Re: [Freesurfer] ICV accuracy
Thanks, Bruce. That seemed to work well. Jared -- Jared Conley Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 221 Longwood Ave., RF 394 P: 617.525.6238 Bruce Fischl wrote: Hi Jared, you can load the source (nu_noneck.mgz) and target (/autofs/space/tensor_004/users/fischl/dev/freesurfer/average/RB_all_withskull_2006-02-15.gca) volumes in tkregister2 with the transform (transforms/talairach_with_skull.lta) to check the alignment. cheers, Bruce On Thu, 12 Jun 2008, Jared Conley wrote: FreeSurfer Community: A quick question for the group. Our lab was wondering if there is an easy way to assess the accuracy of the intracranial volume (ICV) measurement? Or is this not necessary (never any errors)? Thanks in advance, Jared -- Jared Conley Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 221 Longwood Ave., RF 394 P: 617.525.6238 ___ 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] ICV accuracy
FreeSurfer Community: A quick question for the group. Our lab was wondering if there is an easy way to assess the accuracy of the intracranial volume (ICV) measurement? Or is this not necessary (never any errors)? Thanks in advance, Jared -- Jared Conley Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 221 Longwood Ave., RF 394 P: 617.525.6238 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Aseg.stats file
FreeSurfer Community, Is there an easy, quick way to regenerate the aseg.stats file? This particular file was deleted accidentally for a few subjects and we wondered if we could quickly recreate this file without having to run recon-all again. All the other files in the subject directory are present. Thanks in advance, Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Neuroimaging Research Position Available
Our neuroimaging lab at Brigham and Women's Hospital (Boston) is seeking a part-time (20 hrs/week) post-doc to come join our group and assist in human MRI analysis and post-processing. This individual will take a lead role in the analysis of structural and diffusion tensor MRI studies in an HIV cohort and a separate aging cohort. A candidate with FreeSurfer/FSL experience will have a distinct advantage (but is not requisite). If interested please respond with your CV attached. Thanks, Jared -- Jared Conley Department of Radiology/Neurology Brigham and Women's Hospital Harvard Medical School 221 Longwood Ave, RF 394 Boston, 02115 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Manually editing brainmask.mgz
FreeSurfer community, I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command tkmedit subjid brainmask.mgz and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation file. Any ideas? Thanks, Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Manually editing brainmask.mgz
Hi Jenni, I am trying to edit the greyscale images of the brainmask.mgz. We are trying to generate an ICC map with only grey/white matter and we need to exclude a few structures that are not removed in the skull-stripping step (i.e. some of the cranial nerves, pituitary, etc.). I assume that I begin by using the Edit Voxels tool (a), but I do not know where to go from there. Thanks, Jared Jenni Pacheco wrote: Hi Jared, What happens when you try and edit? What type of editing are you trying to do? Do you have the right tools selected? I'm going to need a little bit more information on what you are doing and what is going wrong. Thanks, Jenni On Mon, 11 Jun 2007, Jared Conley wrote: FreeSurfer community, I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command tkmedit subjid brainmask.mgz and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation file. Any ideas? Thanks, Jared ___ 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] Manually editing brainmask.mgz
Jenni, Thanks; that was easier than I thought. I also appreciate the warning about editing the brainmask.mgz. We will be sure to follow your suggestion and save it as another file before editing it. Thanks again, Jared Jenni Pacheco wrote: Hi Jared, Mechanically, yes - you would use the edit voxels tool and then use the right button to remove the voxels you do not want. I'm not sure I understand exactly what you are trying to do - and if you eventually want to use Freesurfer to obtain surfaces etc, this will not work. I'd suggest saving your brainmask as something else, and edit that - this way you still have a viable brainmask.mgz to obtain results with. Jenni On Mon, 11 Jun 2007, Jared Conley wrote: Hi Jenni, I am trying to edit the greyscale images of the brainmask.mgz. We are trying to generate an ICC map with only grey/white matter and we need to exclude a few structures that are not removed in the skull-stripping step (i.e. some of the cranial nerves, pituitary, etc.). I assume that I begin by using the Edit Voxels tool (a), but I do not know where to go from there. Thanks, Jared Jenni Pacheco wrote: Hi Jared, What happens when you try and edit? What type of editing are you trying to do? Do you have the right tools selected? I'm going to need a little bit more information on what you are doing and what is going wrong. Thanks, Jenni On Mon, 11 Jun 2007, Jared Conley wrote: FreeSurfer community, I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command tkmedit subjid brainmask.mgz and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation file. Any ideas? Thanks, Jared ___ 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] Manually editing brainmask.mgz
Hi Jenni, Sorry for the confusion. We are more familiar with our own registration/segmentation system, where we edit before segmentation not after. Anyway, thank you for the advice. We will edit the aseg.mgz file instead. Thanks again, Jared Jenni Pacheco wrote: Hi Jared, It's still not completely clear to me what you are trying to do. By segmentation values do you just mean the volumes that will come out of the aseg.mgz? If thats what you mean you should make these edits to the aseg.mgz itself. I'm not certain what will happen if you make these edits to the brainmask - but I'd guess the surfaces won't be accurate, some things may not run at all. Jenni On Mon, 11 Jun 2007, Jared Conley wrote: Jenni, Another question for you. What is the consequence of running autorecon2 after editing on the brainmask.mgz file itself. You mentioned something about it not working if we want to obtain surfaces--what did you mean exactly? CSF surfaces? Ideally, we are editing the brainmask.mgz file so that autorecon2 only segments the brain according to our protocol (which eliminates pituitary, cranial nerves). In the end, we only need segmentation results of basal ganglia and the grey/white matter/lat. ventricles. If we could get the intracranial volume measurements that would be ideal, but I don't think this is possible. Thanks, Jared Jenni Pacheco wrote: Hi Jared, Mechanically, yes - you would use the edit voxels tool and then use the right button to remove the voxels you do not want. I'm not sure I understand exactly what you are trying to do - and if you eventually want to use Freesurfer to obtain surfaces etc, this will not work. I'd suggest saving your brainmask as something else, and edit that - this way you still have a viable brainmask.mgz to obtain results with. Jenni On Mon, 11 Jun 2007, Jared Conley wrote: Hi Jenni, I am trying to edit the greyscale images of the brainmask.mgz. We are trying to generate an ICC map with only grey/white matter and we need to exclude a few structures that are not removed in the skull-stripping step (i.e. some of the cranial nerves, pituitary, etc.). I assume that I begin by using the Edit Voxels tool (a), but I do not know where to go from there. Thanks, Jared Jenni Pacheco wrote: Hi Jared, What happens when you try and edit? What type of editing are you trying to do? Do you have the right tools selected? I'm going to need a little bit more information on what you are doing and what is going wrong. Thanks, Jenni On Mon, 11 Jun 2007, Jared Conley wrote: FreeSurfer community, I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command tkmedit subjid brainmask.mgz and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation file. Any ideas? Thanks, Jared ___ 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
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] 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
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] Changing the color in Edit Segmentation tool
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 FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5 Kernel info: Darwin 8.9.1 i386 - ___ 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
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? Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Editing Segmentation Results in TkMedit
I am new to FreeSurfer and am attempting to segment T1 images using the recon-all...autorecon2 command. The segmentation results look quite accurate, but I was wondering how to best edit the results (where there is a need). I noticed on the Wiki a possible option using the TkMedit program. I have tried running the command tkmedit subjid wm.mgz -aux T1.mgz as directed, but it gives me an error. Could someone direct me to the correct tutorial or answer my question directly. Thanks. Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Editing Segmentation Results in TkMedit
Bruce Fischl wrote: could be. Is it set to the right place? On Wed, 16 May 2007, Jared Conley wrote: Bruce Fischl wrote: what is the error? On Wed, 16 May 2007, Jared Conley wrote: I am new to FreeSurfer and am attempting to segment T1 images using the recon-all...autorecon2 command. The segmentation results look quite accurate, but I was wondering how to best edit the results (where there is a need). I noticed on the Wiki a possible option using the TkMedit program. I have tried running the command tkmedit subjid wm.mgz -aux T1.mgz as directed, but it gives me an error. Could someone direct me to the correct tutorial or answer my question directly. Thanks. Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer X11 terminal says Error: Loading volume ... couldn't read the anatomical volume. I am worried that perhaps it's due to my SUBJECTS_DIR environment variable not being properly set, as indicated in the Wiki. Let me know what you think. It is working now. Thanks for the assistance. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Editing Segmentation Results
I am new to FreeSurfer and am attempting to segment T1 images using the recon-all...autorecon2 command. The segmentation results look quite accurate, but I was wondering how to best edit the results (where there is a need). I noticed on the Wiki a possible option using I think either 3D Slicer or the tkmedit program. (I would prefer to use 3D Slicer if possible since this is the program with which I am more familiar). Could someone direct me to the correct tutorial or answer my question directly. Thanks. Jared ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
