Re: [Freesurfer] loading label in tksurfer
Hi Sharmili, this is not an error message. It is sampling the volume label coords onto the surface. What happens next? Does tksurfer display the label? cheers, Bruce On Wed, 29 Jul 2009, Sharmili 57 wrote: Hi ! Thats all it says. The window with the inflated brain shuts down, as soon as i load the labe. But i don't get an error message. ssrit...@beo-01:/data/Psychiatrie/01_Projects_Folder/DA_Sritharan/Freesurfer $ t ksurfer FASC rh inflated surfer: current subjects dir: /data/Psychiatrie/01_Projects_Folder/DA_Sritharan/ Freesurfer surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/Psychiatrie/01_Projects_Folder/DA_Sritharan/Freesurfer surfer: Reading header info from /data/Psychiatrie/01_Projects_Folder/DA_Srithar an/Freesurfer/FASC/mri/T1.mgz surfer: vertices=147680, faces=295356 Loading /apps/prod/i686/freesurfer-4.4.0/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(FASC) surfer: using interface /apps/prod/i686/freesurfer-4.4.0/lib/tcl/tksurfer.tcl Reading /apps/prod/i686/freesurfer-4.4.0/lib/tcl/tkm_common.tcl Reading /apps/prod/i686/freesurfer-4.4.0/lib/tcl/tkm_wrappers.tcl Reading /apps/prod/i686/freesurfer-4.4.0/lib/tcl/fsgdfPlot.tcl Reading /apps/prod/i686/freesurfer-4.4.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % /data/Psychiatrie/01_Projects_Folder/DA_Sritharan/Freesurfer/FASC/label/tfusif orm.rh.label /data/Psychiatrie/01_Projects_Folder/DA_Sritharan/Freesurfer/FASC/l abel/tfusiform.rh.label 2107 nonzero vertices found 2107 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... Thanks for your help Sharmili Date: Wed, 29 Jul 2009 07:59:05 -0400 From: fis...@nmr.mgh.harvard.edu To: sharmil...@hotmail.com Subject: Re: loading label in tksurfer Hi Sharmali, can you just send us the text output in your email message instead of an image? That would be much more helpful. thanks Bruce On Wed, 29 Jul 2009, Sharmili 57 wrote: From: sharmil...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 27 Jul 2009 22:54:21 + Subject: [Freesurfer] FW: loading label in tksurfer Hi ! I've edited a label in tkmedit and now I want to open it with tksurfer, but I get the following error message. Could anyone help me? Best Sharmili Neuigkeiten in Deinem Netzwerk? Findest Du hier! Surfen Sie sicher ? die neue Version ist da. Internet Explorer 8! _ http://redirect.gimas.net/?n=M0907xIMDL Den Nachfolger vom MSN Messenger findest Du hier! _ http://redirect.gimas.net/?n=M0907xBing2 Sparen Sie Zeit, Energie, Nerven. Bing?. Die Suche von Microsoft®___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Adding .mnc
Hello Everyone, I am attempting to add .mnc data but get the following error when trying to convert using: mri_convert subject.mnc subject/mri/orig/001.mgz I am following the tutorial reconstruction slides online. Here is the error: mri_convert EF0114.mnc EF0114/orig/001.mgz $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from EF0114.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (-0, -1, -0) k_ras = (-0, -0, -1) writing to EF0114/orig/001.mgz... sh: EF0114/orig/001.mgz: No such file or directory Broken pipe Thank you in advance for any suggestions, Jesse __ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Adding .mnc
That worked, thank you. I used -force at the end instead of -all and it looks good. Jesse On Wed, Jul 29, 2009 at 10:20 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Jesse, does that directory exist? Are you going to run recon-all afterwards? If so, you might just do: recon-all -i EF0114.mnc -s EF0114 -all cheers, Bruce On Wed, 29 Jul 2009, Jesse Bledsoe wrote: Hello Everyone, I am attempting to add .mnc data but get the following error when trying to convert using: mri_convert subject.mnc subject/mri/orig/001.mgz I am following the tutorial reconstruction slides online. Here is the error: mri_convert EF0114.mnc EF0114/orig/001.mgz $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from EF0114.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (-0, -1, -0) k_ras = (-0, -0, -1) writing to EF0114/orig/001.mgz... sh: EF0114/orig/001.mgz: No such file or directory Broken pipe Thank you in advance for any suggestions, Jesse __ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. -- Jesse Bledsoe, M.A. Clinical Psychology Center for Neurodevelopmental Study Michigan State University 110E Psychology Building East Lansing, MI 48824 __ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Adding .mnc
you should probably use -force and -all On Wed, 29 Jul 2009, Jesse Bledsoe wrote: That worked, thank you. I used -force at the end instead of -all and it looks good. Jesse On Wed, Jul 29, 2009 at 10:20 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Jesse, does that directory exist? Are you going to run recon-all afterwards? If so, you might just do: recon-all -i EF0114.mnc -s EF0114 -all cheers, Bruce On Wed, 29 Jul 2009, Jesse Bledsoe wrote: Hello Everyone, I am attempting to add .mnc data but get the following error when trying to convert using: mri_convert subject.mnc subject/mri/orig/001.mgz I am following the tutorial reconstruction slides online. Here is the error: mri_convert EF0114.mnc EF0114/orig/001.mgz $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from EF0114.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (-0, -1, -0) k_ras = (-0, -0, -1) writing to EF0114/orig/001.mgz... sh: EF0114/orig/001.mgz: No such file or directory Broken pipe Thank you in advance for any suggestions, Jesse __ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Adding .mnc
Right. I wondered why it went so fast - thanks again for the help. It is processing everything now. Jesse On Wed, Jul 29, 2009 at 11:18 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: you should probably use -force and -all On Wed, 29 Jul 2009, Jesse Bledsoe wrote: That worked, thank you. I used -force at the end instead of -all and it looks good. Jesse On Wed, Jul 29, 2009 at 10:20 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Jesse, does that directory exist? Are you going to run recon-all afterwards? If so, you might just do: recon-all -i EF0114.mnc -s EF0114 -all cheers, Bruce On Wed, 29 Jul 2009, Jesse Bledsoe wrote: Hello Everyone, I am attempting to add .mnc data but get the following error when trying to convert using: mri_convert subject.mnc subject/mri/orig/001.mgz I am following the tutorial reconstruction slides online. Here is the error: mri_convert EF0114.mnc EF0114/orig/001.mgz $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from EF0114.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (-0, -1, -0) k_ras = (-0, -0, -1) writing to EF0114/orig/001.mgz... sh: EF0114/orig/001.mgz: No such file or directory Broken pipe Thank you in advance for any suggestions, Jesse __ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. -- Jesse Bledsoe, M.A. Clinical Psychology Center for Neurodevelopmental Study Michigan State University 110E Psychology Building East Lansing, MI 48824 __ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Surface Analysis of the Anterior Cingulate
Rahul, thanks for the ref to the atlas definitions. Is there a similar definition for the cortex mask (?h.cortex.label)? Bruce, yes we are using the latest version. Some of our surfaces seem to exhibit a lot of noise between the anterior cingulate and the corpus callosum, sometimes encroaching on the ac. We are trying to determine if manual editing of the surfaces will improve that region sufficiently to justify the time spent and the introduction of human bias to surface reconstruction. Any advice? -- Stephen Tyree Neuroimaging Computer Scientist Laureate Institute for Brain Research Tulsa, OK, USA On Tue, Jul 28, 2009 at 6:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: sure, you could edit it. You'll want to look at the volume as well. What version are you using? I think we improved this sometime in the past year (using the improved callosum labels) cheers Bruce On Tue, 28 Jul 2009 ra...@nmr.mgh.harvard.edu wrote: Hi Stephen, For the ?h.aparc.annot atlas, the boundary definitions are included in the Desikan et al., 2006 paper (Neuroimage). Best, Rahul One of the regions we are investigating using a surface-based analysis is the anterior cingulate. In some of our surface reconstructions, parts of this region are excluded from the ?h.cortex.label files. What are the criteria that Freesurfer uses to determine those boundaries? Could manual editing around the boundary reliably extend the usable surface in that area? Thanks. -- Stephen Tyree Neuroimaging Computer Scientist Laureate Institute for Brain Research Tulsa, OK, USA ___ 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] Surface Analysis of the Anterior Cingulate
do you mean noise in the surface placement or in the parcellation labels? On Wed, 29 Jul 2009, Stephen Tyree wrote: Rahul, thanks for the ref to the atlas definitions. Is there a similar definition for the cortex mask (?h.cortex.label)? Bruce, yes we are using the latest version. Some of our surfaces seem to exhibit a lot of noise between the anterior cingulate and the corpus callosum, sometimes encroaching on the ac. We are trying to determine if manual editing of the surfaces will improve that region sufficiently to justify the time spent and the introduction of human bias to surface reconstruction. Any advice? -- Stephen Tyree Neuroimaging Computer Scientist Laureate Institute for Brain Research Tulsa, OK, USA On Tue, Jul 28, 2009 at 6:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: sure, you could edit it. You'll want to look at the volume as well. What version are you using? I think we improved this sometime in the past year (using the improved callosum labels) cheers Bruce On Tue, 28 Jul 2009 ra...@nmr.mgh.harvard.edu wrote: Hi Stephen, For the ?h.aparc.annot atlas, the boundary definitions are included in the Desikan et al., 2006 paper (Neuroimage). Best, Rahul One of the regions we are investigating using a surface-based analysis is the anterior cingulate. In some of our surface reconstructions, parts of this region are excluded from the ?h.cortex.label files. What are the criteria that Freesurfer uses to determine those boundaries? Could manual editing around the boundary reliably extend the usable surface in that area? Thanks. -- Stephen Tyree Neuroimaging Computer Scientist Laureate Institute for Brain Research Tulsa, OK, USA ___ 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] Surface Analysis of the Anterior Cingulate
Surface shape is the way I would characterize it. We would at times segment the white/gray/other differently than Freesurfer along that boundary. But at the same time it is hard to tell exactly how it should be segmented, but could possibly be improved by manual edits. -- Stephen Tyree Neuroimaging Computer Scientist Laureate Institute for Brain Research Tulsa, OK, USA On Wed, Jul 29, 2009 at 10:35 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: do you mean noise in the surface placement or in the parcellation labels? On Wed, 29 Jul 2009, Stephen Tyree wrote: Rahul, thanks for the ref to the atlas definitions. Is there a similar definition for the cortex mask (?h.cortex.label)? Bruce, yes we are using the latest version. Some of our surfaces seem to exhibit a lot of noise between the anterior cingulate and the corpus callosum, sometimes encroaching on the ac. We are trying to determine if manual editing of the surfaces will improve that region sufficiently to justify the time spent and the introduction of human bias to surface reconstruction. Any advice? -- Stephen Tyree Neuroimaging Computer Scientist Laureate Institute for Brain Research Tulsa, OK, USA On Tue, Jul 28, 2009 at 6:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: sure, you could edit it. You'll want to look at the volume as well. What version are you using? I think we improved this sometime in the past year (using the improved callosum labels) cheers Bruce On Tue, 28 Jul 2009 ra...@nmr.mgh.harvard.edu wrote: Hi Stephen, For the ?h.aparc.annot atlas, the boundary definitions are included in the Desikan et al., 2006 paper (Neuroimage). Best, Rahul One of the regions we are investigating using a surface-based analysis is the anterior cingulate. In some of our surface reconstructions, parts of this region are excluded from the ?h.cortex.label files. What are the criteria that Freesurfer uses to determine those boundaries? Could manual editing around the boundary reliably extend the usable surface in that area? Thanks. -- Stephen Tyree Neuroimaging Computer Scientist Laureate Institute for Brain Research Tulsa, OK, USA ___ 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
[Freesurfer] mri_convert with old GE-LX data
Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm image mri_convert I.001.s01 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 [matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm image mri_convert I.001.s01 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001 [matl...@occipital functional]$ mri_convert I.001.s01 -it dicom -ot spm image mri_convert I.001.s01 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a dicom file ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert with old GE-LX data
I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images total), and I got the same error messages. (With the -it ge option, it is still looking for the old filename, it seems) [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm image mri_convert I.1 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 [matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm image mri_convert I.1 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001 [matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm image mri_convert I.1 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional/new_func ERROR: /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 is not a dicom file Douglas N Greve wrote: can you rename your files to remove the .s01? Chris Watson wrote: Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm image mri_convert I.001.s01 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 [matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm image mri_convert I.001.s01 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001 [matl...@occipital functional]$ mri_convert I.001.s01 -it dicom -ot spm image mri_convert I.001.s01 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a dicom file ___ 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] mri_convert with old GE-LX data
sorry, it's a little finicky, I think it is looking for a %03d format, meaning I.001 for slices numbers less than 1000, and I.1001 for greater Chris Watson wrote: I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images total), and I got the same error messages. (With the -it ge option, it is still looking for the old filename, it seems) [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm image mri_convert I.1 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 [matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm image mri_convert I.1 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001 [matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm image mri_convert I.1 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional/new_func ERROR: /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 is not a dicom file Douglas N Greve wrote: can you rename your files to remove the .s01? Chris Watson wrote: Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm image mri_convert I.001.s01 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 [matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm image mri_convert I.001.s01 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001 [matl...@occipital functional]$ mri_convert I.001.s01 -it dicom -ot spm image mri_convert I.001.s01 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a dicom file ___ 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 gr...@nmr.mgh.harvard.edu 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] mri_convert with old GE-LX data
It got a little further (with -it ge and without any --in_type flag), but I get this error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm image mri_convert I.001 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d zero frames specified in file - setting to 1 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (nan, nan, nan) j_ras = (nan, nan, nan) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: nan nan nan nan; nan nan nan nan; nan nan nan nan; 0.000 0.000 0.000 1.000; Douglas N Greve wrote: sorry, it's a little finicky, I think it is looking for a %03d format, meaning I.001 for slices numbers less than 1000, and I.1001 for greater Chris Watson wrote: I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images total), and I got the same error messages. (With the -it ge option, it is still looking for the old filename, it seems) [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm image mri_convert I.1 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 [matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm image mri_convert I.1 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001 [matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm image mri_convert I.1 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional/new_func ERROR: /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 is not a dicom file Douglas N Greve wrote: can you rename your files to remove the .s01? Chris Watson wrote: Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm image mri_convert I.001.s01 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 [matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm image mri_convert I.001.s01 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001 [matl...@occipital functional]$ mri_convert I.001.s01 -it dicom -ot spm image mri_convert I.001.s01 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a dicom file ___ 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] mri_convert with old GE-LX data
You can try specifying the input geometry with something like -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 this is undoubtedly wrong, but should allow the command to finish Chris Watson wrote: It got a little further (with -it ge and without any --in_type flag), but I get this error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm image mri_convert I.001 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d zero frames specified in file - setting to 1 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (nan, nan, nan) j_ras = (nan, nan, nan) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: nan nan nan nan; nan nan nan nan; nan nan nan nan; 0.000 0.000 0.000 1.000; Douglas N Greve wrote: sorry, it's a little finicky, I think it is looking for a %03d format, meaning I.001 for slices numbers less than 1000, and I.1001 for greater Chris Watson wrote: I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images total), and I got the same error messages. (With the -it ge option, it is still looking for the old filename, it seems) [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm image mri_convert I.1 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 [matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm image mri_convert I.1 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001 [matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm image mri_convert I.1 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional/new_func ERROR: /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 is not a dicom file Douglas N Greve wrote: can you rename your files to remove the .s01? Chris Watson wrote: Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm image mri_convert I.001.s01 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 [matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm image mri_convert I.001.s01 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001 [matl...@occipital functional]$ mri_convert I.001.s01 -it dicom -ot spm image mri_convert I.001.s01 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a dicom file ___ 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 gr...@nmr.mgh.harvard.edu 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] mri_convert with old GE-LX data
Still get an error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d zero frames specified in file - setting to 1 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: 1.000 0.000 0.000 nan; 0.000 1.000 0.000 nan; 0.000 0.000 1.000 nan; 0.000 0.000 0.000 1.000; Douglas N Greve wrote: You can try specifying the input geometry with something like -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 this is undoubtedly wrong, but should allow the command to finish Chris Watson wrote: It got a little further (with -it ge and without any --in_type flag), but I get this error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm image mri_convert I.001 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d zero frames specified in file - setting to 1 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (nan, nan, nan) j_ras = (nan, nan, nan) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: nan nan nan nan; nan nan nan nan; nan nan nan nan; 0.000 0.000 0.000 1.000; Douglas N Greve wrote: sorry, it's a little finicky, I think it is looking for a %03d format, meaning I.001 for slices numbers less than 1000, and I.1001 for greater Chris Watson wrote: I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images total), and I got the same error messages. (With the -it ge option, it is still looking for the old filename, it seems) [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm image mri_convert I.1 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 [matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm image mri_convert I.1 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001 [matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm image mri_convert I.1 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional/new_func ERROR: /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 is not a dicom file Douglas N Greve wrote: can you rename your files to remove the .s01? Chris Watson wrote: Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm image mri_convert I.001.s01 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 [matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm image mri_convert I.001.s01 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001 [matl...@occipital functional]$ mri_convert I.001.s01 -it dicom -ot spm image mri_convert I.001.s01 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a dicom file ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert with old GE-LX data
sorry, also add -ic 0 0 0 Chris Watson wrote: Still get an error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d zero frames specified in file - setting to 1 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: 1.000 0.000 0.000 nan; 0.000 1.000 0.000 nan; 0.000 0.000 1.000 nan; 0.000 0.000 0.000 1.000; Douglas N Greve wrote: You can try specifying the input geometry with something like -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 this is undoubtedly wrong, but should allow the command to finish Chris Watson wrote: It got a little further (with -it ge and without any --in_type flag), but I get this error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm image mri_convert I.001 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d zero frames specified in file - setting to 1 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (nan, nan, nan) j_ras = (nan, nan, nan) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: nan nan nan nan; nan nan nan nan; nan nan nan nan; 0.000 0.000 0.000 1.000; Douglas N Greve wrote: sorry, it's a little finicky, I think it is looking for a %03d format, meaning I.001 for slices numbers less than 1000, and I.1001 for greater Chris Watson wrote: I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images total), and I got the same error messages. (With the -it ge option, it is still looking for the old filename, it seems) [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm image mri_convert I.1 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 [matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm image mri_convert I.1 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001 [matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm image mri_convert I.1 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional/new_func ERROR: /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 is not a dicom file Douglas N Greve wrote: can you rename your files to remove the .s01? Chris Watson wrote: Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm image mri_convert I.001.s01 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 [matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm image mri_convert I.001.s01 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001 [matl...@occipital functional]$ mri_convert I.001.s01 -it dicom -ot spm image mri_convert I.001.s01 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a dicom file ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert with old GE-LX data
It completed but it's only giving me 1 .img file, and when I loaded it into mricro, it thinks the z dimension is 8000 (the number of slices total). It should give me 400 volumes (20 slices each). So I want image001.img, 002.img, and so on. How can I do this? Do I have to rename the files differently? Douglas N Greve wrote: sorry, also add -ic 0 0 0 Chris Watson wrote: Still get an error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d zero frames specified in file - setting to 1 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: 1.000 0.000 0.000 nan; 0.000 1.000 0.000 nan; 0.000 0.000 1.000 nan; 0.000 0.000 0.000 1.000; Douglas N Greve wrote: You can try specifying the input geometry with something like -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 this is undoubtedly wrong, but should allow the command to finish Chris Watson wrote: It got a little further (with -it ge and without any --in_type flag), but I get this error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm image mri_convert I.001 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d zero frames specified in file - setting to 1 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (nan, nan, nan) j_ras = (nan, nan, nan) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: nan nan nan nan; nan nan nan nan; nan nan nan nan; 0.000 0.000 0.000 1.000; Douglas N Greve wrote: sorry, it's a little finicky, I think it is looking for a %03d format, meaning I.001 for slices numbers less than 1000, and I.1001 for greater Chris Watson wrote: I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images total), and I got the same error messages. (With the -it ge option, it is still looking for the old filename, it seems) [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm image mri_convert I.1 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 [matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm image mri_convert I.1 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001 [matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm image mri_convert I.1 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional/new_func ERROR: /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 is not a dicom file Douglas N Greve wrote: can you rename your files to remove the .s01? Chris Watson wrote: Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm image mri_convert I.001.s01 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 [matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm image mri_convert I.001.s01 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001 [matl...@occipital functional]$ mri_convert I.001.s01 -it dicom -ot spm image mri_convert I.001.s01 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... Starting DICOMRead2()
Re: [Freesurfer] mri_convert with old GE-LX data
Sorry, I don't know how to make our tools do this. It's a one-off on an old data set on a file format that we don't really support anymore, so I'm afraid that you're on your own on this one. doug Chris Watson wrote: It completed but it's only giving me 1 .img file, and when I loaded it into mricro, it thinks the z dimension is 8000 (the number of slices total). It should give me 400 volumes (20 slices each). So I want image001.img, 002.img, and so on. How can I do this? Do I have to rename the files differently? Douglas N Greve wrote: sorry, also add -ic 0 0 0 Chris Watson wrote: Still get an error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d zero frames specified in file - setting to 1 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: 1.000 0.000 0.000 nan; 0.000 1.000 0.000 nan; 0.000 0.000 1.000 nan; 0.000 0.000 0.000 1.000; Douglas N Greve wrote: You can try specifying the input geometry with something like -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 this is undoubtedly wrong, but should allow the command to finish Chris Watson wrote: It got a little further (with -it ge and without any --in_type flag), but I get this error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm image mri_convert I.001 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d zero frames specified in file - setting to 1 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (nan, nan, nan) j_ras = (nan, nan, nan) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: nan nan nan nan; nan nan nan nan; nan nan nan nan; 0.000 0.000 0.000 1.000; Douglas N Greve wrote: sorry, it's a little finicky, I think it is looking for a %03d format, meaning I.001 for slices numbers less than 1000, and I.1001 for greater Chris Watson wrote: I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images total), and I got the same error messages. (With the -it ge option, it is still looking for the old filename, it seems) [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm image mri_convert I.1 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 [matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm image mri_convert I.1 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001 [matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm image mri_convert I.1 -it dicom -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.1... Starting DICOMRead2() dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 dcmdir = /raid2/fmri5/LDProj/BOSEN/functional/new_func ERROR: /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 is not a dicom file Douglas N Greve wrote: can you rename your files to remove the .s01? Chris Watson wrote: Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot spm image mri_convert I.001.s01 -it lx -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... genesisRead(): can't determine file name format for /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 [matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot spm image mri_convert I.001.s01 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001.s01... fname_format : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d genesisRead(): error opening file /raid2/fmri5/LDProj/BOSEN/functional/I.001 [matl...@occipital
