Yes it's in RIH_E1_SurferOutput/mri. Would the double forward slashes before RIH_E1_SurferOutput have effect? ________________________________________ From: Douglas N Greve [gr...@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 [gr...@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 [gr...@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-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >>> [gr...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>> >>> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] >>> on behalf of Borzello, Mia >>> Sent: Sunday, April 01, 2012 10:59 PM >>> To: freesurfer@nmr.mgh.harvard.edu<mailto: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.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu<mailto: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 >> >> >> > -- > 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 > > > -- 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 . 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