4-stable-pub-v3.0.3 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /pkg/brainmap/freesurfer FSFAST_HOME /pkg/brainmap/freesurfer/fsfast SUBJECTS_DIR/disk/k2/freesurfer/neuromorph_v1_flash/ FUNCTIONALS_DIR /pkg/brainmap/freesurfer/sessions MINC_BIN_DIR/pkg/brainmap/freesurfer/mni/bin MINC_LIB_DIR/pkg/brainmap/freesurfer/mni/lib PERL5LIB/pkg/brainmap/freesurfer/mni/lib/perl5/5.8.0 GSL_DIR /pkg/brainmap/freesurfer/lib/gsl QTDIR /usr/lib/qt-3.3 TCLLIBPATH /pkg/brainmap/freesurfer/lib/tcltktixblt/lib FSL_DIR /pkg/brainmap/freesurfer/fsl [EMAIL PROTECTED] ~]$ which tkmedit /pkg/brainmap/freesurfer/bin//tkmedit cd /disk/k2/freesurfer/neuromorph_v1_flash/ Thanks in advance. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] printing out from tksurfer and tkmedit
Can you say exactly what you're doing so we can try to reproduce it? On Wed, Jul 12, 2006 at 10:46:34PM -0700, Chacko Cherian wrote: when i want to print-out the outputs using Save TIFF as it isn't giving me any results.Is there something else that I need to do to save the outputs as TIFF files?? --- Bruce Fischl [EMAIL PROTECTED] wrote: but you could write a tcl script to do it automatically On Fri, 30 Jun 2006, Kevin Teich wrote: How can I can I print out the display images from tksurfer and tkmedit other than manually saving them into tiff and then printing them.IS there any way to print them directly? No, sorry, saving TIFFs is the only output that tkmedit and tksurfer do of that kind. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer rendering offscreen
Sorry, that isn't supported in tksurfer. Tksurfer has a lot of inefficient redrawing as it is a very old program and has a lot of old spaghetti code that isn't being updated. I'm working on moving all the tksurfer features into scuba. On Wed, Jun 21, 2006 at 12:13:51PM -0700, Don Hagler wrote: In older versions of tksurfer, it was possible to set a renderoffscreen flag (in a tcl script) that would make it possible to render images in the background. I find this very valuable for rendering large batches of stats. I would like to store surface-painted timeseries data in mgh format and render each frame in order to make a movie. Since the old version of tksurfer will not read mgh files, I need to use the new one for this. But rendering onscreen is very annoying because it means you can't use your computer for hours (if rendering lots of images). The problem seems to be that tksurfer is opening a window and drawing it twice before the tcl script even begins to be interpreted. Is this something that can be fixed? Just in general, why should time be wasted drawing the surface twice upon opening? And can the tcl script be interpreted *before* any open_window or redraw commands are given? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer hemodynamic waveforms for group analysis
If you're still having trouble with the time course loading, can you send me the command line you're using and the data you are trying to load? On Wed, Jun 07, 2006 at 07:35:49PM -0400, Doug Greve wrote: It is definitely possible to display time courses in tksurfer, but I usually load them from the cmd line with -timecourse. I don't think I've ever done it from the gui. Kevin will have to look into that error. If you'd like to try loading from the cmd line then: cd fegroup/bold/ISI1TR_BERT_ERFIRsm5pf5tpefsub/sph You will need to paint the HDRs onto fsaverage: mri_surf2surf --hemi lh --sval h-lh.bhdr --tval h-lh-fsaverage.mgh --srcsubject ico --trgsubject fsaverage --noreshape Do the same thing for sig: cd AV-REST mri_surf2surf --hemi lh --sval sig-lh.bhdr --tval sig-lh-fsaverage.mgh --srcsubject ico --trgsubject fsaverage --noreshape This will create: h-lh-fsaverage.mgh You can then: tksurfer fsaverage lh inflated -overlay AV-REST/sig-lh-fsaverage.bhdr -timecourse h-lh-fsaverage.mgh doug [EMAIL PROTECTED] wrote: Dear Fellow Freesurfers, I am trying to display HDR waveforms (time courses) for group level FIR analyses in tksurfer. When opening the group analysis data with tkmedit and a functional overlay, obviously some sort of time course data is loaded, because I can scroll back and forth between the different time points/frames of the functional overlay (for the specific contrast that I loaded). However the load timecourse function does not seem to be working. When attempting to load a hemodynamic waveform, I receive either an error (func_load_timecourse: error in FunD_New) without opening the HDR window, or then the time course volume is interpreted as encoded scalar volume and only one time point, of only one contrast, is shown in the HDR window. I have tried downloading all possible and impossible files related to the group analysis (.hdr/.bhdr/.bfloat/.dat/.mat/.w) from both within the specific contrast directory or the one higher level, but they all fail in either of the two ways above. The wiki, in this case, was not very helpful in trying to discover which file to load: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization Is this function currently functional? If so, which file should I load? Details: group brain = fsaverage STUDY_DIR = /space/cognito/21/users/raij/avml_fmri_mctogether/ SUBJECTS_DIR = /space/cognito/5/users/raij/subjects_mri/ environment = nmr-std-env on machine ai (FreeSurfer vs 3) group analysis name = fegroup, analysis = ISI1TR_BERT_ERFIRsm5pf5tpefsub example contrast: AV-REST Thanks for your help! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] How to disable jumping tool windows? Environment variables?
Both tkmedit and tksurfer have tool windows which jump to a location below their respective main image windows whenever the image windows are moved or adjusted. This prevents the image windows from being enlarged to full screen height, because the tool windows then jump to bottom of screen, and behind the main window. Is there some way to signal these two apps not to move the tool windows? Sorry, no, that's a feature. :) If you're only doing volume viewing and don't need surface viewing or some of the other esoteric tkmedit tools, you may want to try scuba, which works much better when enlarged to full-screen size. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
Are you sure the volume is conformed? On Thu, May 18, 2006 at 12:14:30PM -0400, Mark Pinsk wrote: I just installed the latest release on my mac ox 10.4 Trying to set control points on a monkey volume, and something wierd keeps happening... I will middle-click to set the control point, and the green cross will appear, but when I move to another location to set another control point, the first point disappears. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fill stats
Unless Doug has a tool for this, then no; it can't be done within tksurfer. Sorry. On Thu, May 04, 2006 at 06:16:31PM -0400, Chris Baker wrote: Yes- we're trying to select labels based on negative regions. If there's no way to do this, is there a way to change which is the positive and which the negative contrast in sfa-sess or does it always take the first condition as being the positive contrast. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Manual intervention for skull stripping
I have a three button mouse on a Mac machine (the middle button being a scroller as well). When I clicked on the middle button, the screen appears with all icons of the programs that I have opened. Huh. It sounds like you have some kind of special mouse driver that is mapping your middle mouse button to a different task. You'll probably need to disable it for the X11 program. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer overlay display
No, sorry. On Thu, Apr 13, 2006 at 04:59:17PM -0400, anthony gallo wrote: Hello, How can the color scale bar of the overlay display be changed so that it only shows positive values? I know if you use the truncate function in Configure Overlay Display that takes the color for the negative values off the display but the scale itself still shows negative values. If further clarity is needed please let me know. Thanks! -Anthony -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] color scale bar
if you are using the overlay color display how can you configure the scale? In the paper Measuring the thickness of the human cerebral cortex from magnetic resonance images the images show the overlay color bar in many different scales. Thanks What do you mean by the scale of the color, and what program are you talking about? Both tkmedit and tksurfer have dialog boxes for this, opened by choosing View - Configure - (Functional) Overlay... from the menu bar. There are details on how these dialogs work in the relevant wiki pages: https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide_2fTkMeditWorkingWithData_2fTkMeditFunctionalVolumes https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide_2fTkSurferWorkingWithData_2fTkSurferOverlay -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer - view - information - distance
It's the screen distance from the cursor or point clicked to the vertex it's reporting as the one the mouse is over or clicked. On Mon, Apr 10, 2006 at 02:09:25PM -0400, anthony gallo wrote: tksurfer - view - information - distance what is the reference point for this command, ie when the cursor is on point x with a value of, say 0.02 what is that the distance of? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: tcl command to raise tksurfer window
how do we raise the tksurfer window into the foreground in a tcl script (in case it is obscured by other windows)? Sorry, there's no way to do that. There's also no way to set the backgroud color in the window. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] cortical labels
but I would still like to know if there is anyway to build an mgz image of the grey volume segmented accordingly to ?h.aparc.annot. I hope you can help me. In tksurfer, you can import an annotation as a segmentation file. This will fill the voxels between surfaces with the label in the annotation file. Then you can save this segmentation as a new volume. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tcl script - rotate and save graphics
outputs about 85-90 dpi images. Is there an option for vector graphics or high resolution tiff or png images? Best, Darren ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Darren L. Weber, Ph.D. Visiting Postdoctoral Scholar Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself. --Thomas Willis (The Anatomy of the Brain and Nerves, 1664) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tcl script - rotate and save graphics
If you are using a recent dev version of tksurfer, then try the function: save_tiff filename If you enter this into the shell and it doesn't work, then you have an older version. Our new release will have this function. There is (finally) some documentation for scripting commands in tksurfer, although it is for the newer dev version. https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide_2fTkSurferScripting I would like a short tcl script to rotate each hemisphere through all the main views (lateral, medial, dorsal, ventral, anterior, posterior) and output a graphics file with the name of the subject and the view in the file name. I've found rotate_brain_[xyz] and save_rgb, but the latter does not permit a file name for the output graphics. I would like high-resolution graphics for publications, but the save_rgb outputs about 85-90 dpi images. Is there an option for vector graphics or high resolution tiff or png images? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: mk-fieldsign problems
viewing eccen and polar to the location of the ring and wedge. is there a map somewhere that can be loaded that tells me what order the colours run from fovea to periphery and from vertical to horizontal meridian etc.? thanks again for your help! jane -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer script
If you have a .w file: set val filename sclv_read_from_dotw layer If it's a volume: sclv_read_from_volume layer filename registration type [registration file name] Where layer is an index 0-8 for the layer to load it into, registration type is 0 for file, 1 for find, and 2 for identity, and the registration file name is optional if you choose 0 for the reg type. On Thu, Dec 29, 2005 at 10:55:19AM +1100, Fornito, Alexander wrote: Thanks Kevin. Is it possible to load overlays through a script as well? Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Kevin Teich [mailto:[EMAIL PROTECTED] Sent: Wed 28/12/2005 11:40 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer script labl_load_color_table filename On Wed, Dec 28, 2005 at 04:06:08PM +1100, Fornito, Alexander wrote: Is there any way to load a colour look-up table through tksurfer scripting? I can't seem to see any options in the usage. -- Kevin Teich -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer script
labl_load_color_table filename On Wed, Dec 28, 2005 at 04:06:08PM +1100, Fornito, Alexander wrote: Is there any way to load a colour look-up table through tksurfer scripting? I can't seem to see any options in the usage. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] overlay thickness maps
There are a couple things that could be wrong. Make sure that calculating an identity registration is the proper thing to be doing here. Doug can probably tell you more about this. Next, is the file actually loading? Make sure that the output to the shell doesn't have any errors, and that there's a new line in the label/value area with the overlay's name on it. Make sure that there are actually values in that line as you move the mouse aroudn over the surface. If there are, do View-Configure-Overlay and see if you can set the threshold so that it encompasses the values, as the default threshold might be incorrect. On Fri, Dec 23, 2005 at 03:42:31PM -0500, Kirk, Gregory wrote: I would like to overlay lh.thickness, rh.thickness on inflated for single subject, not the glm results, how to do that is well documented from the tutorial/tutorial group study tried tksurfer subject lh inflated - got the gray surface next file-load overlay - $SUBJECTS_DIR/subject/surf choose lh.thickness * calculate identity map it redraws the surface but there is no colormap of the thickness -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Script: setfile sulc
I'll save the tiff question for kevint It's just: save_tiff filename Newbie questions: I'm doing some stuff inn a script (with the -tcl option in freesurfer). This is very nice, but I have problems with the following: 1) I don't get the curvature file to work. I've tried with: setfile sulc (and then the full path to the file). No error, but the files effects isn't being added. 2) Is it possible to save as tif from the script? (I use now: set rgb and save_rgb) Regards! Henrik Ormåsen IT analyselab, Psykologi -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tksurfer tcl script LoadCurvature
On Thu, Nov 17, 2005 at 03:51:01PM +0100, Henry Luetcke wrote: is there a tcl-script command for loading a curvature file in tksurfer? It depends what version you're using, but if it's relatively recent: set curv FILE_NAME read_binary_curv; If yes, what is it and what is the syntax? Actually, is there a reference document with all the script commands for tksurfer? Sorry, not really. But if you have something you want to try and do, let me know and I'll give you the commands for it. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer on debian
If freesurfer is adopting some kind of open-source license (hoorrah!), can we do away with the requirement for a license file? We use the license file requests to keep track of how many people are using FreeSurfer, so probably not. Are there any components/dependencies of freesurfer that are not open-source? When it releases, there won't be. The main requirements are things like the MNI tools, GSL, and tcl/tk/tix/blt, but most of those are installed by default on most Linux distros. Does anyone have detailed instructions for a) compiling freesurfer? b) installation of freesurfer on debian? We will include instructions with the release. It will be a standard autoconf setup (configure make make install). I'm pretty sure it should compile on Debian without a problem. Is anyone working on creating a debian package for freesurfer? For that matter, has anyone created any rpm packages for freesurfer? That isn't in the works right now, but maybe somebody can make packages for their favorite distribution(s) and share with the rest of us. :) Debian already has a package for minc tools, see http://packages.debian.org/stable/science/minc-tools but this does not include all the MNI tools (eg, n3 and mritotal). We're currently compiling against 1.4, if that helps you plan ahead. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] difference between dev version and the final stable version?
I have a question about the current dev release - how different is the new 'stable' release going to be different from it? Probably not very different, but we are still working on a few critical bug fixes, and adding some final touches to the GUI programs. Can I start processing some brains using dev release and then continue processing using new 'stable' release? The nature of the bug fixes might make this a problem. In general we don't recommend mixing versions within the same study or series of result comparisons. We are working on improving our ability to detect changes in results from version to version, but we're not there yet. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Permission denied
Recently moved freesurfer from one system to another, but I am having trouble executing it. ./csurf: Permission denied. I have license in the right folder. Has anyone experienced the same problem. Make sure it is executable. Try: chmod a+x csurf -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_watershed
Alternatively, depending on what version of tkmedit you have, you can use the -mm-main min max option to specify an out-of-range min and max visible value on the command line. As Xiao said, normally the min and max visible values that determine the color scale are preset to the actual min and max values in the volume. In the View-Configure-Brightness / Constrast dialog box, you cannot specify values outside of this range. However, if on the command, you do: tkmedit bert T1 -mm-main 0 500 This will set the min and max visible values to 0 and 500, even though 500 is above the max value in the volume. Note that your version of tkmedit may not have this option, so if you get an error when trying this, ignore this email. :) On Fri, 19 Aug 2005, Xiao Han wrote: Hi Sasha, If you use tkmedit to visualize the results, then the contrast change you saw may be just due to the display problem (not exactly a problem) of tkmedit. You can move the mouse around the image to actually see whether the image intensity values were changed or not. I used mri_watershed a lot, and never saw it changed the original image intensity (in the brain region). But tkmedit will adjust its display contrast according to the dynamic range of the original image. So once skull is removed, the max and min intensity values of the image are very likely to be different, and the image will then look differently in tkmedit. -Xiao On Fri, 19 Aug 2005, florent segonne wrote: Dear Sasha, mri_watershed was initially designed to skull strip orig images, without any preprocessing step, such as intensity normalization or contrast modification. So, This certainly seems like a reasonable thing to do. However, mri_watershed might normalize intensities during the process but should NOT generate skull-stripped images with different intensities. We'll quickly look into this and let you know if this is a bug that needs to be fixed. Cheers, Florent On Fri, 19 Aug 2005, Sasha Wolosin wrote: We use an anatomical analysis program called Brain Image in our lab. We would like to speed up our analysis in Brain Image by replacing manual skull stripping with FreeSurfer's automated skull strip program. For this we would need to do a skull strip alone, without adjusting intensity values or contrast. Is this possible? Is this a reasonable thing to do? I have run mri_watershed with the input from orig on several subjects, and the output volume looks much brighter than the orig volume. Does mri_watershed normalize intensities or change the contrast in order to strip the skull? Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] .tcl file for tksurfer
setfile label /space/ventzl/1/users/SUBJECTS_DIR/mano002/label/dACC-rh.label The command to load a label is: labl_load fileName -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Label colours
Can labels be loaded in different colours in tkmedit? No, sorry. The only thing you can do is convert your lables into a volume and load it as a segmentation volume. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Editing labels
I've been trying to edit some labels in tkmedit and have noticed that if I save a label in tkmedit and then project it back onto the surface in tksurfer, it appears fragmented (ie., speckled). This happens even if I save a label that was created in tksurfer in tkmedit without even editing it (ie., create label in tksurfer, load it in tkmedit, save it in tkmedit (without editing), and then load it back in tksurfer). I don't understand why this should happen, particulalry in the latter case, as the label should remain unchanged. Can anyone explain why this might happen? Thanks, Alex Does your data have a voxel resolution different than 1mm squared? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] command line problems with tkmedit/tksurfer
Does it still work with csurf? Do you have libglut installed? If so, find libglut.so and make sure that there's a link from libglut.so.3 to it. On Tue, 2 Aug 2005, David Soscia wrote: Guys, I am having trouble getting volumes/surfaces to show when I use the command line to try to bring them up. Prior, I was just using the csurf interface to bring up all my volumes, but now that I've make my first final surface I'm trying to get the pial surface using the command line. I type in... tksurfer /up/to/the/directory/before/mri, surf, tmp, scripts, etc lh pial (or others, they all dont work) and i get this error every time... tksurfer: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory it does the same thing when i try to open something with tkmedit...any ideas on what the problem is? Dave David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Scripts in TkSurfer
I have a question about creating scripts for TkSurfer. I really know next to
nothing about scripts in general so these are rather basic questions. There
seems to be a lot of scripting commands for TkMedit but not for TkSurfer. Is
there a general list of the basic commands?
First of all, the scripting langugage for tkmedit and tksurfer is Tcl, so
you should get an introduction to Tcl on the web or from a book. The
syntax is pretty simple.
You will start up tksurfer from the command line normally, so you can load
your subject and surface from there. Then, you pass the script you want to
run with the -tcl option. For example:
tksurfer bert lh inflated -tcl my_script.tcl
my_script.tcl would be a text file with your script commands.
Display the color bar
in a for loop
Overlay a .w file Redraw the image
Save as a .rgb image
end loop
To turn on the color bar:
set colscalebarflag 1
To read a .w file, use the commands:
set val filename
sclv_read_binary_values field
Where filename is the .w file name and field is 0-9, signifying which
overlay layer you want to load this into. If you load an overlay into a
layer that is already filled, it will replace what's there.
You will need to force a redraw of the screen after loading an overlay, so
use this command:
redraw
To save an rgb image:
set rgb filename
save_rgb
Where filename is the name of the RGB file you want to create.
There are different kinds of loops available, but if you want to loop over
a series of elements in a list, such as file names to load, you can use:
foreach varname list {
}
This will iterate over all the elements in list, setting varname to
each. For example:
set colscalebarflag 1
foreach file_name { overlay1.w overlay2.w overlay3.w } {
set val $file_name
sclv_read_binary_values 0
redraw
set rgb ${file_name}-capture.rgb
save_rgb
}
This will load overlay1.w and create overlay1.w-capture.rgb, then
overlay2.w and create overlay2.w-capture.rgb, and so on.
You may need to use full file names if you don't want to load everything
from the current directory and save all the RGBs there. Tcl has a nice set
of functions in the file command to do stuff like join paths, extract
file names, and chop off extensions, e.g.:
set path [file join path to my data]
- path becomes /path/to/my/data
set file_name [file tail /path/to/my/data/overlay1.w]
- file_name becomes overlay1.w
set simple_file_name [file name overlay1.w]
- simple_file_name becomes overlay1
So:
set base_directory [file join path to my data]
set file_name overlay1.w
set val [file join $base_directory $file_name]
...
set rgb_directory [file join path to my rgbs]
set rgb [file join $rgb_directory [file tail [file name
$val]]].rgb
This will set val to /path/to/my/data/overlay1.w, and rgb to
/path/to/my/rgbs/overlay1.rgb
There's a lot here, so I would suggest starting out with an introduction
to Tcl, then creating a simple script to load and display an overlay file,
then gradually add to it.
--
Kevin Teich
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Re: [Freesurfer] unload segmentation?
when I've loaded the aseg in tkmedit, is it possible to unload it, or do I have to close tkmedit to view a volume without it again? Sorry, there's no way to unload a segementation volume. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] unload segmentation?
To clarify, this will turn off the display of the volume, not free up the memory. Not sure which you were initially asking. On Tue, 2 Aug 2005, Brian T. Quinn wrote: toggle it on and off with Ctrl-G On Tue, 2 Aug 2005 [EMAIL PROTECTED] wrote: when I've loaded the aseg in tkmedit, is it possible to unload it, or do I have to close tkmedit to view a volume without it again? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: tkregister problem
/annecy_019/users/knutsen/050126Edgar/mystudy/log/surf-sess.PPA.pl_fa.log - -- -- Session: 050126Edgar -- lh hemisphere -- grep: /autofs/space/annecy_019/users/knutsen/050126Edgar/session.info: No such file or directory wfile is /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig-0-lh.w tcl file --- set val /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig-0-lh.w sclv_read_binary_values 0 set curv lh.curv read_binary_curv; set curvflag 1; source /usr/local/freesurfer/dev/lib/tcl/readenv.tcl open_window rotate_brain_y 90 sclv_set_current_field 0 redraw - -- /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA/pl_fa tksurfer -edgar2 lh inflated -tcl /tmp/surf-sess-18404.tcl -- Segmentation fault Fri Jul 22 11:05:10 EDT 2005 -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem filling labels
Ah, I think the version of tksurfer you are using is much newer than the one that should be associated with the script. What do you get if you try: tksurfer --all-info On Sat, 9 Jul 2005 [EMAIL PROTECTED] wrote: Hi, It used to work in the past, but I don't know what might have changed. The machines run uptodate each night to stay current with Redhat patches, but I'm not sure what might have been updated right before this stopped working. As for tksurfer --version freesurfer_alpha/bin/Linux/tksurfer --version $ I'm not sure what the means though, as it's not a number, just the dollar sign. Does this give you any clues? Thanks so much for helping me out with this. Xander Original message Date: Fri, 8 Jul 2005 13:17:45 -0400 (EDT) From: Kevin Teich [EMAIL PROTECTED] Subject: Re: [Freesurfer] Problem filling labels To: [EMAIL PROTECTED] I can't duplicate this at all. Has this ever worked for you, or did it stop working? Can you give me the output of tksurfer --version On Fri, 8 Jul 2005 [EMAIL PROTECTED] wrote: In the Fill box the one I am trying to use is Up to and including boundaries by itself, but I've also tried the other possible combinations in a hope that it would work. Also, this error always happens regardless of whatever else I've done. Xander Original message Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) From: Kevin Teich [EMAIL PROTECTED] Subject: Re: [Freesurfer] Problem filling labels To: Xander Meadow [EMAIL PROTECTED] Cc: freesurfer@nmr.mgh.harvard.edu What were your settings in the Fill dialog box? Does this always happen, or only with a specific combination of options? On Thu, 7 Jul 2005, Xander Meadow wrote: Hi, I was trying to make an ROI on an inflated surface. Specifically I can recreate the error if I: Mark a bunch of vertices Create fill boundary clear all marked vertices mark a vertex within the filled boundary then try to fill it. I did all this via the GUI. Does this help? Is there anything else I can tell you that might help? Xander On Jul 7, 2005, at 3:43 PM, Kevin Teich wrote: Here is the file you requested: Hm, that appears to be OK. What action were you performing when you got the error? Can you send me the file: $FREESURFER_HOME/lib/tcl/tksurfer.tcl On Thu, 7 Jul 2005 [EMAIL PROTECTED] wrote: Hi, I'm having trouble filling labels using Freesurfer version 0.9(33y). I'm running RedHat Enterprise WS v.4. I looked through the mail archives and found that this problem has happened in the past, the post is here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00042.html I get the same error: Error: Wrong # args: fill_flood_from_cursor dont_cross_boundary dont_cross_label dont_cross_cmid dont_cross_fthresh use_multiple_seeds action argument I have a .xdebug_tkmedit if it would help debug this issue. Does anyone know what I can do to fix this? Thank you very much. -- Kevin Teich -- Kevin Teich -- Kevin Teich -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem filling labels
Yes, delete tksurfer.new.tcl. We stopped using tksurfer.new.tcl a while before that release and removed it from the distribution, but unfortunately, our upgrade script did not erase it. So you probably upgraded an old installation with the 2004 version, and it didn't remove the old tksurfer.new.tcl. tksurfer is hardcoded to first look for and use tksurfer.new.tcl, then tksurfer.tcl. This is for 'historical reasons'. On Sat, 9 Jul 2005 [EMAIL PROTECTED] wrote: Hi, I just opened up freesurfer and did some stuff and I got the following in the logs: surfer: using interface /opt/freesurfer_alpha/lib/tcl/tksurfer.new.tcl The /opt/freesurfer_alpha is correct, but I'm not sure what the tksurfer.new.tcl is. Inside freesurfer_alpha/lib I've got a tcl and tcl.new directory. Iniside those folders I've got: tcl.new/tksurfer.new.tcl tcl.new/tksurfer.tcl tcl/tksurfer.new.tcl.020617 tcl/tksurfer.tcl.020318 tcl/tksurfer.tcl tcl/tksurfer.tcl.040219 tcl/tksurfer.new.tcl tcl/tksurfer.tcl.020107 tcl/tksurfer.tcl.120400 But I don't know which of these I should be using. Is there a way I can check which of these is the correct one? Also, in which preference file to I tell Freesurfer to look at the correct tksurfer.tcl file? Thanks very much. Xander Original message Date: Fri, 8 Jul 2005 17:35:18 -0400 (EDT) From: Kevin Teich [EMAIL PROTECTED] Subject: Re: [Freesurfer] Problem filling labels To: Xander Meadow [EMAIL PROTECTED] Actually, I just veried that those are the correct versions to be used together. The only other thing I can think of is that the binary is finding a different version of the script. When you run tksurfer, look for a line of output that looks like: surfer: using interface .../tksurfer.tcl and make sure the .../ part is $FREESURFER_HOME/lib/tcl. Then make sure that 'which tksurfer' is pointing to the same $FREESURFER_HOME installation. On Fri, 8 Jul 2005, Xander Meadow wrote: I'm not entirely sure where we got our current version from. If the easiest thing to do would be just e-mail me the new script then I am definitely in favor of that. I have other machines with freesurfer on them, and it's likely they all have this problem, would the easiest thing to do, be to just download a new fresh copy of freesurfer from the freesurfer website? But, please if it's not too much trouble, send me the new script so I can install that and start drawing. Thank you again so much for helping me with this. Xander On Jul 8, 2005, at 3:39 PM, Kevin Teich wrote: Yes, that version is from 2004, while the script file you're using is from 2003. Did you get a new version from us at some point? If so, you should've gotten a corresponding tksurfer.tcl file. If not, I can give you one. On Fri, 8 Jul 2005, Xander Meadow wrote: freesurfer_alpha/bin/tksurfer --all-info ProgramName: tksurfer ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 05/07/08-20:36:58-GMT CVS: $Id: tksurfer.c,v 1.61 2004/01/05 20:36:23 fischl Exp $ User: xmeadow Machine: andrew Platform: Linux PlatformVersion: 2.6.9-11.ELsmp CompilerName: GCC CompilerVersion: 29600 Xander On Jul 8, 2005, at 3:26 PM, Kevin Teich wrote: Ah, I think the version of tksurfer you are using is much newer than the one that should be associated with the script. What do you get if you try: tksurfer --all-info On Sat, 9 Jul 2005 [EMAIL PROTECTED] wrote: Hi, It used to work in the past, but I don't know what might have changed. The machines run uptodate each night to stay current with Redhat patches, but I'm not sure what might have been updated right before this stopped working. As for tksurfer --version freesurfer_alpha/bin/Linux/tksurfer --version $ I'm not sure what the means though, as it's not a number, just the dollar sign. Does this give you any clues? Thanks so much for helping me out with this. Xander Original message Date: Fri, 8 Jul 2005 13:17:45 -0400 (EDT) From: Kevin Teich [EMAIL PROTECTED] Subject: Re: [Freesurfer] Problem filling labels To: [EMAIL PROTECTED] I can't duplicate this at all. Has this ever worked for you, or did it stop working? Can you give me the output of tksurfer --version On Fri, 8 Jul 2005 [EMAIL PROTECTED] wrote: In the Fill box the one I am trying to use is Up to and including boundaries by itself, but I've also tried the other possible combinations in a hope that it would work. Also, this error always happens regardless of whatever else I've done. Xander Original message Date: Thu, 7 Jul 2005 17:27:20 -0400 (EDT) From: Kevin Teich [EMAIL PROTECTED] Subject: Re: [Freesurfer] Problem filling labels To: Xander Meadow [EMAIL PROTECTED] Cc: freesurfer@nmr.mgh.harvard.edu What were your settings in the Fill dialog box? Does this always happen, or only with a specific combination of options? On Thu, 7 Jul 2005, Xander Meadow wrote: Hi, I was trying to make an ROI
re: [Freesurfer] Newbie and some question
Thanks a lot. Those really help. However, I don't have the root permission to install those libraries into the required directory. So, I guess that I should use the static version of tkmedit and tksurfer. Could you show me where I can find them? Thanks again. Sorry, but we don't distribute a static version any more. You'll have to install tcl/tk 8.3. Best, Thanh --- Bell, Andrew (NIH/NIMH) [EMAIL PROTECTED] wrote: Thanh Ngo, Welcome to FreeSurfer :) I'm no expert but maybe I can help. I had the same problem (many people have) with the libtk8.3.so and libtcl8.3so libraries (I assume you're getting a shared library error). Before you try to get the static version to work, try this: Have you searched your computer for these files? FreeSurfer seems to want them to be in the /usr/lib directory. If you have these files but they are in a different directory, create a symbolic link to them: e.g., if the files are in /opt/tcltk/lib cd /usr/lib ln -s /opt/tcltk/lib/libtk8.3.so libtk8.3.so ln -s /opt/tcltk/lib/libtcl8.3.so libtcl8.3.so If you don't have these files, you should download them (make sure you get version 8.3.x!). If you look on the FreeSurfer Download page, there is a link below the table with the main downloads that takes you to the most up-to-date binaries. I believe these files are posted there. If you have newer versions of tcl/tk (e.g., 8.4 or 8.5), you need to install the older versions as well (make sure to FORCE the install) -- at least this was the only way I could get it to work. Hope this helps! Andy Andrew H. Bell, PhD Laboratory of Brain and Cognition National Institute of Mental Health Bethesda, Maryland USA O: (301) 496-5625 x260 [EMAIL PROTECTED] Yahoo! Sports Rekindle the Rivalries. Sign up for Fantasy Football http://football.fantasysports.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] where to download freesurfer-Linux-rh9-20050415.tar.gz
I jsut wonder where to download the freesurfer-Linux-rh9-20050415.tar.gz. Is this program release ? or someone can tell me where to download it. thanks It was a pre-release build. We're still working on a new public release. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] static version for tksurfer
Hi ! I have the same problem with tksurfer as they detail in the mail (see link). http://www.mail-archive.com/freesurfer@mail.nmr.mgh.harvard.edu/msg00642.html I installed last version of freesurfer (20040218) wich doesn't have tksurfer.static. Perhaps it's in an earlier version... Can somebody send it to me ? Hi, We don't have a static version any more, sorry; we found that most users could resolve these problems on their end. Are you getting any error messages, or just a blank window? What kind of video card do you have, and do you have the latest graphic drivers installed, including any GL related libraries? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freeglut problem
Hi all I've installed Freesurfer and when I open csurf to edit segmentation on images, I get the following error: /usr/local/freesurfer/bin/Linux/tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory Now, I've installed Freeglut and still get the above error. I can see the libglut.so.3 library in /usr/local/lib and this is in my $PATH. Is /usr/local/lib in your /etc/ld.so.conf file? If not, add it, run ldconfig as root, and try again. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit problems
So obviously it's still having a problem with the newer versions of Tcl. Does anyone have an idea of how to fix this without uninstalling the newer Tcl/Tk? Right now there is no other solution. We're just finishing up a new build that will be tailored to specific Linux distros, so one of these should work for you. Sorry! -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tksurfer Error
tksurfer: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory. Do you have glut installed? If you are running a Red Hat box, you can check by: $ rpm -qa | grep glut Or just looking for libglut* in /usr/lib or /usr/local/lib. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] new binaries for tkmedit and tksurfer
Did you install tix with FinkCommander? Be sure to install all the necessary libraries: http://surfer.nmr.mgh.harvard.edu/cgi-bin/fom?file=55 On Wed, 16 Feb 2005, Wan Park wrote: hi kevin, i reinstalled fink and installed the blt package. then i copied the new binaries. now i cannot open the tkedit nor the tksurfer. these are the messages i receive: when i press volume: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished when i press surface: Command Finished env tksurferinterface=csurf patchname= /usr/local/freesurfer_package/freesurfer/bin/Darwin/tksurfer -22970 rh white -tcl /tmp/TmpTclSurf.20719 dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tksurfer can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished any suggestion? thanks a lot, wan On Feb 14, 2005, at 2:15 PM, Kevin Teich wrote: Do you have BLT installed via Fink or FinkCommander? On Sun, 13 Feb 2005, Wan Park wrote: hi teich, i went to this place: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ tkmedit_tksurfer-20050211-Darwin.tar.gz and I Unziped it in a temp directory, then move bin/tkmedit and bin/tksurfer into your freesurfer/bin/Darwin directory, and the lib/tcl/* files into freesurfer/lib/tcl. now when i put: $tksurfer i receive this new message: dyld: tksurfer can't open library: /sw/lib/libBLT.2.dylib (No such file or directory, errno = 2) Trace/BPT trap [ogden:freesurfer_package/freesurfer/subjects] wpark% how can i solve this problem? thanks wan -- Kevin Teich -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] new binaries for tkmedit and tksurfer
Do you have BLT installed via Fink or FinkCommander? On Sun, 13 Feb 2005, Wan Park wrote: hi teich, i went to this place: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ tkmedit_tksurfer-20050211-Darwin.tar.gz and I Unziped it in a temp directory, then move bin/tkmedit and bin/tksurfer into your freesurfer/bin/Darwin directory, and the lib/tcl/* files into freesurfer/lib/tcl. now when i put: $tksurfer i receive this new message: dyld: tksurfer can't open library: /sw/lib/libBLT.2.dylib (No such file or directory, errno = 2) Trace/BPT trap [ogden:freesurfer_package/freesurfer/subjects] wpark% how can i solve this problem? thanks wan -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error in the visualization of the parcellation
Can you send me the annotation file? On Thu, 3 Feb 2005, Wan Park wrote: hi, i am using a mac G5. after successfully doing the talairach (thanks tosa and quinn) i went through and i did the parcellation: (last part) labeling surface... relabeling using gibbs priors... 000: 12553 changed, 169800 examined... 001: 3181 changed, 48112 examined... 002: 1021 changed, 16263 examined... 003:473 changed, 5771 examined... 004:281 changed, 2658 examined... 005:157 changed, 1570 examined... 006: 69 changed, 848 examined... 007: 34 changed, 397 examined... 008: 19 changed, 211 examined... 009: 9 changed, 120 examined... 010: 8 changed, 47 examined... 011: 8 changed, 49 examined... 012: 2 changed, 44 examined... 013: 0 changed, 11 examined... 000: 538 total segments, 417 labels (5917 vertices) changed 001: 158 total segments, 44 labels (399 vertices) changed 002: 116 total segments, 2 labels (13 vertices) changed 003: 114 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 172 changed) writing output to /usr/local/freesurfer_package/freesurfer/subjects/22970/label/ rh.aparc.annot... writing colortable into annotation file... classification took 4 minutes and 49 seconds. i tried to see it and wrote: tksurfer 22970 rh inflated en then file label import annot /usr/local/freesurfer_package/freesurfer/subjects/22970/label/rh.aparc.annot but i receive this message: [ogden:freesurfer_package/freesurfer/subjects] wpark% tksurfer 22970 rh inflated surfer: current subjects dir: /usr/local/freesurfer_package/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer_package/freesurfer/subjects surfer: /usr/local/freesurfer_package/freesurfer/subjects/22970/mri/T1/COR- .info INFO: Src volume /tmp/mritotal_4912/orig_8_dxyz.mnc INFO: Target volume /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc INFO: Volume /tmp/mritotal_4912/orig_8_dxyz.mnc cannot be found. ncopen: filename /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc: Invalid dimension id or name miopen: MINC package entry point Error opening /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc mincRead(): error reading volume from file /usr/local/mni/share/mni_autoreg/average_305_8_dxyz.mnc surfer: vertices=169800, faces=339596 surfer: using interface /usr/local/freesurfer_package/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/fsgdfPlot.tcl Couldn't load libtclfsgdf.dylib. Reading /usr/local/freesurfer_package/freesurfer/lib/tcl/tkUtils.tcl Read /usr/local/freesurfer_package/freesurfer/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % reading colortable from annotation file... colortable with 85 entries read (originally /space/neo/5/recon/christophe/Simple_surface_labels2002.txt) reading colortable from annotation file... *** malloc_zone_calloc[11526]: arguments too large: 3221210976,520 CTABreadFrom: could not allocate -1073756320 bin table Cannot allocate memory Bus error [ogden:freesurfer_package/freesurfer/subjects] wpark% could you please help me with this? thanks, wan -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Mac OSX Installation Questions
I am a new user of FreeSurfer. I am seeking a set of explicit instruction for installing Mac OSX (10.3.7) binaries on a G4 platform. I keep getting lost at the level of finding and using minc_tools. Can anyone improve my knowledge base and attitude. What are you getting stuck on? Did you see this: http://surfer.nmr.mgh.harvard.edu/cgi-bin/fom?file=55 -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] full surface cuts
Try: 1) Make your cut points (in clockwise or counter-clockwise order). 2) Click the Cut Closed Line button. 3) Visibly check that the cut line is contiguous; if not, make additinal cut points and use the Cut Line tool. 4) Left click one of the regions to be kept. 5) Click Fill Uncut Area button. On Sun, 16 Jan 2005, Joongnam Yang wrote: Hi, I followed the manual instructions on full surface cuts, but not working. Here is what I did. (1) cut five relaxation cuts. (2) right-click. (3) left-click one of regions that are to be kept. (4) select Fill Uncut Area button, The image refrehses, but no change is made on the image. The circular midline region is supposed to be cut off. (I looked at the archive; someone had this problem, but she just said later she figured it out and no comment on it was given) Thanks. Nam. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ascii information file for a label
I wonder if there is a way to save all information above (index, spherical coordinates, overlaid functionals values) into an ascii text file for all vertexes located within a certain label (patch)? The only thing close to this is the Save Summary function for time courses. But it's not going to save all the information you want, so, sorry, but no. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ascii information file for a label
That's true; you'll get an index, original RAS coordinates, and the overlay value for each vertex in the label. On Thu, 6 Jan 2005, Bruce Fischl wrote: if you save a label with a statistical overlay, the stat field in the label (the last field in each row) should have the statistic at that point. Isn't that right Kevin? Bruce On Thu, 6 Jan 2005, Kevin Teich wrote: I wonder if there is a way to save all information above (index, spherical coordinates, overlaid functionals values) into an ascii text file for all vertexes located within a certain label (patch)? The only thing close to this is the Save Summary function for time courses. But it's not going to save all the information you want, so, sorry, but no. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] thresh_zstat1.img
Hi, Have you tried changing the threshold parameters, in the View-Configure-Overlay dialog box? On Fri, 19 Nov 2004, Joongnam Yang wrote: Hi all, I did, (1) use mri_vol2surf to convert thresh_zstat*.img into thresh_zstat1-lh.w (2) use the *.w file to overlay it onto flattened surface. The resulting overlaid image (TkSurfer) doesn't show as much activation as that of thresh_zstat*.img (in FEAT). I see only a few tiny dots, not large areas of activation. Coud someone tell me in which direction I should explore it further? Nam. ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problems installing freesurfer on Mac OS X (Darwin)
If you launch tixwish, can you then type the following command and get
this result?
% info commands tix
tix
%
Try commenting out the line in csurf tht calls tixwish4.1.7.4 and
replacing it with the following:
exec tixwish $0 ${1+$@}
On Thu, 11 Nov 2004, Catherine Schevon wrote:
Hi,
I have been trying to get freesurfer installed on my Mac, and ran into a
problem getting csurf to run. I figured out to put the correct path to
tclsh into csurf (it's in /usr/bin, not /bin), but now I get an error
message:
$ tcsh
% source fs_setup
Setting up enviroment for FreeSurfer/FS-FAST
$ Id: FreeSurferEnv.csh,v 1.3 2003/08/05 19:19:16 kteich Exp $
FREESURFER_HOME /freesurfer
FSFAST_HOME /freesurfer/fsfast
AFNI_DIR/freesurfer/afni
FSL_DIR /freesurfer/fsl
SUBJECTS_DIR/freesurfer/subjects
WARNING: /freesurfer/afni/Darwin does not exist.
WARNING: /freesurfer/fsl/bin does not exist.
[mccec-061135:/freesurfer] cschevon% csurf
tix not found--setenv problem?
%
Also, I notice that the tixwish command doesn't seem to execute when it's
run from csurf, although it does create a window when I run it from the
command line.
Any suggestions would be most welcome!
Cathy
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[Freesurfer] Update mri_convert and mri_parse_sdcmdir
Thanks to Keith Schneider, we discovered memory related problems when reading Siemens DICOM files. This update should fix those bugs. There are two programs, mri_convert and mri_parse_sdcmdir, and they should go into your $FREESURFER_HOME/bin/$OS directory. Darwin: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_convert-20041012-Darwin.tar.gz Linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_convert-20041012-Linux.tar.gz -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] license key
Hello, I received a license key by email, but cannot find where in the license it should go. Thanks, Margaret It should go in a file named .license and placed in your FREESURFER_HOME directory. Note the leading dot in the filename. -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem to source FreeSurfer.cshrc
Where did you get the version you are trying to install, and what instructions are you using to install it? On Wed, 29 Sep 2004, Sepideh Sadaghiani wrote: Hello, I'm trying to install FreeSurfer0.8 on linux. Since the linux computer doesn't have an internet connection, I write off what from the shell: [EMAIL PROTECTED] sepirat]$ ls etc/ FreeSurfer.cshrc [EMAIL PROTECTED] sepirat]$tcsh : Command not found. : Command not found. : label not found. [EMAIL PROTECTED] ~]$ source etc/FreeSurfer.cshrc : Command not found. : Command not found. : label not found. [EMAIL PROTECTED] ~]$ newdefs newdefs: Command not found. I don't have a solid unix background. Is this a problem with tcsh? Sep -- +++ GMX DSL Premiumtarife 3 Monate gratis* + WLAN-Router 0,- EUR* +++ Clevere DSL-Nutzer wechseln jetzt zu GMX: http://www.gmx.net/de/go/dsl ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Update for mris_register
There is an updated version of mris_register available for download. Darwin: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Darwin.tar.gz Linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Linux.tar.gz Download the tarfile and expand it in your FREESURFER_HOME/bin/OS/ directory. -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer.static
Hello, Try this: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/tksurfer-040505-Linux.tar.gz I added a build of tksurfer.static to that archive. It is a build from May 5th, but contains some necessary bug fixes, and should still be fine with yout 2/18 installation. On Fri, 20 Aug 2004, Maria Virginia Centeno wrote: Hi ! I have the same problem with tksurfer as they detail in the mail (see link). http://www.mail-archive.com/[EMAIL PROTECTED]/msg00642.html I installed last version of freesurfer (20040218) wich doesn't have tksurfer.static. Perhaps it's in an earlier version... Can somebody send it to me ? Thanks Marivi 100mb gratis, Antivirus y Antispam Correo Yahoo!, el mejor correo web del mundo ¡Tenelo ya! -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] csurf problem on RedHat Linux EL2.15
You can try downloading the source and compiling it yourself: http://opengl.org/resources/libraries/glut.html On Thu, 12 Aug 2004, Xiaojian Kang wrote: Hi, I am trying to run csurf (Feb 2004 version) on RedHat Linux Enterprise 2.15 system. We choose this version of Linux because it supports AMD64 (64-bit). I can start csurf interface, but cannot run either tkmedit or tksurfer, the error megs are: /usr/local/FreeSurfer/bin/Linux/tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory /usr/local/FreeSurfer/bin/Linux/tksurfer: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory I searched the web. Linux EL 2.15 has no libglut.so. I didn't find libglut.so for AMD64. Anybody has the similar problem? Any ideas? Thanks a lot. XJ Kang -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit cpu usage
Is it normal for tkmedit to saturate the cpu when freesurfer is idle? Yes. This is fixed in the next version. -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer
I am loading the bfloats through tksurfer, not tkmedit, using the File-Load Overlay dialogue window. Sorry about that, I was confused for a minute. I just built a version from that date and it can load a bfloat volume correctly. Can you try loading the volume in tkmedit? If it can't load there, there might be a problem with the volume itself. Another source of potential error is a mismatch between the tksurfer binary and its interface file (tksurfer.tcl); have you ever tried doing an upgrade or replaced some files in your distribution that might have caused this? You can check by getting the versions of both. Send me the output of the following commands: tksurfer --all-info head $FREESURFER_HOME/lib/tcl/tksurfer.tcl - Original Message - From: Kevin Teich [EMAIL PROTECTED] Date: Thursday, June 3, 2004 3:56 pm Subject: Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer Maybe it's the case that that version of tkmedit can't load bfloats that way. Have you tried specifying directory and stem, i.e.: /path/to/data/beta_doss-thickness-250-lh for beta_doss-thickness-250-lh_000.bfloat? I tried a number of other files and got the same error in all cases. 1) From the same glm analysis, on the same average7 surface: beta_doss-thickness-250-lh_000.bfloat beta_doss-thickness-250-rh_000.bfloat (in a different session with the rh surface) 2) and from a different glm analysis: y_doss-thickness-250-lh_000.bfloat (with a different average7 surface from that study) Are there any others I should try to load? On Thu, 3 Jun 2004, Robert D Twomey wrote: Thanks for your prompt response. Is this the most current version of FreeSurfer? We have the 07-24-2003 version, however I am sure that we saw this working with this version of Freesurfer last summer. If possible we would prefer to stick with our current version and avoid updating and re-installation. What input are you giving to load the bfloat? In tksurfer File-Load Overlay, we specified the file y_doss- thickness-250lh_000.bfloat Robert - Original Message - From: Kevin Teich [EMAIL PROTECTED] Date: Thursday, June 3, 2004 3:10 pm Subject: Re: [Freesurfer] scatter plot of multiple subjects thickness data in tksurfer On Thu, 3 Jun 2004, Robert D Twomey wrote: Hi Brian, Thanks for the e-mail. Unfortunately we are still having problems getting the graph window to appear. Here is what we have: 1) load the y values into tksurfer to see scatter plots. We tried to load the .bfloat file as an overlay, and got this message in the log window: sclv_read_bfloat_values: error in FunD_New Not a directory 2) Here are the messages I get in the log window when loading y_doss-thickness-250lh.fsgd file (No graph window appears): INFO: ignoring tag Creator INFO: ignoring tag SmoothSteps INFO: ignoring tag SUBECTS_DIR INFO: ignoring tag SynthSeed Read one slice only. Did you put all the slices in the same directory? WARNING: Could not get the graph title. WARNING: Could not get the measurement label. WARNING: Could not get the subject name. WARNING: Could not get the data file name. ERROR: Could not get number of classes. Thanks for your help, Robert ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich -- Kevin Teich -- Kevin Teich -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_normalize update
The processing of control points in volume/surface creation in mri_normalize, used by csurf and recon-all, is broken for certain types of data in the 20040218 release. Please download one of these updates if you are having trouble: Darwin, 872KB: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_normalize-20040311-Darwin.tar.gz Linux, 1263KB: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_normalize-20040311-Linux.tar.gz To unpack, move the file you download to your freesurfer/ directory, cd there, and run tar zxvf filename. It will install bin/OS/mri_normalize. -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
