Re: [Freesurfer] reg- feat2anat error
Hi, Actually I have the same problem. Here is my log file, Regards Uzay Doug Greve [EMAIL PROTECTED] wrote: Actually, I wanted the log file found in featdir/reg/freesurfer/reg-feat2anat.log. doug Furlong, Carolyn wrote: Hi niiRead(): unsupported timing pattern in Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz sorry for the delay, Best wishes Carolyn can you send the log file? Furlong, Carolyn wrote: Hi, When I try to register my functional data to anatomical data using reg-feat2anat --feat feat_directory --subject subject_name I get the following error message ERROR: could not read ///example_func.nii.gz as 24 What does this mean? And how can I fix this? Best wishes Carolyn - ___ 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 -- 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 - We won't tell. Get more on shows you hate to love (and love to hate): Yahoo! TV's Guilty Pleasures list.Thu May 17 10:05:02 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/brain.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz reading from /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.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/brain.mgz --mov /usr/local/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/brain.mgz movable volume /usr/local/fsl/etc/standard/avg152T1_brain.img reg file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat LoadVol0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 INFO: loading target /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.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 /usr/local/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 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 Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat -om
Re: [Freesurfer] tkmedit
Hi Martin, you only need to do it if there is a connection from mis-segmented eye muscle as wm to the body of the wm. cheers, Bruce On Wed, 16 May 2007, Martin Chang wrote: Hi, I have a question about using tkmedit. Up until now, our group has been editing out the eye muscles after autorecon-1 and editing out the optic nerve after autorecon-2. I know on earlier versions of freesurfer it was highly recommended to do so because the program would sometimes crash otherwise. However, using the newer version, the program seems to know to not include eye muscles in the pial matter boundary, and the optic nerve does create a region of high curvature at that point, but it doesn't crash the program. I was wondering, in your own analyses, did you do editing at each step (excluding situations that are obviously out of the norm), and would it be a bad thing not to edit those regions in the majority of cases? Thanks, Martin Chang _ PC Magazines 2007 editors choice for best Web mailaward-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-usocid=TXT_TAGHM_migration_HM_mini_pcmag_0507 ___ 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] tkmedit
Hi Martin, You should be fine not editing these regions routinely - only, of course, if they pose a problem for your surfaces. For the most part, also, you should be fine to run the entire stream and do any edits that may be needed after the fact - instead of running stepwise and checking each output along the way. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Martin Chang Sent: Thursday, May 17, 2007 12:34 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] tkmedit Hi, I have a question about using tkmedit. Up until now, our group has been editing out the eye muscles after autorecon-1 and editing out the optic nerve after autorecon-2. I know on earlier versions of freesurfer it was highly recommended to do so because the program would sometimes crash otherwise. However, using the newer version, the program seems to know to not include eye muscles in the pial matter boundary, and the optic nerve does create a region of high curvature at that point, but it doesn't crash the program. I was wondering, in your own analyses, did you do editing at each step (excluding situations that are obviously out of the norm), and would it be a bad thing not to edit those regions in the majority of cases? Thanks, Martin Chang _ PC Magazine's 2007 editors' choice for best Web mail-award-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-usocid=TXT_TAGHM_migratio n_HM_mini_pcmag_0507 ___ 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] recon-all exited with ERRORS
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] 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] reg- feat2anat error
I think this may have been a problem with our nifti reader that I fixed a few months ago. I see from the log file that you are using a freesurfer version that is about a year old. So, can you try using the versions of reg-feat2anat, mri_convert, and tkregister2 that I put in tp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve? The last two are binaries compiled for Linux. doug uzay emir wrote: Hi, Actually I have the same problem. Here is my log file, Regards Uzay Doug Greve [EMAIL PROTECTED] wrote: Actually, I wanted the log file found in featdir/reg/freesurfer/reg-feat2anat.log. doug Furlong, Carolyn wrote: Hi niiRead(): unsupported timing pattern in Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz sorry for the delay, Best wishes Carolyn can you send the log file? Furlong, Carolyn wrote: Hi, When I try to register my functional data to anatomical data using reg-feat2anat --feat feat_directory --subject subject_name I get the following error message ERROR: could not read ///example_func.nii.gz as 24 What does this mean? And how can I fix this? Best wishes Carolyn ___ 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 -- 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 We won't tell. Get more on shows you hate to love http://us.rd.yahoo.com/evt=49980/*http://tv.yahoo.com/collections/265 (and love to hate): Yahoo! TV's Guilty Pleasures list. http://us.rd.yahoo.com/evt=49980/*http://tv.yahoo.com/collections/265 Thu May 17 10:05:02 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/brain.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz reading from /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.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/brain.mgz --mov /usr/local/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/brain.mgz movable volume /usr/local/fsl/etc/standard/avg152T1_brain.img reg file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat LoadVol0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 INFO: loading target /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.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 /usr/local/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 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
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
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
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] recon-all exited with ERRORS
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
