Re: [Freesurfer] tkmedit crashes/freezes
were these processed any differently? The .xdebug_tkmedit should be in pwd wherever you ran it from. Bruce On Tue, 29 Aug 2006, Derin Cobia wrote: Kevin- Yeah, either way. In my infinite wisdom I thought that scrolling slower would help, but not so. Nick- I'm unable to locate a .xdebug_tkmedit file in either the freesurfer or subjects directory. Would it be somewhere else? It looks like we're using the 1.0-8178 Nvidia driver for our Quadro FX card, but their site shows a 1.0-8762 as the latest. I'll see if we can update it today, maybe that will help. On the side... why are my intensity values infinite for the following subject? I've briefly checked brainmask.mgz, and differing intensities appear. Any ideas? Thanks. -Derin # [EMAIL PROTECTED] WM Segmentation Mon Aug 28 04:00:48 CDT 2006 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM: nan +- nan [10.0 -- -10.0] GM: nan +- nan [10.0 -- -10.0] mri_segment: class statistics not finite - check input volume! Linux gizmo 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Aug 28 04:00:54 CDT 2006 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Regarding missing DICOM fields
Hi Doug, Thanks for the quick response. These are for single images. These older files are missing 0020,0032 (ImagePositionPatient) and 0020,0037 (ImageOrientationPatient). It is my understanding that 20,37 is used to establish the direction cosines. The scans were all acquired in the axial plane. Is it possible to 'fake' the 20,37 field by inserting the values: 1\0\0\0\1\0 ? We also know which way the slices are supposed to be sorted, is it possible to insert values into 20,32 in order to have freesurfer able to 'know' the proper sorting order? As I said in my first email, I am afraid not... But I figured it would not hurt to ask. Thanks! Cheers, Niels On 8/28/06, Doug Greve [EMAIL PROTECTED] wrote: Which diom tags do you mean? I think we can get away with not having the Patient Orientation (tag 20,20) -- I'm not sure why I required it in the first place. ImagePositionPatient (tag 20,32) is considerably more important as this is one of the ways the slices are sorted and the direction cosines estabilished. Are these for mosaics? doug Niels Bergsland wrote: Hi, We have some old scans that were originally in ACR-NEMA format which we have converted to DICOM. The problem is that they are missing both the ImagePositionPatient and ImageOrientationPatient fields. Is there anyway to use freesurfer without having these two fields? Based on the post by Doug which I found at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html , I am afraid not... Thank you for any help. Regards, Niels Bergsland ___ 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
Re: [Freesurfer] tkmedit crashes/freezes
Sorry, visual artifacts- yes (still there), crashing/freezing- no (but I've been trying hard). It's only been about an hour since the update, I'll keep you posted. So, should I worry about the artifacts affecting output? If I scroll through the slices long enough, they eventually all disappear. -Derin OK, so since you updated the graphics driver, you've had no problems with either the visual artifacts or the crashing/freezing? If there have been no problems, we'll assume the graphics driver fixed it. Otherwise, let us know. On Tue, Aug 29, 2006 at 01:24:09PM -0500, Derin Cobia wrote: Bruce, No, I processed all of them the same way (converted files, -autorecon1, etc). The scan quality differs among them, but I tossed the really bad ones. Here is the xdebug file. Also, is what I'm seeing in this slice (see attached jpg) something to worry about? If I scroll through other slices, then come back to it, the artifacts are gone. This happens randomly on various slices on some of the subjects, but it never stays. I have updated the drivers for the video card, and haven't had any issues (yet). I'll keep my eye on it. Thanks for your help. -Derin were these processed any differently? The .xdebug_tkmedit should be in pwd wherever you ran it from. Bruce On Tue, 29 Aug 2006, Derin Cobia wrote: Kevin- Yeah, either way. In my infinite wisdom I thought that scrolling slower would help, but not so. Nick- I'm unable to locate a .xdebug_tkmedit file in either the freesurfer or subjects directory. Would it be somewhere else? It looks like we're using the 1.0-8178 Nvidia driver for our Quadro FX card, but their site shows a 1.0-8762 as the latest. I'll see if we can update it today, maybe that will help. On the side... why are my intensity values infinite for the following subject? I've briefly checked brainmask.mgz, and differing intensities appear. Any ideas? Thanks. -Derin # [EMAIL PROTECTED] WM Segmentation Mon Aug 28 04:00:48 CDT 2006 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM: nan +- nan [10.0 -- -10.0] GM: nan +- nan [10.0 -- -10.0] mri_segment: class statistics not finite - check input volume! Linux gizmo 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Aug 28 04:00:54 CDT 2006 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 ___ 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] preprocessing question
Could you tell me the transformation vector that is used to convert a e.g.(181x217x181) array to a FS (256^3) array. I would like to backtransform from FS to native space. Thanks, Fred --- Doug Greve [EMAIL PROTECTED] wrote: Which way do you want to go? Convert FS volumes back into the native space or the other way around? To convert native space vols into FS, run something like: tkregister2 --s subjectname --mov mri/orig/001.mgz --regheader --reg reg.dat This will bring up both the conformed and nonconf volumes, and there should be an exact registration. Once you're confidient of that, you can add --noedit in which case it will simply produce reg.dat without bringing up the gui. Then you can run mri_vol2vol --mov anynativevolume --fstarg --o anynativevolume.inconformedspace.mgz The new volume will be in the conformed (orig.mgz) space. doug Goldman, Aaron (NIH/NIMH) [C] wrote: Hi, I have a few datasets I ran in freesurfer that were originally in 181x217x181 format. As usual, these were converted to 256^3 early in the process. Basically, I'd like to run some comparison stats between the freesurfer volumes and the same subjects run in a couple other programs (that are still 181x217x181), and was wondering what the best way would be to reobtain an exact overlay between the two. Thanks, -Aaron- ___ 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 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] preprocessing question
Hi Frederick, mri_info will give you the various transformations back to native (i.e. scanner) RAS coords. cheers, Bruce On Tue, 29 Aug 2006, Frederick Klauschen wrote: Could you tell me the transformation vector that is used to convert a e.g.(181x217x181) array to a FS (256^3) array. I would like to backtransform from FS to native space. Thanks, Fred --- Doug Greve [EMAIL PROTECTED] wrote: Which way do you want to go? Convert FS volumes back into the native space or the other way around? To convert native space vols into FS, run something like: tkregister2 --s subjectname --mov mri/orig/001.mgz --regheader --reg reg.dat This will bring up both the conformed and nonconf volumes, and there should be an exact registration. Once you're confidient of that, you can add --noedit in which case it will simply produce reg.dat without bringing up the gui. Then you can run mri_vol2vol --mov anynativevolume --fstarg --o anynativevolume.inconformedspace.mgz The new volume will be in the conformed (orig.mgz) space. doug Goldman, Aaron (NIH/NIMH) [C] wrote: Hi, I have a few datasets I ran in freesurfer that were originally in 181x217x181 format. As usual, these were converted to 256^3 early in the process. Basically, I'd like to run some comparison stats between the freesurfer volumes and the same subjects run in a couple other programs (that are still 181x217x181), and was wondering what the best way would be to reobtain an exact overlay between the two. Thanks, -Aaron- ___ 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 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] Regarding missing DICOM fields
No, I don't have anything which allows you to specify them yourself. On the other hand, you can work-around this with something like: mri_probedicom --i slice1.dcm --o slice1.dat slice1.dat will be a binary file of the pixel data from the file slice1.dcm. You can do this for each slice, then assemble the data into a real format. Not fun, but possible. Other tools out there might not require the direction cosines. doug Niels Bergsland wrote: Hi Doug, Thanks for the quick response. These are for single images. These older files are missing 0020,0032 (ImagePositionPatient) and 0020,0037 (ImageOrientationPatient). It is my understanding that 20,37 is used to establish the direction cosines. The scans were all acquired in the axial plane. Is it possible to 'fake' the 20,37 field by inserting the values: 1\0\0\0\1\0 ? We also know which way the slices are supposed to be sorted, is it possible to insert values into 20,32 in order to have freesurfer able to 'know' the proper sorting order? As I said in my first email, I am afraid not... But I figured it would not hurt to ask. Thanks! Cheers, Niels On 8/28/06, Doug Greve [EMAIL PROTECTED] wrote: Which diom tags do you mean? I think we can get away with not having the Patient Orientation (tag 20,20) -- I'm not sure why I required it in the first place. ImagePositionPatient (tag 20,32) is considerably more important as this is one of the ways the slices are sorted and the direction cosines estabilished. Are these for mosaics? doug Niels Bergsland wrote: Hi, We have some old scans that were originally in ACR-NEMA format which we have converted to DICOM. The problem is that they are missing both the ImagePositionPatient and ImageOrientationPatient fields. Is there anyway to use freesurfer without having these two fields? Based on the post by Doug which I found at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html , I am afraid not... Thank you for any help. Regards, Niels Bergsland ___ 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 -- 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
Re: [Freesurfer] Regarding missing DICOM fields
Thanks for the help Doug! I will let you know how it goes. Niels On 8/29/06, Doug Greve [EMAIL PROTECTED] wrote: No, I don't have anything which allows you to specify them yourself. On the other hand, you can work-around this with something like: mri_probedicom --i slice1.dcm --o slice1.dat slice1.dat will be a binary file of the pixel data from the file slice1.dcm. You can do this for each slice, then assemble the data into a real format. Not fun, but possible. Other tools out there might not require the direction cosines. doug Niels Bergsland wrote: Hi Doug, Thanks for the quick response. These are for single images. These older files are missing 0020,0032 (ImagePositionPatient) and 0020,0037 (ImageOrientationPatient). It is my understanding that 20,37 is used to establish the direction cosines. The scans were all acquired in the axial plane. Is it possible to 'fake' the 20,37 field by inserting the values: 1\0\0\0\1\0 ? We also know which way the slices are supposed to be sorted, is it possible to insert values into 20,32 in order to have freesurfer able to 'know' the proper sorting order? As I said in my first email, I am afraid not... But I figured it would not hurt to ask. Thanks! Cheers, Niels On 8/28/06, Doug Greve [EMAIL PROTECTED] wrote: Which diom tags do you mean? I think we can get away with not having the Patient Orientation (tag 20,20) -- I'm not sure why I required it in the first place. ImagePositionPatient (tag 20,32) is considerably more important as this is one of the ways the slices are sorted and the direction cosines estabilished. Are these for mosaics? doug Niels Bergsland wrote: Hi, We have some old scans that were originally in ACR-NEMA format which we have converted to DICOM. The problem is that they are missing both the ImagePositionPatient and ImageOrientationPatient fields. Is there anyway to use freesurfer without having these two fields? Based on the post by Doug which I found at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html , I am afraid not... Thank you for any help. Regards, Niels Bergsland ___ 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 -- 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
