There does not appear to be an error at the end. doug
On 04/02/2012 12:58 PM, Borzello, Mia wrote:
mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz mri_convert -i /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000... Starting DICOMRead2() dcmfile = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 dcmdir = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003 Ref Series No = 6 Found 138 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1.25 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 136 ndcmfiles = 136 PE Dir = UNKNOWN (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data 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 ct.mgz... ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 10:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
Can you paste the terminal output into the email instead of sending a pic?
On 4/2/12 9:54 AM, Borzello, Mia wrote:
Morning guys,
I ran the MRI recon Saturday and today was trying to convert the CT dicoms to mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", but got an error. I'm sure there's a better way to do this, but i attached a screenshot of the error (I don't know how to copy and paste since ctrl + c doesn't work.)
Thanks! Mia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Sunday, April 01, 2012 10:59 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] coreg error
Hey guys,
When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz file. but when i use spmregister, it says that spm.reg.dat is unrecognizable. How can i remedy this?
Thanks so much! Mia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
is PE Dir = UNKNOWN okay?
when i run this command "spmregister --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig", i get the following error: ERROR: Flag spm.reg.dat unrecognized. --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 1:39 PM To: Borzello, Mia; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
There does not appear to be an error at the end. doug
On 04/02/2012 12:58 PM, Borzello, Mia wrote:
mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz mri_convert -i /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000... Starting DICOMRead2() dcmfile = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 dcmdir = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003 Ref Series No = 6 Found 138 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1.25 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 136 ndcmfiles = 136 PE Dir = UNKNOWN (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data 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 ct.mgz... ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 10:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
Can you paste the terminal output into the email instead of sending a pic?
On 4/2/12 9:54 AM, Borzello, Mia wrote:
Morning guys,
I ran the MRI recon Saturday and today was trying to convert the CT dicoms to mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", but got an error. I'm sure there's a better way to do this, but i attached a screenshot of the error (I don't know how to copy and paste since ctrl + c doesn't work.)
Thanks! Mia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Sunday, April 01, 2012 10:59 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] coreg error
Hey guys,
When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz file. but when i use spmregister, it says that spm.reg.dat is unrecognizable. How can i remedy this?
Thanks so much! Mia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
You need a space between ct.mgz and --reg. PE Dir unknown is ok.
On 04/02/2012 01:43 PM, Borzello, Mia wrote:
is PE Dir = UNKNOWN okay?
when i run this command "spmregister --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig", i get the following error: ERROR: Flag spm.reg.dat unrecognized. --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 1:39 PM To: Borzello, Mia; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
There does not appear to be an error at the end. doug
On 04/02/2012 12:58 PM, Borzello, Mia wrote:
mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz mri_convert -i /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000... Starting DICOMRead2() dcmfile = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 dcmdir = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003 Ref Series No = 6 Found 138 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1.25 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 136 ndcmfiles = 136 PE Dir = UNKNOWN (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data 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 ct.mgz... ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 10:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
Can you paste the terminal output into the email instead of sending a pic?
On 4/2/12 9:54 AM, Borzello, Mia wrote:
Morning guys,
I ran the MRI recon Saturday and today was trying to convert the CT dicoms to mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", but got an error. I'm sure there's a better way to do this, but i attached a screenshot of the error (I don't know how to copy and paste since ctrl + c doesn't work.)
Thanks! Mia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Sunday, April 01, 2012 10:59 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] coreg error
Hey guys,
When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz file. but when i use spmregister, it says that spm.reg.dat is unrecognizable. How can i remedy this?
Thanks so much! Mia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
K I corrected that. I reran, and this was the error (below)..is there a way to change the double forward slashes? I'm not sure how that happened.
thanks!
spmregister --s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig Log file is ./spmregister.log Mon Apr 2 13:47:24 EDT 2012 --s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig $Id: spmregister,v 1.39 2011/03/02 20:16:40 nicks Exp $ matlab matlab fmt img UseSPMGetSpace 1 ERROR: /autofs/homes/009/miaborz/subjects//RIH_E1_SurferOutput/mri/orig.mgz not found in either COR or MGZ formats ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 1:45 PM To: Borzello, Mia Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
You need a space between ct.mgz and --reg. PE Dir unknown is ok.
On 04/02/2012 01:43 PM, Borzello, Mia wrote:
is PE Dir = UNKNOWN okay?
when i run this command "spmregister --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig", i get the following error: ERROR: Flag spm.reg.dat unrecognized. --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 1:39 PM To: Borzello, Mia; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
There does not appear to be an error at the end. doug
On 04/02/2012 12:58 PM, Borzello, Mia wrote:
mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz mri_convert -i /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000... Starting DICOMRead2() dcmfile = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 dcmdir = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003 Ref Series No = 6 Found 138 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1.25 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 136 ndcmfiles = 136 PE Dir = UNKNOWN (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data 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 ct.mgz... ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 10:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
Can you paste the terminal output into the email instead of sending a pic?
On 4/2/12 9:54 AM, Borzello, Mia wrote:
Morning guys,
I ran the MRI recon Saturday and today was trying to convert the CT dicoms to mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", but got an error. I'm sure there's a better way to do this, but i attached a screenshot of the error (I don't know how to copy and paste since ctrl + c doesn't work.)
Thanks! Mia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Sunday, April 01, 2012 10:59 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] coreg error
Hey guys,
When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz file. but when i use spmregister, it says that spm.reg.dat is unrecognizable. How can i remedy this?
Thanks so much! Mia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
It says that it cannot find a file. Does that file exist?
On 04/02/2012 01:50 PM, Borzello, Mia wrote:
K I corrected that. I reran, and this was the error (below)..is there a way to change the double forward slashes? I'm not sure how that happened.
thanks!
spmregister --s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig Log file is ./spmregister.log Mon Apr 2 13:47:24 EDT 2012 --s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig $Id: spmregister,v 1.39 2011/03/02 20:16:40 nicks Exp $ matlab matlab fmt img UseSPMGetSpace 1 ERROR: /autofs/homes/009/miaborz/subjects//RIH_E1_SurferOutput/mri/orig.mgz not found in either COR or MGZ formats ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 1:45 PM To: Borzello, Mia Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
You need a space between ct.mgz and --reg. PE Dir unknown is ok.
On 04/02/2012 01:43 PM, Borzello, Mia wrote:
is PE Dir = UNKNOWN okay?
when i run this command "spmregister --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig", i get the following error: ERROR: Flag spm.reg.dat unrecognized. --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 1:39 PM To: Borzello, Mia; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
There does not appear to be an error at the end. doug
On 04/02/2012 12:58 PM, Borzello, Mia wrote:
mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz mri_convert -i /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000... Starting DICOMRead2() dcmfile = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 dcmdir = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003 Ref Series No = 6 Found 138 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1.25 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 136 ndcmfiles = 136 PE Dir = UNKNOWN (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data 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 ct.mgz... ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 10:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
Can you paste the terminal output into the email instead of sending a pic?
On 4/2/12 9:54 AM, Borzello, Mia wrote:
Morning guys,
I ran the MRI recon Saturday and today was trying to convert the CT dicoms to mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", but got an error. I'm sure there's a better way to do this, but i attached a screenshot of the error (I don't know how to copy and paste since ctrl + c doesn't work.)
Thanks! Mia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Sunday, April 01, 2012 10:59 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] coreg error
Hey guys,
When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz file. but when i use spmregister, it says that spm.reg.dat is unrecognizable. How can i remedy this?
Thanks so much! Mia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
Yes it's in RIH_E1_SurferOutput/mri. Would the double forward slashes before RIH_E1_SurferOutput have effect? ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 1:51 PM To: Borzello, Mia Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
It says that it cannot find a file. Does that file exist?
On 04/02/2012 01:50 PM, Borzello, Mia wrote:
K I corrected that. I reran, and this was the error (below)..is there a way to change the double forward slashes? I'm not sure how that happened.
thanks!
spmregister --s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig Log file is ./spmregister.log Mon Apr 2 13:47:24 EDT 2012 --s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig $Id: spmregister,v 1.39 2011/03/02 20:16:40 nicks Exp $ matlab matlab fmt img UseSPMGetSpace 1 ERROR: /autofs/homes/009/miaborz/subjects//RIH_E1_SurferOutput/mri/orig.mgz not found in either COR or MGZ formats ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 1:45 PM To: Borzello, Mia Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
You need a space between ct.mgz and --reg. PE Dir unknown is ok.
On 04/02/2012 01:43 PM, Borzello, Mia wrote:
is PE Dir = UNKNOWN okay?
when i run this command "spmregister --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig", i get the following error: ERROR: Flag spm.reg.dat unrecognized. --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 1:39 PM To: Borzello, Mia; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
There does not appear to be an error at the end. doug
On 04/02/2012 12:58 PM, Borzello, Mia wrote:
mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz mri_convert -i /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000... Starting DICOMRead2() dcmfile = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 dcmdir = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003 Ref Series No = 6 Found 138 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1.25 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 136 ndcmfiles = 136 PE Dir = UNKNOWN (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data 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 ct.mgz... ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 10:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
Can you paste the terminal output into the email instead of sending a pic?
On 4/2/12 9:54 AM, Borzello, Mia wrote:
Morning guys,
I ran the MRI recon Saturday and today was trying to convert the CT dicoms to mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", but got an error. I'm sure there's a better way to do this, but i attached a screenshot of the error (I don't know how to copy and paste since ctrl + c doesn't work.)
Thanks! Mia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Sunday, April 01, 2012 10:59 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] coreg error
Hey guys,
When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz file. but when i use spmregister, it says that spm.reg.dat is unrecognizable. How can i remedy this?
Thanks so much! Mia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
It looks like it does not exist
ls /autofs/homes/009/miaborz/subjects//RIH_E1_SurferOutput/mri/orig.mgz ls: /autofs/homes/009/miaborz/subjects//RIH_E1_SurferOutput/mri/orig.mgz: No such file or directory
make sure your $SUBJECTS_DIR is set correctly
On 04/02/2012 01:53 PM, Borzello, Mia wrote:
Yes it's in RIH_E1_SurferOutput/mri. Would the double forward slashes before RIH_E1_SurferOutput have effect? ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 1:51 PM To: Borzello, Mia Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
It says that it cannot find a file. Does that file exist?
On 04/02/2012 01:50 PM, Borzello, Mia wrote:
K I corrected that. I reran, and this was the error (below)..is there a way to change the double forward slashes? I'm not sure how that happened.
thanks!
spmregister --s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig Log file is ./spmregister.log Mon Apr 2 13:47:24 EDT 2012 --s RIH_E1_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig $Id: spmregister,v 1.39 2011/03/02 20:16:40 nicks Exp $ matlab matlab fmt img UseSPMGetSpace 1 ERROR: /autofs/homes/009/miaborz/subjects//RIH_E1_SurferOutput/mri/orig.mgz not found in either COR or MGZ formats ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 1:45 PM To: Borzello, Mia Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
You need a space between ct.mgz and --reg. PE Dir unknown is ok.
On 04/02/2012 01:43 PM, Borzello, Mia wrote:
is PE Dir = UNKNOWN okay?
when i run this command "spmregister --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig", i get the following error: ERROR: Flag spm.reg.dat unrecognized. --s RIH_E1_SurferOutput --mov ct.mgz--reg spm.reg.dat --fsvol orig ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 1:39 PM To: Borzello, Mia; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
There does not appear to be an error at the end. doug
On 04/02/2012 12:58 PM, Borzello, Mia wrote:
mri_convert -i ~/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz mri_convert -i /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 -o ct.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000... Starting DICOMRead2() dcmfile = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003/I0000 dcmdir = /homes/9/miaborz/subjects/RIH-E1_PostOp_CT/S0000/SE0003 Ref Series No = 6 Found 138 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1.25 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 136 ndcmfiles = 136 PE Dir = UNKNOWN (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data 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 ct.mgz... ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 10:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] coreg error
Can you paste the terminal output into the email instead of sending a pic?
On 4/2/12 9:54 AM, Borzello, Mia wrote:
Morning guys,
I ran the MRI recon Saturday and today was trying to convert the CT dicoms to mgz format using the command "mri_convert -i first ct.dicom -o ct.mgz", but got an error. I'm sure there's a better way to do this, but i attached a screenshot of the error (I don't know how to copy and paste since ctrl + c doesn't work.)
Thanks! Mia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Sunday, April 01, 2012 10:59 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] coreg error
Hey guys,
When i run mri_convert to get ct.mgz, everything runs, and i get a ct.mgz file. but when i use spmregister, it says that spm.reg.dat is unrecognizable. How can i remedy this?
Thanks so much! Mia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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@nmr.mgh.harvard.edu
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Borzello, Mia -
Douglas N Greve