RE: [Freesurfer] Converting DICOMs
Hi Doug, Thanks for your speedy response. The image comes up fine in SPM, but not in other programs like MRIcro or FSLview, where the anterior of the image in the axial plane faces down instead of up. Is there any (relatively) straightforward I can adjust this through mri_convert? Thanks again, Alex -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Wed 10/4/2006 2:03 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Converting DICOMs On Wed, 4 Oct 2006, Fornito, Alexander wrote: Hi, I'm new to fMR and am using mri_convert to convert from siemens dicom to analyze/spm format.I ran the command below and had a couple of questions: 1 - Why does the first INFO: line say that 807 files were found when only 805 were input? That's just the number of files in the directory (includes . and .., which is where the extra 2 come from) 2 - Why were only 800 of 805 files converted? Of the 805 files, 800 of them belonged to the series you were converting. The other files were either non-dicom or dicoms but not in your series (eg, a localizer). 3 - As it says at the end of the output, the axial plane is flipped. Is there any way I can prevent this? The axial plane is not actually flipped. The msg: INFO: set hdr.hist.orient to 'transverse flipped' means that a flag in the header is set to 'transverse flipped'. I don't know what software packages actually use this info. SPM will/should read the .mat file created instead of the orient field in the hdr. doug Thanks for your help, Alex mri_convert -it siemens_dicom 21851740 -ot spm ../test mri_convert -it siemens_dicom 21851740 -ot spm ../test reading from 21851740... Getting Series No Scanning Directory INFO: Found 807 files in /data/flanders/work/alex/freesurfer/subjects_pace/epi_test/04271947 INFO: Scanning for Series Number 2 INFO: found 800 files in series INFO: loading series header info. INFO: sorting. RunNo = 1 INFO: ( 64 60 21), nframes = 800, ismosaic=1 Numaris Version: syngo MR 2004V 4VB11D Maj = 4, Min=1, MinMin = 1 Computing TR with number of slices Repetition Time = 1420, TR = 29820 ms FileName /data/flanders/work/alex/freesurfer/subjects_pace/epi_test/04271947/21851800 Identification NumarisVersyngo MR 2004V 4VB11D ScannerModel Avanto PatientName Fornito^Alex^^^Mr Date and time StudyDate 20060427 StudyTime 192350.703000 SeriesTime192556.781000 AcqTime 192554.055005 Acquisition parameters PulseSeq epfid2d1_60 Protocol ep2d_800 PhEncDir COL EchoNo0 FlipAngle 78 EchoTime 26 InversionTime 26 RepetitionTime1420 PhEncFOV 206.25 ReadoutFOV220 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows300 NImageCols320 NFrames 800 SliceArraylSize 21 IsMosaic 1 ImgPos106.2426 139.4769 -20.2630 VolRes 3.4375 3.4375 5. VolDim 64 60 21 Vc -0.9981 -0.0053 0.0606 Vr 0. -0.9962 -0.0873 Vs 0.0608 -0.0872 0.9943 VolCenter -0.3610 31.5859 29.5993 TransferSyntaxUID 1.2.840.10008.1.2.1 should never get here INFO: no Siemens slice order reversal detected (good!). TR=29820.00, TE=26.00, TI=26.00, flip angle=78.00 i_ras = (-0.998149, -0.00531035, 0.0605839) j_ras = (3.3967e-08, -0.996181, -0.0873174) k_ras = (0.0608162, -0.0871557, 0.994337) writing to ../test... Analyze Output Matrix -3.431 0.000 0.304 109.370; -0.018 -3.424 -0.436 143.355; 0.208 -0.300 4.972 -25.143; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' INFO: set hdr.hist.orient to 'transverse flipped' ... Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] functional overlay onto the occiptal patch with fieldsign
Hi Dear FreeSurfers, I'm using the new version of FreeSurfer to process retinotopic data. I can view the finial results of eccen, polar and fieldsign on the occiptal patch. Now I want to overlay another block designed activations onto the fieldsign patch with file---load overlay--select the corresponding fsig_000.bfloat---select register.dat---OK, but actually no activations appeared on the patch altough the fsig_000.bfloat can be shown on the overlay layer. Would smeone let me know how to overlay the functional activations onto the retinotopic patch? Thanks in advance! Lei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] roisummary and FIR
Hi, I am running roisummary with an FIR analysis with a 25s timewindow, 5s prestim and TR=2.5s. I In the summary output I receive 10 nestpercond but shouldn't I receive 11 with these parameters? timecourse: -5.0 -2.5 0.0 2.5 5.0 7.5 10.0 12.5 15.0 17.5 20.0 timepoint: 01 2 3 4 56789 10 I did not mask the roi. If I should only receive 10 nestpercond which timepoint is left out? Thanks in advance. Cameron ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] functional overlay onto the occiptal patch with fieldsign
Are you sure the viewing threshold is set correctly for that data? Check out the View-Configure-Overlay dialog box and try changing the values. On Wed, Oct 04, 2006 at 03:22:54PM +0200, [EMAIL PROTECTED] wrote: Hi Dear FreeSurfers, I'm using the new version of FreeSurfer to process retinotopic data. I can view the finial results of eccen, polar and fieldsign on the occiptal patch. Now I want to overlay another block designed activations onto the fieldsign patch with file---load overlay--select the corresponding fsig_000.bfloat---select register.dat---OK, but actually no activations appeared on the patch altough the fsig_000.bfloat can be shown on the overlay layer. Would smeone let me know how to overlay the functional activations onto the retinotopic patch? Thanks in advance! Lei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] roisummary and FIR
Hi Cameron, there's no missing time point, that window does cover 25 sec as the last time point covers 20-22.5. doug Cameron Ellis wrote: Hi, I am running roisummary with an FIR analysis with a 25s timewindow, 5s prestim and TR=2.5s. I In the summary output I receive 10 nestpercond but shouldn't I receive 11 with these parameters? timecourse: -5.0 -2.5 0.0 2.5 5.0 7.5 10.0 12.5 15.0 17.5 20.0 timepoint: 01 2 3 4 56789 10 I did not mask the roi. If I should only receive 10 nestpercond which timepoint is left out? Thanks in advance. Cameron ___ 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] roisummary and FIR
I THINK your last timepoint shld be 17.5 which covers from 17.5 - 20 and makes the timewindow 25 sec. so, yu will have 10 timepoints in total. Balaji Cameron Ellis Hi, I am running roisummary with an FIR analysis with a 25s timewindow, 5s prestim and TR=2.5s. I In the summary output I receive 10 nestpercond but shouldn't I receive 11 with these parameters? timecourse: -5.0 -2.5 0.0 2.5 5.0 7.5 10.0 12.5 15.0 17.5 20.0 timepoint: 01 2 3 4 56789 10 I did not mask the roi. If I should only receive 10 nestpercond which timepoint is left out? Thanks in advance. Cameron ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Balaji M Lakshmanan M.S. Research Technologist Mass. General Hospital (East) e-mail: [EMAIL PROTECTED] Phone: 617-726-9189 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] corrupted curvature file
Hi Balaji, from the surf dir mris_curvature -a 10 -w ./lh.white mv lh.white.H lh.curv should do it Bruce On Wed, 4 Oct 2006, Balaji Lakshmanan wrote: Dear all, One of our subjects have a corrupted curvature file(lh.curv) due to some overwriting. This subject was reconstructed using older version of freesurfer. I would like to know which step/command should I rerun in order to retrieve this file. Thanks in advance, Balaji ___ 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
