Re: [Freesurfer] reg- feat2anat error-problem
Thank you,it is working now. However, I have anorientation problem with automatic registration results. This problem has been mentioned before but i could not find any reply. I think this is something related following lines where I found it in the reg- feat2anat log file. Regards Uzay - INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file - INFO: using NIfTI-1 sform - INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file - - INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com Fri May 18 11:13:12 EEST 2007 /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig /home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat --feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya Linux localhost.localdomain 2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 i686 i686 i386 GNU/Linux mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz $Id: mri_convert.c,v 1.141 2007/04/26 05:31:21 greve Exp $ reading from /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz... TR=11.00, TE=4.92, TI=4.92, flip angle=15.00 i_ras = (-1, 2.56273e-11, 6.83856e-10) j_ras = (-1.17877e-09, -2.94451e-16, -1) k_ras = (3.0538e-12, 1, -9.84868e-13) writing to Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz... example_func ras_good_flag --- Initializing exf2anat from crude std2anat tkregister2 --targ /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit target volume /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz movable volume /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img reg file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat LoadVol0 $Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $ Diagnostic Level -1 INFO: loading target /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Ttarg: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img Tmov: -2.000 0.000 0.000 91.000; 0.000 0.000 2.000 -91.000; 0.000 -2.000 0.000 109.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) Input registration matrix (computed) 1.000 0.000 0.000 1.414; -0.000 -0.000 1.000 -30.612; 0.000 -1.000 -0.000 -44.496; 0.000 0.000 0.000 1.000; --- Input registration matrix 1.000 0.000 0.000 1.414; -0.000 -0.000 1.000 -30.612; 0.000 -1.000 -0.000 -44.496; 0.000 0.000 0.000 1.000; subject = subject-unknown RegMat --- 1.000 0.000 0.000 1.414; -0.000 -0.000 1.000 -30.612; 0.000 -1.000 -0.000 -44.496; 0.000 0.000 0.000 1.000; register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat written FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8, ref det = -1 mri_matrix_multiply -fsl -bin -iim Akkaya_Zuhre_1_9++.feat//reg/example_func2standard.mat -iim
[Freesurfer] probabilistic labels
Hi, Is there a way to get probabilistic labels for ?h.sphere.reg? If I understand it right, mris_ca_label oand mris_divide_parcellation only return the MAP solution of the probabilistic labels. Thanks, Wanmei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] probabilistic labels
Hi Wanmei, do you want the full posterior density? Bruce On Fri, 18 May 2007, Wanmei Ou wrote: Hi, Is there a way to get probabilistic labels for ?h.sphere.reg? If I understand it right, mris_ca_label oand mris_divide_parcellation only return the MAP solution of the probabilistic labels. Thanks, Wanmei ___ 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
Re: [Freesurfer] Changing the color in Edit Segmentation tool
In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the Sgmtn label (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the Sgmtn label line says Right-accumbens-intens and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks. Kevin Teich wrote: 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? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all exited with ERRORS
Hi Annie, The aparc+aseg has the aseg subcortical labels in the wm regions, and has the parcellation labels along the cortex. This is overlaid on volumes in tkmedit. A description and a snapshot is shown at the bottom of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData Jenni On Fri, 18 May 2007, Annie Chiu wrote: Hi Jenni, Thanks very much for your speedy reply. Before understanding whether I need aparc+aseg, could you let me know what the file entails? Thanks again, Annie On 5/17/07 5:48 PM, Jenni Pacheco [EMAIL PROTECTED] wrote: Hi Annie, I think what's happening is that it's failing in the aparc+aseg step, but you can verify this by looking at the status log in your subjects scripts/recon-all-status.log This step uses some previously generated input to make a new segmentation. The lh.ribbon.mgz is a newer addition to the recon-all stream, currently run in autorecon2. If your data is old it may not have this, and so the aparc+aseg can not be generated. You can either survive without the aparc+aseg if you don't want it, or you can generate the ?h.ribbon.mgz by running recon-all -cortribbon -s subjid and then trying recon-all -aparc2aseg -s subjid But first, do verify with the status log that this is the step thats failing! Jenni On Thu, 17 May 2007, Chiu, Annie (NIH/NINDS) [F] wrote: Hello all, Using the most updated version of freesurfer, I ran autorecon3 on a set of data obtained with an old version of the software (the first version) and I obtained the following error message: Loading rh annotations from /home/chiuan/freesurfer/subjects/becker2ANNIE/label/rh.aparc.annot Have color table for lh white annotation Have color table for rh white annotation Loading lh ribbon mask from /home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz ERROR: loading aseg /home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz Linux mushrat.ninds.nih.gov 2.6.9-42.0.2.ELsmp #1 SMP Thu Aug 17 18:00:32 EDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed May 16 22:24:13 EDT 2007 Could someone please clarify? Thanks in advance, Annie ___ 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
Re: [Freesurfer] Changing the color in Edit Segmentation tool
Hi Jared, How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there? jenni On Fri, 18 May 2007, Jared Conley wrote: In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the Sgmtn label (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the Sgmtn label line says Right-accumbens-intens and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks. Kevin Teich wrote: 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? ___ 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
Re: [Freesurfer] Changing the color in Edit Segmentation tool
Jenni Pacheco wrote: Hi Jared, How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there? jenni On Fri, 18 May 2007, Jared Conley wrote: In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the Sgmtn label (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the Sgmtn label line says Right-accumbens-intens and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks. Kevin Teich wrote: 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? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Thanks, Jenni for the assistance. Yes, I have gone to Tools/Configure Segmentation Brush.../Segmentation Brush Info in the TkMedit Tools window. In the Segmentation Brush Info window, I have selected my desired structure color (with the Main Anatomical used as source) and still no change in the Sgmnt label when I attempt to edit the segmentation. ___ 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
When you are editing the segmentation, are you using the middle button to change the label? jenni On Fri, 18 May 2007, Jared Conley wrote: Jenni Pacheco wrote: Hi Jared, How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there? jenni On Fri, 18 May 2007, Jared Conley wrote: In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the Sgmtn label (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the Sgmtn label line says Right-accumbens-intens and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks. Kevin Teich wrote: 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? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Thanks, Jenni for the assistance. Yes, I have gone to Tools/Configure Segmentation Brush.../Segmentation Brush Info in the TkMedit Tools window. In the Segmentation Brush Info window, I have selected my desired structure color (with the Main Anatomical used as source) and still no change in the Sgmnt label when I attempt to edit the segmentation. ___ 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
Jenni Pacheco wrote: When you are editing the segmentation, are you using the middle button to change the label? jenni On Fri, 18 May 2007, Jared Conley wrote: Jenni Pacheco wrote: Hi Jared, How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there? jenni On Fri, 18 May 2007, Jared Conley wrote: In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the Sgmtn label (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the Sgmtn label line says Right-accumbens-intens and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks. Kevin Teich wrote: 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? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Thanks, Jenni for the assistance. Yes, I have gone to Tools/Configure Segmentation Brush.../Segmentation Brush Info in the TkMedit Tools window. In the Segmentation Brush Info window, I have selected my desired structure color (with the Main Anatomical used as source) and still no change in the Sgmnt label when I attempt to edit the segmentation. Jenni, Thanks--it was a button issue. It is working now! I was confused because I was following the Wiki directions (http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide_2fTkMeditWorkingWithData_2fTkMeditSegmentations?action=highlightvalue=TkMedit) and on my Mac, it is Button 3 (according to System Preferences) that paints a label in the segmentation, not Button 2 as indicated. I didn't know what you meant by the middle button, but I started to experiment and discovered it was Button 3 that paints the label. Thanks again for your help. Should I change this Wiki page to indicate that it is Button 3 or is this just an issue for those who use Macs with the new standard Mac mouse? Best, Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Where to get mri_binarize?
I would like to use mri_binarize but don't seem to have it (running stable 3.0.3). Where can I get it? Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222 E-mail: [EMAIL PROTECTED] ___ 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
It's a MAC thing. With a standard three-button mouse it's the middle button that adds the label. If you use a MAC mouse or other non 3-button mouse there are other keystrokes which you may have to do in order to have the middle button option. sorry, Jenni On Fri, 18 May 2007, Jared Conley wrote: Jenni Pacheco wrote: When you are editing the segmentation, are you using the middle button to change the label? jenni On Fri, 18 May 2007, Jared Conley wrote: Jenni Pacheco wrote: Hi Jared, How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there? jenni On Fri, 18 May 2007, Jared Conley wrote: In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the Sgmtn label (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the Sgmtn label line says Right-accumbens-intens and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks. Kevin Teich wrote: 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? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Thanks, Jenni for the assistance. Yes, I have gone to Tools/Configure Segmentation Brush.../Segmentation Brush Info in the TkMedit Tools window. In the Segmentation Brush Info window, I have selected my desired structure color (with the Main Anatomical used as source) and still no change in the Sgmnt label when I attempt to edit the segmentation. Jenni, Thanks--it was a button issue. It is working now! I was confused because I was following the Wiki directions (http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide_2fTkMeditWorkingWithData_2fTkMeditSegmentations?action=highlightvalue=TkMedit) and on my Mac, it is Button 3 (according to System Preferences) that paints a label in the segmentation, not Button 2 as indicated. I didn't know what you meant by the middle button, but I started to experiment and discovered it was Button 3 that paints the label. Thanks again for your help. Should I change this Wiki page to indicate that it is Button 3 or is this just an issue for those who use Macs with the new standard Mac mouse? Best, Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Where to get mri_binarize?
Dan, You can get a copy here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/dev/ Nick On Fri, 2007-05-18 at 13:46 -0400, Dan Dillon wrote: I would like to use mri_binarize but don’t seem to have it (running stable 3.0.3). Where can I get it? Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222 E-mail: [EMAIL PROTECTED] ___ 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
Re: [Freesurfer] reg- feat2anat error-problem
What do you mean there was an orientation problem? If you use analyze files, then it relies on the FSL reg to std space being correct. Is it? uzay emir wrote: Thank you,it is working now. However, I have anorientation problem with automatic registration results. This problem has been mentioned before but i could not find any reply. I think this is something related following lines where I found it in the reg- feat2anat log file. Regards Uzay - INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file - INFO: using NIfTI-1 sform - INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file - - INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com Fri May 18 11:13:12 EEST 2007 /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig /home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat --feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya Linux localhost.localdomain 2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 i686 i686 i386 GNU/Linux mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz $Id: mri_convert.c,v 1.141 2007/04/26 05:31:21 greve Exp $ reading from /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz... TR=11.00, TE=4.92, TI=4.92, flip angle=15.00 i_ras = (-1, 2.56273e-11, 6.83856e-10) j_ras = (-1.17877e-09, -2.94451e-16, -1) k_ras = (3.0538e-12, 1, -9.84868e-13) writing to Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz... example_func ras_good_flag --- Initializing exf2anat from crude std2anat tkregister2 --targ /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit target volume /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz movable volume /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img reg file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat LoadVol0 $Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $ Diagnostic Level -1 INFO: loading target /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Ttarg: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img Tmov: -2.000 0.000 0.000 91.000; 0.000 0.000 2.000 -91.000; 0.000 -2.000 0.000 109.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) Input registration matrix (computed) 1.000 0.000 0.000 1.414; -0.000 -0.000 1.000 -30.612; 0.000 -1.000 -0.000 -44.496; 0.000 0.000 0.000 1.000; --- Input registration matrix 1.000 0.000 0.000 1.414; -0.000 -0.000 1.000 -30.612; 0.000 -1.000 -0.000 -44.496; 0.000 0.000 0.000 1.000; subject = subject-unknown RegMat --- 1.000 0.000 0.000 1.414; -0.000 -0.000 1.000 -30.612; 0.000 -1.000 -0.000 -44.496; 0.000 0.000 0.000 1.000; register: file
