Re: [Freesurfer] mri_convert problem
Have you made sure that you have read permission to open those files? What is the output of `ls -l asta.mgh`? And asta.nii doesn’t seem to be a file in your working directory. Best, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Pierpaolo Croce Date: Thursday, April 8, 2021 at 11:32 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_convert problem External Email - Use Caution Dear List, I have installed the ubuntu version of freesurfer (creating the VM as in the tutorial) I would like to run the following command: mri_convert -c -oc 0 0 0 asta.mgh orig.mgz I always get the error in the screen shot. Can someone help me? also using asta.nii format -- Ing. Pierpaolo Croce, PhD. Institute for Advanced Biomedical Technologies - ITAB and Department of Neuroscience and Imaging University of Chieti "G. D'Annunzio" Via dei Vestini, 33 66013 Chieti, Italy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert problem
Do you have read permission to the file? Also, you can convert straight to mgz, not need to use nii as an intermediate. doug On 3/15/13 5:13 AM, Valtina Pouegue wrote: Hi, I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error; - [esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gz mri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc... mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc [esther@m3012-04 ~]$ I look up, and the file is at the rith place Could you help me.. Thanks VP ] ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_convert problem
I get this error-esther@m3012-04 ~]$ mri_info $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mncmincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.mnc---I check in the directory enad the file is right there, Date: Fri, 15 Mar 2013 09:24:22 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem Hi Valtina you can convert directly without going through nii. What happens when you run ls -l on that file? Or mri_info? cheers Bruce On Fri, 15 Mar 2013, Valtina Pouegue wrote: Hi, I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error; - [esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gz mri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc... mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc [esther@m3012-04 ~]$ I look up, and the file is at the rith place Could you help me.. Thanks VP] The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_convert problem
can you run ls -l and mri_info on it? On Fri, 15 Mar 2013, Valtina Pouegue wrote: I get this error- esther@m3012-04 ~]$ mri_info $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.m nc ---I check in the directory enad the file is right there, Date: Fri, 15 Mar 2013 09:24:22 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem Hi Valtina you can convert directly without going through nii. What happens when you run ls -l on that file? Or mri_info? cheers Bruce On Fri, 15 Mar 2013, Valtina Pouegue wrote: Hi, I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error; - [esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gz mri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc... mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc [esther@m3012-04 ~]$ I look up, and the file is at the rith place Could you help me.. Thanks VP] The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_convert problem
just: mri_convert full path to minc file volume.mgz cheers Bruce On Fri, 15 Mar 2013, Valtina Pouegue wrote: Sorry, I am also a beginner in Linux environment. Now it works. I try : - esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA total 13892 -rwxr--r-- 1 esther esther 14224696 12 mar 23:33 t1_icbm_normal_1mm_pn3_rf20.mnc [esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc -rwxr--r-- 1 esther esther 14224696 12 mar 23:33/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20. mnc And this -- Volume information for/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20. mnc type: MINC dimensions: 181 x 217 x 181 voxel sizes: 1., 1., 1. type: SHORT (4) fov: 217.000 dof: 0 xstart: -90.5, xend: 90.5 ystart: -108.5, yend: 108.5 zstart: -90.5, zend: 90.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 1., y_r = 0., z_r = 0., c_r = 0.5000 : x_a = 0., y_a = 1., z_a = 0., c_a = -17.5000 : x_s = 0., y_s = 0., z_s = 1., c_s = 18.5000 Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 1. 0. 0. -90. 0. 1. 0. -126. 0. 0. 1. -72. 0. 0. 0. 1. voxel-to-ras determinant 1 ras to voxel transform: 1. -0. -0. 90. -0. 1. -0. 126. -0. -0. 1. 72. 0. 0. 0. 1. --- which command shoul I use for convert direct from MNC to mgz^ Thanks Date: Fri, 15 Mar 2013 10:00:04 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem can you run ls -l and mri_info on it? On Fri, 15 Mar 2013, Valtina Pouegue wrote: I get this error- esther@m3012-04 ~]$ mri_info $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t 1_icbm_normal_1mm_pn3_rf20.m nc ---I check in the directory enad the file is right there, Date: Fri, 15 Mar 2013 09:24:22 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem Hi Valtina you can convert directly without going through nii. What happens when yo u run ls -l on that file? Or mri_info? cheers Bruce On Fri, 15 Mar 2013, Valtina Pouegue wrote: Hi, I have a problem of conversion. I would like to convert mnc file to mg z. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error; - [esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gz mri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc... mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc [esther@m3012-04 ~]$ I look up, and the file is at the rith place Could you help me.. Thanks VP] The information in this e-mail is intended only for the person to whom i t is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you i n error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only
Re: [Freesurfer] mri_convert problem
Thanks a lot! Date: Fri, 15 Mar 2013 13:09:41 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem just: mri_convert full path to minc file volume.mgz cheers Bruce On Fri, 15 Mar 2013, Valtina Pouegue wrote: Sorry, I am also a beginner in Linux environment. Now it works. I try : - esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA total 13892 -rwxr--r-- 1 esther esther 14224696 12 mar 23:33 t1_icbm_normal_1mm_pn3_rf20.mnc [esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc -rwxr--r-- 1 esther esther 14224696 12 mar 23:33/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20. mnc And this -- Volume information for/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20. mnc type: MINC dimensions: 181 x 217 x 181 voxel sizes: 1., 1., 1. type: SHORT (4) fov: 217.000 dof: 0 xstart: -90.5, xend: 90.5 ystart: -108.5, yend: 108.5 zstart: -90.5, zend: 90.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 1., y_r = 0., z_r = 0., c_r = 0.5000 : x_a = 0., y_a = 1., z_a = 0., c_a = -17.5000 : x_s = 0., y_s = 0., z_s = 1., c_s = 18.5000 Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 1. 0. 0. -90. 0. 1. 0. -126. 0. 0. 1. -72. 0. 0. 0. 1. voxel-to-ras determinant 1 ras to voxel transform: 1. -0. -0.90. -0. 1. -0. 126. -0. -0. 1.72. 0. 0. 0. 1. --- which command shoul I use for convert direct from MNC to mgz^ Thanks Date: Fri, 15 Mar 2013 10:00:04 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem can you run ls -l and mri_info on it? On Fri, 15 Mar 2013, Valtina Pouegue wrote: I get this error- esther@m3012-04 ~]$ mri_info $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t 1_icbm_normal_1mm_pn3_rf20.m nc ---I check in the directory enad the file is right there, Date: Fri, 15 Mar 2013 09:24:22 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem Hi Valtina you can convert directly without going through nii. What happens when yo u run ls -l on that file? Or mri_info? cheers Bruce On Fri, 15 Mar 2013, Valtina Pouegue wrote: Hi, I have a problem of conversion. I would like to convert mnc file to mg z. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error; - [esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gz mri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc... mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc [esther@m3012-04 ~]$ I look up, and the file is at the rith place Could you help me.. Thanks VP] The information in this e-mail is intended only for the person to whom i t is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you i n error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you
[Freesurfer] mri_convert problem
Hi, I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error; -[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gzmri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc...mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc[esther@m3012-04 ~]$ I look up, and the file is at the rith place Could you help me..Thanks VP] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_convert problem
There is a tag in this file that our DICOM reader does not recognize: 280092 DCM Unrecognized VR code (??) in readVRLength Unfortunately, we're using a 3rd party dicom reader that is quite brittle, and I don't know a way around it. Can you convert to nifti using MRIcro and then use mri_convert to convert to mgz? doug Gabriel Go.Es. wrote: Dear FS users I'm using FS v5 to convert some dicom images to mgz running the comand: mri_convert -it dicom -ot mgz 01.DCM 001.mgz And get the error: ERROR: /root/trabajo/freesurfer/subjects/sujeto1/mri/orig/MPRAGE1/01.DCM is not a dicom file But when I try to open the file in MRIcro it is a dicom (philips) file (see attached file), can any one help me with this? Regards, Gabriel ___ 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_convert problem
Thanks Doug, The answer is yes, I can convert to NIfTY with using MRIcro (DCM2nii) and then use mri_convert to convert to mgz but, how can I be sure that this will not change the handedness???' Bests, Gabriel Date: Tue, 1 Feb 2011 10:59:56 -0500 From: gr...@nmr.mgh.harvard.edu To: gabriel...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem There is a tag in this file that our DICOM reader does not recognize: 280092 DCM Unrecognized VR code (??) in readVRLength Unfortunately, we're using a 3rd party dicom reader that is quite brittle, and I don't know a way around it. Can you convert to nifti using MRIcro and then use mri_convert to convert to mgz? doug Gabriel Go.Es. wrote: Dear FS users I'm using FS v5 to convert some dicom images to mgz running the comand: mri_convert -it dicom -ot mgz 01.DCM 001.mgz And get the error: ERROR: /root/trabajo/freesurfer/subjects/sujeto1/mri/orig/MPRAGE1/01.DCM is not a dicom file But when I try to open the file in MRIcro it is a dicom (philips) file (see attached file), can any one help me with this? Regards, Gabriel ___ 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_convert problem
Hi, I'm trying to run mri_convert to convert CT dicoms into nifti format but I keep getting the following error: [multnomah:CT] (nmr-std-env) mri_convert -i 1.2.840.10008.5.1.4.1.22342498128.100.dcm -o ct.nii mri_convert -i 1.2.840.10008.5.1.4.1.22342498128.100.dcm -o ct.nii file not found or unknown file type for file 1.2.840.10008.5.1.4.1.22342498128.100.dcm I'm running this from /autofs/space/multnomah_002/users/Cashlab/MG13/CT. I think the sources and directory are OK because I ran mri_convert to convert this same subject's MRI into mgz without problems. Is there a problem with the dicoms format then? How can I bypass this? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert problem
Rodrigo, These appear to be from a NeuroLogica CereTom scanner, and while they appear to be in dicom format, I cannot get mri_convert to recognize them. However, mricro does read them, and can convert them to analyze (which mri_convert can convert to .nii). Converting to analyze loses orientation info though. I can point you at the converted file if you want. Nick On Mon, 2009-04-27 at 11:13 -0400, Rodrigo Zepeda wrote: Hi, I'm trying to run mri_convert to convert CT dicoms into nifti format but I keep getting the following error: [multnomah:CT] (nmr-std-env) mri_convert -i 1.2.840.10008.5.1.4.1.22342498128.100.dcm -o ct.nii mri_convert -i 1.2.840.10008.5.1.4.1.22342498128.100.dcm -o ct.nii file not found or unknown file type for file 1.2.840.10008.5.1.4.1.22342498128.100.dcm I'm running this from /autofs/space/multnomah_002/users/Cashlab/MG13/CT. I think the sources and directory are OK because I ran mri_convert to convert this same subject's MRI into mgz without problems. Is there a problem with the dicoms format then? How can I bypass this? Thanks! ___ 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: problem with multiple echoes in Genesis images
Problem: mri_convert creates a NIFTI image that splits the dual echo, but pads with empty slices to the full size, e.g. a dual echo of size 256 x 256 with 108 slices will become a 4D volume with 256 x 256 x 108 x 2 instead of 256 x 256 x 54 x 2. The -nth 0 or -nth 1 option will return a volume of 54 slices, but only half of them with image data and again the lower half empty. This does not seem to happen for DICOM. Does the program look at the echo number tag or just de-interleave based on slice order? I noticed DICOM headers have the echo number set correctly, but Genesis headers all seem to list all slices as echo #2. If that's the source of the problem the behavior of mri_convert is not wrong (since it is getting wrong input), but unexpected. In that case: Is there an option to suppress/ignore all echo fields and read all as one volume? Environment: FREESURFER_HOME: /Programs/install/freesurfer Build stamp: freesurfer-Darwin-tiger-stable-pub-v4.0.1 Kernel info: Darwin 8.11.0 Power Macintosh Command: mri_convert -ot nii GE_DualEcho_PD_axial_3mm/I.001 aTestGEDual.nii Output generated $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from GE_DualEcho_PD_axial_3mm/I.001... fname_format : GE_DualEcho_PD_axial_3mm/I.%03d multi-echo genesis file detected (2 echoes)... TR=3000.00, TE=30.00, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (0, 0, 1) writing to aTestGEDual.nii... Many thanks. Dominik __ DOMINIK MEIER, PH.D. Center for Neurological Imaging Brigham Women's Hospital, Harvard Medical School 221 Longwood Avenue, RF396, Boston, MA 02115 Phone: 617 278-0800 Fax: 617 264-5154 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert problem while unpacking functionals
Dear FreeSurfers, Our group has encountered an error while unpacking the first set of data we acquired on Bay 2 since the upgrade. Here's our command line: unpacksdcmdir -src 07120620/ -targ . -generic -scanonly SUBJ.out We then modify the .out file from 1localizer ok 512 512 3 1 74858975 2 AAScout ok 128 128 128 2 74859004 3T1_MPRAGE_sag ok 256 256 128 1 74856609 4 gre_2d_2mm ok 256 256 55 1 74855396 5 gre_2d_2mm ok 256 256 55 1 74852997 6 field_mapping_2mmthickness ok 128 128 35 2 74853893 7 field_mapping_2mmthickness ok 128 128 35 1 74851708 8 ep2d_t1w ok 64 64 35 1 74848994 9 epzshim_cjw02_nonalternat ok 64 64 35 222 74849554 10 epzshim_cjw02_nonalternat ok 64 64 35 222 74846612 11 epzshim_cjw02_nonalternat ok 64 64 35 222 74843672 12 epzshim_cjw02_nonalternat ok 64 64 35 222 74837495 to 3 T1_MPRAGE_sag COR T1_MPRAGE 8 ep2d_t1w bshort f 9 epzshim_cjw02_nonalternat bshort f 10 epzshim_cjw02_nonalternat bshort f 11 epzshim_cjw02_nonalternat bshort f 12 epzshim_cjw02_nonalternat bshort f and save as SUBJ.cfg Next command line is: unpacksdcmdir -src 07120620/ -targ .. -cfg SUBJ.cfg -fsfast We get this error when it encounters the first functional run: - Run 9 - Mon Dec 10 12:43:27 EST 2007 9 epzshim_cjw02_nonalternat bshort f ERROR: mri_convert child process exited abnormally We've re-run the second unpack command after putting different functional runs (or even single functional runs) in the first position processed, and the same error message occurs each time. We've also tried the process on functional runs that do not have a z-shim (thought that might be causing trouble), but the error still comes up. Any ideas? Thanks in advance. Dan Dillon (on behalf of Elena Goetz) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert problem while unpacking functionals
Is this data on line here at the NMR center? Can you point me to it? Dan Dillon wrote: Dear FreeSurfers, Our group has encountered an error while unpacking the first set of data we acquired on Bay 2 since the upgrade. Here's our command line: unpacksdcmdir -src 07120620/ -targ . -generic -scanonly SUBJ.out We then modify the .out file from 1localizer ok 512 512 3 1 74858975 2 AAScout ok 128 128 128 2 74859004 3T1_MPRAGE_sag ok 256 256 128 1 74856609 4 gre_2d_2mm ok 256 256 55 1 74855396 5 gre_2d_2mm ok 256 256 55 1 74852997 6 field_mapping_2mmthickness ok 128 128 35 2 74853893 7 field_mapping_2mmthickness ok 128 128 35 1 74851708 8 ep2d_t1w ok 64 64 35 1 74848994 9 epzshim_cjw02_nonalternat ok 64 64 35 222 74849554 10 epzshim_cjw02_nonalternat ok 64 64 35 222 74846612 11 epzshim_cjw02_nonalternat ok 64 64 35 222 74843672 12 epzshim_cjw02_nonalternat ok 64 64 35 222 74837495 to 3 T1_MPRAGE_sag COR T1_MPRAGE 8 ep2d_t1w bshort f 9 epzshim_cjw02_nonalternat bshort f 10 epzshim_cjw02_nonalternat bshort f 11 epzshim_cjw02_nonalternat bshort f 12 epzshim_cjw02_nonalternat bshort f and save as SUBJ.cfg Next command line is: unpacksdcmdir -src 07120620/ -targ .. -cfg SUBJ.cfg -fsfast We get this error when it encounters the first functional run: - Run 9 - Mon Dec 10 12:43:27 EST 2007 9 epzshim_cjw02_nonalternat bshort f ERROR: mri_convert child process exited abnormally We've re-run the second unpack command after putting different functional runs (or even single functional runs) in the first position processed, and the same error message occurs each time. We've also tried the process on functional runs that do not have a z-shim (thought that might be causing trouble), but the error still comes up. Any ideas? Thanks in advance. Dan Dillon (on behalf of Elena Goetz) ___ 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] mri_convert problem while unpacking functionals
I can unpack these without a problem locally. Nick is preparing a new minor stable release in which these fixes will be present. doug ps. If you just can't wait, you can get new versions of the following (linux) binaries mri_convert mri_parse_sdcmdir mri_probedicom here:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ doug Dan Dillon wrote: Dear FreeSurfers, Our group has encountered an error while unpacking the first set of data we acquired on Bay 2 since the upgrade. Here's our command line: unpacksdcmdir -src 07120620/ -targ . -generic -scanonly SUBJ.out We then modify the .out file from 1localizer ok 512 512 3 1 74858975 2 AAScout ok 128 128 128 2 74859004 3T1_MPRAGE_sag ok 256 256 128 1 74856609 4 gre_2d_2mm ok 256 256 55 1 74855396 5 gre_2d_2mm ok 256 256 55 1 74852997 6 field_mapping_2mmthickness ok 128 128 35 2 74853893 7 field_mapping_2mmthickness ok 128 128 35 1 74851708 8 ep2d_t1w ok 64 64 35 1 74848994 9 epzshim_cjw02_nonalternat ok 64 64 35 222 74849554 10 epzshim_cjw02_nonalternat ok 64 64 35 222 74846612 11 epzshim_cjw02_nonalternat ok 64 64 35 222 74843672 12 epzshim_cjw02_nonalternat ok 64 64 35 222 74837495 to 3 T1_MPRAGE_sag COR T1_MPRAGE 8 ep2d_t1w bshort f 9 epzshim_cjw02_nonalternat bshort f 10 epzshim_cjw02_nonalternat bshort f 11 epzshim_cjw02_nonalternat bshort f 12 epzshim_cjw02_nonalternat bshort f and save as SUBJ.cfg Next command line is: unpacksdcmdir -src 07120620/ -targ .. -cfg SUBJ.cfg -fsfast We get this error when it encounters the first functional run: - Run 9 - Mon Dec 10 12:43:27 EST 2007 9 epzshim_cjw02_nonalternat bshort f ERROR: mri_convert child process exited abnormally We've re-run the second unpack command after putting different functional runs (or even single functional runs) in the first position processed, and the same error message occurs each time. We've also tried the process on functional runs that do not have a z-shim (thought that might be causing trouble), but the error still comes up. Any ideas? Thanks in advance. Dan Dillon (on behalf of Elena Goetz) ___ 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] mri_convert problem?
Hi Jessica, it looks like you successfully ran this yesterday. Is this
still a problem?
doug
On Sat, 15 Sep 2007, Jessica Andrews-Hanna wrote:
Hi -
Does anyone know if there is a problem with mri_convert used within the
context of unpacksdcmdir? When I type the following at the command line
(which we've used several times successfully in the past in the Buckner lab):
ssh nexlin6
source /space/freesurfer/nmr-std-env
cd /space/nexus/20/users/jandrews/FDN/070814_4TT00316/scripts
unpacksdcmdir -src `/usr/pubsw/bin/findsession 070814_4TT00316 | grep PATH |
awk '{print $3}'` -targ ../ -cfg 070814_4TT00316_unpack_fsl.cfg -unpackerr
I get the following error:
mri_convert /space/archive/133/siemens/
TrioTim-35006-20070814-165946-67/67-3-1.dcm ..//anat/
003/070814_4TT00316_mpr003.nii --sdcmlist ..//anat/003/flf -ot nii --
nspmzeropad 3 --in_type siemens_dicom
ERROR: mri_convert
child killed: segmentation violation
Here's some useful information using bugr:
-
FREESURFER_HOME: /usr/local/freesurfer/stable4
Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.0-20070914
RedHat release: CentOS release 4.4 (Final)
Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64
NMR Center info (/space/freesurfer exists):
machine: nexlin6
SUBJECTS_DIR: /space/sake/3/users/inverse/subjects
PWD: /space/nexus/20/users/jandrews/FDN/070814_4TT00316/scripts
Thanks very much,
Jessica___
Freesurfer mailing list
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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
___
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[Freesurfer] mri_convert problem?
Hi -
Does anyone know if there is a problem with mri_convert used within
the context of unpacksdcmdir? When I type the following at the
command line (which we've used several times successfully in the past
in the Buckner lab):
ssh nexlin6
source /space/freesurfer/nmr-std-env
cd /space/nexus/20/users/jandrews/FDN/070814_4TT00316/scripts
unpacksdcmdir -src `/usr/pubsw/bin/findsession 070814_4TT00316 | grep
PATH | awk '{print $3}'` -targ ../ -cfg
070814_4TT00316_unpack_fsl.cfg -unpackerr
I get the following error:
mri_convert /space/archive/133/siemens/
TrioTim-35006-20070814-165946-67/67-3-1.dcm ..//anat/
003/070814_4TT00316_mpr003.nii --sdcmlist ..//anat/003/flf -ot nii --
nspmzeropad 3 --in_type siemens_dicom
ERROR: mri_convert
child killed: segmentation violation
Here's some useful information using bugr:
-
FREESURFER_HOME: /usr/local/freesurfer/stable4
Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.0-20070914
RedHat release: CentOS release 4.4 (Final)
Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64
NMR Center info (/space/freesurfer exists):
machine: nexlin6
SUBJECTS_DIR: /space/sake/3/users/inverse/subjects
PWD: /space/nexus/20/users/jandrews/FDN/070814_4TT00316/scripts
Thanks very much,
Jessica
___
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[Freesurfer] mri_convert problem
I am trying to convert Dicom files to mgz format and I keep getting the same error even when I try some variations on what I am typing in the terminal. I have already set my subjects directory to /home/amc/freesurferstable/subjects, which is where my first data set is located, /1593-4. First I change the directory to /subjects, then I type the following with the error: [EMAIL PROTECTED] subjects]$ recon-all -i 1593-4/Image0001.dcm -s 1593-4 program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ $Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ WM removal version $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ### ERROR: Flag -i unrecognized. -i 1593-4/Image0001.dcm -s 1593-4 I dont know why it doesnt recognize the -i flag...but this is repeatedly the wall I am running into. Any ideas? Dave ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert problem
to convert Dicom files to mgz try to use following: mri_convert -it dicom -i dicom_file -o your_file.mgz to get more options type mri_convert -- help Silvester [EMAIL PROTECTED] wrote: I am trying to convert Dicom files to mgz format and I keep getting the same error even when I try some variations on what I am typing in the terminal. I have already set my subjects directory to /home/amc/freesurferstable/subjects, which is where my first data set is located, /1593-4. First I change the directory to /subjects, then I type the following with the error: [EMAIL PROTECTED] subjects]$ recon-all -i 1593-4/Image0001.dcm -s 1593-4 program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ $Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ WM removal version $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ### ERROR: Flag -i unrecognized. -i 1593-4/Image0001.dcm -s 1593-4 I dont know why it doesnt recognize the -i flag...but this is repeatedly the wall I am running into. Any ideas? Dave ___ 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 problem
Dave, It looks like a version of recon-all from 2004 is being used, which predates the -i flag. Have you installed the newest version of freesurfer (v3.0)? Or use mri_convert to create the 001.mgz, 002.mgz input files in your subjid/mri/orig directory, and run recon-all from there. Nick I am trying to convert Dicom files to mgz format and I keep getting the same error even when I try some variations on what I am typing in the terminal. I have already set my subjects directory to /home/amc/freesurferstable/subjects, which is where my first data set is located, /1593-4. First I change the directory to /subjects, then I type the following with the error: [EMAIL PROTECTED] subjects]$ recon-all -i 1593-4/Image0001.dcm -s 1593-4 program versions used $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ $Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ WM removal version $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ### ERROR: Flag -i unrecognized. -i 1593-4/Image0001.dcm -s 1593-4 I dont know why it doesnt recognize the -i flag...but this is repeatedly the wall I am running into. Any ideas? Dave ___ 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 problem?
I've been getting this error message whenever I try to convert to .mgz format: mri_convert /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz reading from /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img... INFO: analyzeRead(): min = 0, max = 1000 TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.027317, -0.986145, 0.163619) j_ras = (0.0506652, -0.164836, -0.985019) k_ras = (-0.998342, 0.018618, -0.054466) writing to /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz... gzip: stdout: Operation not permitted Broken pipe --- Is this a problem with mri_convert or am I doing something wrong that's preventing mri_convert from working properly? Thanks, - Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert problem?
does the output dir exists? Do you have write permission? On Mon, 21 Nov 2005, Daniel Goldman wrote: I've been getting this error message whenever I try to convert to .mgz format: mri_convert /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz reading from /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img... INFO: analyzeRead(): min = 0, max = 1000 TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.027317, -0.986145, 0.163619) j_ras = (0.0506652, -0.164836, -0.985019) k_ras = (-0.998342, 0.018618, -0.054466) writing to /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz... gzip: stdout: Operation not permitted Broken pipe --- Is this a problem with mri_convert or am I doing something wrong that's preventing mri_convert from working properly? Thanks, - Daniel ___ 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
