[Freesurfer] Version compatability
Hi, Is it a problem combining results from data processed using versions 3.03, 3.04, and 3.05? I have some data processed on 3.03 but I'm updating other machines and I'd like to install 3.05. Thanks, Alex Alex Fornito JN Peters Research Fellow 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 1861 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert orientation
Hi, I'm trying to convert a series of siemens dicom mosaic format files to analyze format, while reorienting at the same time. Running the command below converts and reorients only the filename specified in the command line (which is the first file in the series), whereas leaving out the --out_orientation flag converts all the files in the series. Is it only possible to convert AND reorient one file at a time? Or is there something I'm missing that would allow me to convert and reorient all the files in the series with a single command? Thanks, Alex mri_convert -it siemens_dicom 93663320 -ot analyze test_ --out_orientation LPS Alex Fornito JN Peters Research Fellow 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 1861 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 https
[Freesurfer] Converting DICOMs
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? 2 - Why were only 800 of 805 files converted? 3 - As it says at the end of the output, the axial plane is flipped. Is there any way I can prevent this? 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] ROI Curvature
No, I don't need signed values necessarily. So just to double-check then, higher mean curvature for averaged across a gyral ROI label would mean the gyrus has a more steeply peaked appearance, whereas high values for a sulcal label would, conversely, mean the sulcus resembles a shraply bended valley? 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] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 10:21 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature p.s. sorry, the mean and Gaussian curvatures displayed in mris_anatomical_stats are absolute value. I forgot this, sorry. The integrate Gaussian curvature is actually a topological invariant, so doesn't tell you much about the surface. Do you really need signed mean curvaature averaged over a region? If so, you could specify -T curv, so that the thickness is actually the curvature, and it will give you the mean and std. Bruce On Fri, 26 May 2006, Fornito, Alexander wrote: Yup. That looks fine. 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] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 9:44 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature when you overlay the ?h.curv file on the inflated surface does it look correct? Are there both red and green regions? On Fri, 26 May 2006, Fornito, Alexander wrote: I mainly interested in the mean curvature. This is output for a gyral ROI: % 1001365: wm vol surf area gray vol thick mean thick var integ rect. mean curv integ rect. Gauss curv fold index intr curv ind 647773 395 12973.145 0.780 0.151 0.027 4.123 0.572 This is for a sulcal ROI; % 1001365: wm vol surf area gray vol thick mean thick var integ rect. mean curv integ rect. Gauss curv fold index intr curv ind 647773 563 16932.992 0.567 0.121 0.068 48.616 4.783 Cheers, Alex 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] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 5/26/2006 8:32 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature which curvature values. Can you send the output? On Fri, 26 May 2006, Fornito, Alexander wrote: Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned? 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] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature Hi Alex, the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check. cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote: Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive
[Freesurfer] ROI Curvature
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing? Thanks in advance, Alex 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] 3T problems
Hi Bruce, It doesn't look good; actually, I can't see anything when I load it in tkmedit. If I re-run the alignment with mritotal as described in the manual (Final objective function value = 0.38553751), I do get an image, although it appears shrunken. Not sure what might cause this, or how to fix. 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] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 4/28/2006 1:35 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 3T problems did you check the talairach? On Fri, 28 Apr 2006, Fornito, Alexander wrote: Hi, I'm trying to segment some Siemens 3T images (200x200x256; 1mm3) and have encountered some problems at autorecon1 - the normalization seems to label some of the background as white matter. Needless to say, the skullstrip fails spectacularly. I've attached a snapshot of the T1 image showing the problem.Any ideas as to why this might occur? I'm running recon-all version 1.104 Thanks, Alex 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Repeated-measures in mris_glm
make_average_subject did the trick. However, although I can load the lh results as an overlay in tksurfer, if I try to adjust the display settings through View Configure Overlay, tksurfer crashes and I get the message below. I don't have this problem when overlaying the rh results. tksurfer average lh smoothwm surfer: current subjects dir: /data/nelson/work/alex/freesurfer/subjects_twins surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/nelson/work/alex/freesurfer/subjects_twins ERROR: cound not stat /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1/COR-.info. Does it exist? mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgh, -1): could not open file surfer: Reading header info from /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz surfer: vertices=163842, faces=327680 corRead(): can't open file /data/nelson/work/alex/freesurfer/subjects_twins/average/surf/../mri/orig/COR-.info MRISreadVertexPosition(/data/nelson/work/alex/freesurfer/subjects_twins/average/surf/lh.orig): could not open file /data/nelson/work/alex/freesurfer/subjects_twins/average/surf/lh.orig No such file or directory MRISreadOriginalProperties: could not read surface file /data/nelson/work/alex/freesurfer/subjects_twins/average/surf/lh.orig No such file or directory surfer: single buffered window Xlib: extension XFree86-DRI missing on display :0.0. surfer: using interface /usr/local/freesurfer-dev20050905/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer-dev20050905/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer-dev20050905/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer-dev20050905/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer-dev20050905/lib/tcl/tkUtils.tcl Read /usr/local/freesurfer-dev20050905/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % offset is 0.25 surfer: reading canonical coordinates from surfer: /data/nelson/work/alex/freesurfer/subjects_twins/average/surf/lh.sphere.reg too big, x major ticks can't be 8002 Abort 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] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 4/13/2006 1:45 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm Try using make_average_subject. That will create a T1 volume. Alternatively, you can run make_average_volume, which will just do the volume (make_average_subject will re-do the volume). Or even faster would be to copy the T1 volume from average7 or talairach into your average subject mri dir. You can do this and see if the problem goes away. doug Fornito, Alexander wrote: I craeted the average using make_average_surface. An average/mri/T1 directory gets created, but nothing is in there. There is no T1 volume at all. Is this because I'm using an older version of recon-all (v 1.104 2005/09/07)? Could this also explain my trouble creating scatterplots? 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] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Wed 4/12/2006 2:42 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm How did you create the average subject? Is there a T1.mgz in the mri dir? If so, you might have an old version of tksurfer that is looking for COR files instead of mgz. Fornito, Alexander wrote: That did the trick, but I'm having trouble displaying the results. First issue is that I can't seem to load my average surface in tksurfer from the command line.I get the following: tksurfer average rh inflated surfer: current subjects dir: /data/nelson/work/alex/freesurfer/subjects_twins surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/nelson/work/alex/freesurfer/subjects_twins ERROR: cound not stat /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1/COR-.info. Does it exist? mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgh, -1): could not open file zcat: /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz.gz: No such file or directory mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz, -1): read error surfer: ### Could not find anatomical
RE: [Freesurfer] Repeated-measures in mris_glm
I craeted the average using make_average_surface. An average/mri/T1 directory gets created, but nothing is in there. There is no T1 volume at all. Is this because I'm using an older version of recon-all (v 1.104 2005/09/07)? Could this also explain my trouble creating scatterplots? 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] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Wed 4/12/2006 2:42 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm How did you create the average subject? Is there a T1.mgz in the mri dir? If so, you might have an old version of tksurfer that is looking for COR files instead of mgz. Fornito, Alexander wrote: That did the trick, but I'm having trouble displaying the results. First issue is that I can't seem to load my average surface in tksurfer from the command line.I get the following: tksurfer average rh inflated surfer: current subjects dir: /data/nelson/work/alex/freesurfer/subjects_twins surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/nelson/work/alex/freesurfer/subjects_twins ERROR: cound not stat /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1/COR-.info. Does it exist? mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgh, -1): could not open file zcat: /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz.gz: No such file or directory mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz, -1): read error surfer: ### Could not find anatomical header information. What I do instead is load a subject's surface and then click load Surface, and select the average one. When I load the sigt file as an overlay, what should I specify as the registration matrix? Clicking calculate identity matrix seems to work, so I'm assuming this is ok? After doing this, I can visualize the SPM ok, but have trouble when I try to obtain scatterplots for a gven vertex. tksurfer closes and I get the error below.(I've tried specifying markers and colors in the FSGD but it doesn't seem to make a difference) I'm using recon-all-nmr,v 1.104 2005/09/07. gdfReadHeader: reading /data/nelson/work/alex/freesurfer/subjects_twins/stats/twin_qualcheck_fsgd.txt WARNING: Marker for class class_subj1 was invalid. WARNING: Color for class class_subj1 was invalid. WARNING: Marker for class class_subj2 was invalid. WARNING: Color for class class_subj2 was invalid. WARNING: Marker for class class_subj3 was invalid. WARNING: Color for class class_subj3 was invalid. WARNING: Marker for class class_subj4 was invalid. WARNING: Color for class class_subj4 was invalid. WARNING: Marker for class class_subj5 was invalid. WARNING: Color for class class_subj5 was invalid. surfer: dmin=0.8701, vno=132952, x=14.6850, y=-30.1178, z=47.7694 % surfer: curv=0.00, fs=0.00 % surfer: val=2.132707, val2=0.00 % surfer: amp=2.132707, angle=0.00 deg (0.00) Thanks again, A Oh, I'm sorry. I see the problem now. When I said to create a class for each subject, I meant for each person, not for each FreeSurfer subject. So there should only be 5 classes, not 10. So do something like this: Class class_subj1 Class class_subj2 Class class_subj3 Class class_subj4 Class class_subj5 Variables Time Input time1_subj1 class_subj1 -1 Input time2_subj1 class_subj1 +1 ... doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: I still get the same error message. Maybe I've coded the variable wrong? gdfReadHeader: reading ./test_fsgd.txt INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) = ncols (11) 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] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 4/11/2006 11:43 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Repeated-measures in mris_glm Yes, mris_preproc is new with stable. In your FSGD file, try specifying the title as a single string without spaces. doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: Hi Doug, Is mri_preproc a new addition to the stable version? I'm using recon-all-nmr,v 1.104 2005/09/07 and can't seem to find it. I tried running the analysis through mris_glm as per option 1 as you described, but came across a problem. Command
[Freesurfer] Repeated-measures in mris_glm
Hi, I'd like to run a simple repeated-measures analysis tetsing for change in thickness measures between 2 time points. There is no between-subjects factor, only the effect of time. Do I just set up a standard DOSS FSGD file, or do I use a different format? The tutorial only covers between-subjects designs. Thanks, Alex 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Repeated-measures in mris_glm
Hi Doug, Is mri_preproc a new addition to the stable version? I'm using recon-all-nmr,v 1.104 2005/09/07 and can't seem to find it. I tried running the analysis through mris_glm as per option 1 as you described, but came across a problem. Command, error, and my FSGD are below. Thanks, Alex Command: mris_glm --surfmeas thickness --hemi lh --trgsubj ../average --fsgd ./test_fsgd.txt doss --beta ./beta_doss_thickness-100_lh bfloat --var ./var_doss_thickness-100_lh.w paint --y ./y_doss_thickness-100_lh_000.bfloat --nsmooth 100 gdfReadHeader: reading ./test_fsgd.txt INFO: ignoring tag 1 INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) = ncols (11) My FSGD: GroupDescriptorFile 1 Title Time 1 vs Time 2 Class class_time1_subj1 Class class_time1_subj2 Class class_time1_subj3 Class class_time1_subj4 Class class_time1_subj5 Class class_time2_subj1 Class class_time2_subj2 Class class_time2_subj3 Class class_time2_subj4 Class class_time2_subj5 Variables Time Input time1_subj1 class_time1_subj1 -1 Input time1_subj2 class_time1_subj2 -1 Input time1_subj3 class_time1_subj3 -1 Input time1_subj4 class_time1_subj4 -1 Input time1_subj5 class_time1_subj5 -1 Input time2_subj1 class_time2_subj1 1 Input time2_subj2 class_time2_subj2 1 Input time2_subj3 class_time2_subj3 1 Input time2_subj4 class_time2_subj4 1 Input time2_subj5 class_time2_subj5 1 DefaultVariable Time 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] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 4/11/2006 9:31 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm There are two ways to do it: 1. You can use DOSS, making each subject it's own class. Then create one Variable. For a given input, set the variable to either +1 or -1 depending upon whether it corresponds to the first or second time point. Then create a contrast as [0 0 0 0 ... 0 0 0 1], where there are as many 0s as subjects. The last 1 will correspond to the Time Point variable. 2. Alternatively, if you are using mris_preproc, you can specify --paired-diff, then just use a one-sample group mean test. See the --help. This may be easier, and will also allow you to add a between subject factor. doug Fornito, Alexander wrote: Hi, I'd like to run a simple repeated-measures analysis tetsing for change in thickness measures between 2 time points. There is no between-subjects factor, only the effect of time. Do I just set up a standard DOSS FSGD file, or do I use a different format? The tutorial only covers between-subjects designs. Thanks, Alex 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 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] Repeated-measures in mris_glm
I still get the same error message. Maybe I've coded the variable wrong? gdfReadHeader: reading ./test_fsgd.txt INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) = ncols (11) 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] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 4/11/2006 11:43 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Repeated-measures in mris_glm Yes, mris_preproc is new with stable. In your FSGD file, try specifying the title as a single string without spaces. doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: Hi Doug, Is mri_preproc a new addition to the stable version? I'm using recon-all-nmr,v 1.104 2005/09/07 and can't seem to find it. I tried running the analysis through mris_glm as per option 1 as you described, but came across a problem. Command, error, and my FSGD are below. Thanks, Alex Command: mris_glm --surfmeas thickness --hemi lh --trgsubj ../average --fsgd ./test_fsgd.txt doss --beta ./beta_doss_thickness-100_lh bfloat --var ./var_doss_thickness-100_lh.w paint --y ./y_doss_thickness-100_lh_000.bfloat --nsmooth 100 gdfReadHeader: reading ./test_fsgd.txt INFO: ignoring tag 1 INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) = ncols (11) My FSGD: GroupDescriptorFile 1 Title Time 1 vs Time 2 Class class_time1_subj1 Class class_time1_subj2 Class class_time1_subj3 Class class_time1_subj4 Class class_time1_subj5 Class class_time2_subj1 Class class_time2_subj2 Class class_time2_subj3 Class class_time2_subj4 Class class_time2_subj5 Variables Time Input time1_subj1 class_time1_subj1 -1 Input time1_subj2 class_time1_subj2 -1 Input time1_subj3 class_time1_subj3 -1 Input time1_subj4 class_time1_subj4 -1 Input time1_subj5 class_time1_subj5 -1 Input time2_subj1 class_time2_subj11 Input time2_subj2 class_time2_subj21 Input time2_subj3 class_time2_subj31 Input time2_subj4 class_time2_subj41 Input time2_subj5 class_time2_subj51 DefaultVariable Time 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] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 4/11/2006 9:31 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm There are two ways to do it: 1. You can use DOSS, making each subject it's own class. Then create one Variable. For a given input, set the variable to either +1 or -1 depending upon whether it corresponds to the first or second time point. Then create a contrast as [0 0 0 0 ... 0 0 0 1], where there are as many 0s as subjects. The last 1 will correspond to the Time Point variable. 2. Alternatively, if you are using mris_preproc, you can specify --paired-diff, then just use a one-sample group mean test. See the --help. This may be easier, and will also allow you to add a between subject factor. doug Fornito, Alexander wrote: Hi, I'd like to run a simple repeated-measures analysis tetsing for change in thickness measures between 2 time points. There is no between-subjects factor, only the effect of time. Do I just set up a standard DOSS FSGD file, or do I use a different format? The tutorial only covers between-subjects designs. Thanks, Alex 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 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] MNI coords
You're right, I actually did move them a while ago and completely forgot. The command did the trick though. Thanks! 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] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 4/6/2006 11:03 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] MNI coords Hi Alex, you should get the MNI coords for all your subjects - recon-all runs the MNI talairach procedure. Did you move things around on disk? I think there are times that it can't find the xform anymore because it is in a different location than when you ran recon-all. See if there is a talairach.xfm in the subjects mri/transforms directory for one of the ones you don't get MNI coords. If it's there and you're not getting MNI coords, try using mri_add_xform_to_header full path to talairach.xfm input vol output vol cheers, Bruce On Thu, 6 Apr 2006, Fornito, Alexander wrote: Hi Bruce, I tried using the volume scanner coords (which were identical to the RAS coords), but this didn't seem to do the trick; the cutting plane was still skewed away from the true midline. After re-running some of my images using the volume scanner coords, I've noticed that I now have the MNI coords. However, I still didn't get them for some images. Is there a flag or command that I can specify to ensure that I do obtain the MNI coords? Thanks, Alex 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] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 3/30/2006 11:41 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MNI coords Hi Alex, try volume scanner coords for the subjects that don't have the MNI coords. Sorry, I know this is more confusing than it needs to be. In the new version you just specify voxel coords :) Bruce On Thu, 30 Mar 2006, Fornito, Alexander wrote: Hi, I need to manually specify a seed point for the corpus callosum cutting plane on some of my images, although some of them don't seem to have the MNI coordiates available through clicking view information in tkmedit. Not sure why this is the case, since other images do have this info. Specifying the RAS coord doens't fix the problem. I'm using recon-all version 1.104 2005/09/07 (I'm trying to finish off a study using the dev version and wold dearly like to avoid re-processing everyone with a newer version!!). Any help is much appreciated. Many thanks, Alex 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 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] MNI coords
Hi, I need to manually specify a seed point for the corpus callosum cutting plane on some of my images, although some of them don't seem to have the MNI coordiates available through clicking view information in tkmedit. Not sure why this is the case, since other images do have this info. Specifying the RAS coord doens't fix the problem. I'm using recon-all version 1.104 2005/09/07 (I'm trying to finish off a study using the dev version and wold dearly like to avoid re-processing everyone with a newer version!!). Any help is much appreciated. Many thanks, Alex 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] MNI coords
No problem. Thanks again! 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] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 3/30/2006 11:41 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MNI coords Hi Alex, try volume scanner coords for the subjects that don't have the MNI coords. Sorry, I know this is more confusing than it needs to be. In the new version you just specify voxel coords :) Bruce On Thu, 30 Mar 2006, Fornito, Alexander wrote: Hi, I need to manually specify a seed point for the corpus callosum cutting plane on some of my images, although some of them don't seem to have the MNI coordiates available through clicking view information in tkmedit. Not sure why this is the case, since other images do have this info. Specifying the RAS coord doens't fix the problem. I'm using recon-all version 1.104 2005/09/07 (I'm trying to finish off a study using the dev version and wold dearly like to avoid re-processing everyone with a newer version!!). Any help is much appreciated. Many thanks, Alex 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 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] tcl and annotations
Hi, Is there any way to 'automatically' save the labels in an annotation file using a -tcl script (or some other way) for a set of subjects? Thanks Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert orientation
Hi, I'm trying to reorient some analyze files using mri_convert. The files are in LAS format and I'd like to get them in LPI format. i run the command below, but get the message: mri_convert: unknown flag --in-orientation mri_convert -it analyze 101_lh_bound_gs -ot analyze ./101_lh_bound_gs_r.img --in-orientation LAS --out-orientation LPI Any help is much appreciated! Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] control points
Hi, I've generally been successful in using control points to get the white surfaces into darker areas, where the white matter appears similar to grey matter. I'm wandering if it's possible to use control points (or any other remedy) to get make the white matter segmentation less 'harsh', i.e., for some of my images, the white surface seems to consistently eat into the grey matter, so I wonder if it's possible to lower the threshold of what it calls grey in some way. Thanks Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Essential ingredients for labels
It was a bug at our end. Sorry!! Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 17/01/2006 11:42 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Essential ingredients for labels Hi Alex, send us the label and we'll have a look. Bruce On Tue, 17 Jan 2006, Fornito, Alexander wrote: Hi, I'm trying to create some custom labels using matlab, but haven't had much luck. From what I've read on the FAQ page, the last two columnns are optional, so I've left them out. My label file therefore has 4 columns - vertex ID, and x y z, with the total number of vertices at the top. When I try to load the label in tksurfer I get a message saying % tksurfer: could not parse 401th line in /data/flanders/work/alex/freesurfer/subjects_fe/101/matlab_results/101_rh.label Where 401th line is the final line in the label file. I'm not sure if this is because I've ommitted the final two columns usually present in the standard label files, or if there's something else I'm missing. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ 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] Essential ingredients for labels
Hi, I'm trying to create some custom labels using matlab, but haven't had much luck. From what I've read on the FAQ page, the last two columnns are optional, so I've left them out. My label file therefore has 4 columns - vertex ID, and x y z, with the total number of vertices at the top. When I try to load the label in tksurfer I get a message saying % tksurfer: could not parse 401th line in /data/flanders/work/alex/freesurfer/subjects_fe/101/matlab_results/101_rh.label Where 401th line is the final line in the label file. I'm not sure if this is because I've ommitted the final two columns usually present in the standard label files, or if there's something else I'm missing. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Which white?
Hi, I've got a few reltively simple questions that I'm sure I've seen the answers to before but can't seem to find them again. What is the difference between ?h.orig, ?h.white, and ?h.smoothwm? Which one is automatically brought up in tkmedit when ?h.pial is loaded as a surface? Which is usd in the thickness calculations? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] rh and lh neighbour error
Hi, I've been getting the following error message when running autorecon2-wm with some of my images.Any idea as to what might be causing this? Thanks, Alex Fill Fri Jan 6 14:15:18 EST 2006 Using transforms/talairach.lta mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz /data/flanders/work/alex/freesurfer/subjects_fe/1000795_fixwm/mri logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.120 0.025 -0.148 4.472; 0.007 1.256 0.182 -50.337; 0.160 -0.148 1.109 -29.027; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.120 0.025 -0.148 4.472; 0.007 1.256 0.182 -50.337; 0.160 -0.148 1.109 -29.027; 0.000 0.000 0.000 1.000; mri_fill: could not find any points where lh and rh wm are nbrs INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst reading segmented volume aseg.mgz... INFO: Modifying dst c_(r,a,s), using the transform dst ERROR: mri_fill exited with non-zero status Linux flanders 2.4.26 #2 SMP Tue Dec 14 03:07:23 EST 2004 i686 GNU/Linux recon-all exited with errors at Fri Jan 6 14:16:07 EST 2006 Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] .sulc in tksurfer
Great, thanks. On another issue, I've noticed that using mris_convert to convert ?h.area to ascii produces the same area values in the resulting file, irrepsective of whether pial or white surfaces are specified in the command. This contrasts mris_anatomical_stats, which gives different values. Is it possible to extract pial and white surface area separately for sulcal and gyral regions? Thanks again, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 5/01/2006 12:42 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] .sulc in tksurfer yes, that makes sense. On Wed, 4 Jan 2006, Fornito, Alexander wrote: Hi Bruce, I'm trying to extract thickness for sulci and gyri separately. From what I understand, positive .sulc values suggest sulci and negative .sulc values suggest gyri. I'd like to play around with this distinction (e.g., call everything with a .sulc value .35 'gyral'), and am wandering if adjusting the midpoint in tksurfer allows me to precisly visualize what changing this threshold does. Basically, I'd like to know if it's correct for me to pick a midpoint I'm happy with in tksurfer, say .35, than go back and split the .thickness file into vertices with .sulc values above and below .35, knowing that this distinction between sulcal and gyral will correspond to the one shown by the colour display I visualized in tksurfer. I'm pretty sure the values in the tksurfer threshold midpoint scale correspond to those in the curvature file, since they seem to change depednig on the curvature file loaded (e.g., the range for .sulc files is different to the range for .thickness files). Just want to double-check. Hope this makes sense, Alex the threshold midpoint in the curvature display just sets where the transition is from red to green (or light gray to dark gray if using binary colors) On Wed, 4 Jan 2006, Fornito, Alexander wrote: Hi, Does the 'threshold midpoint' value in tksurfer's curvature display control correspond to values in the .sulc file (assuming the .sulc file is loaded), or are they arbitrary values? For example, if I set the value to .50, does this make all vertices with a .sulc value of .50 or less lighter (lighter, if using binary colouring)? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ 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] tksurfer script
Thanks Kevin. Is it possible to load overlays through a script as well? Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Kevin Teich [mailto:[EMAIL PROTECTED] Sent: Wed 28/12/2005 11:40 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer script labl_load_color_table filename On Wed, Dec 28, 2005 at 04:06:08PM +1100, Fornito, Alexander wrote: Is there any way to load a colour look-up table through tksurfer scripting? I can't seem to see any options in the usage. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Sulcal depth
Hi Doug, I tried what you suggested but don't think sure I've got it right. I'm trying to extract thickness for gyri and sulci separately in labels that I have created and saved as an annotation. I began by using mri_surf2surf to convert the thickness and sulc files to mgh - no errors, although trying to load either in tkmedit just brings up a straight, coloured line running ear to ear (not sure if this is what to expect) . I then comverted the annot file to mgh using mri_label2vol - seemed ok (although one of the labels in the annot did not seem to appear in the resulting volume). I then ran mri_segstats and got the following: mri_segstats --seg annot_vol.mgh --sum ./annot_stats.txt --in 101_thickness_conv.mgh --ctab /usr/local/freesurfer-dev20050905/alex_ACC_colour_LUT.txt --mask 101_sulc_conv.mgh --masksign pos Loading annot_vol.mgh Loading 101_thickness_conv.mgh Loading 101_sulc_conv.mgh NOT INVERTING There were 28632 voxels in the mask Segmentation fault Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 10:33 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth you might be able to use mri_segstats. Give it the thickness file as --in, and use the sulc as the mask and use a threshold of 0 (or close to 0). Note, you might have to convert the thickness and sulc from curv format to mgh (use mri_surf2surf). doug What it require a lot of work? What would be the odds of somehting like that happening in the near future? :) On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral regions separately? I remember seeing a posting about this some time ago, bu can't seem to find it again. Thanks again. Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth not all that easily, although I guess we could write out something from mris_inflate that has the units of mm. On Fri, 23 Dec 2005, Fornito, Alexander wrote: Hi all, From my understanding, ?h.sulc can be used to measure sulcal depth. I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ 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] Sulcal depth
Hi all, From my understanding, ?h.sulc can be used to measure sulcal depth. I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Sulcal depth
What it require a lot of work? What would be the odds of somehting like that happening in the near future? :) On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral regions separately? I remember seeing a posting about this some time ago, bu can't seem to find it again. Thanks again. Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth not all that easily, although I guess we could write out something from mris_inflate that has the units of mm. On Fri, 23 Dec 2005, Fornito, Alexander wrote: Hi all, From my understanding, ?h.sulc can be used to measure sulcal depth. I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ 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] Sulcal depth
Famous last words, but seems simple enough. Will give it a try. Would just like to clarify what the columns represent in curvature files after converting to ascii: The first volumn is the vertx id. The next three columns are the xyz co-ords. The rightmost column is the actual 'curvature value', e.g., in thickness file, it's the thickness associated with that vertex, in the sulc file, it's the integrated the distnace the node moves during inflation, etc.. In which case, for extracting sulcal and gyral regions separately, I'd need to split vertices based on the sign of the final column in the sulc file. Another question: are the xyz coords talairach or native coords? They're not surface coords are they? I would've thought surface coords would be in 2D (although I have been known to get it completely wrong form time to time!). Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 10:36 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth sure, just sum them separately. Would be easy to do in matlab (we did it in our PNAS thickness paper) On Fri, 23 Dec 2005, Fornito, Alexander wrote: What it require a lot of work? What would be the odds of somehting like that happening in the near future? :) On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral regions separately? I remember seeing a posting about this some time ago, bu can't seem to find it again. Thanks again. Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth not all that easily, although I guess we could write out something from mris_inflate that has the units of mm. On Fri, 23 Dec 2005, Fornito, Alexander wrote: Hi all, From my understanding, ?h.sulc can be used to measure sulcal depth. I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ 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] Sulcal depth
So, read_label could be used to load the label in, and then that could be used to pull out the relevant vertices from the .thickness and .sulc files? Also, is there a straightforward way of converting the final column in the .sulc file into mm (as in mm sulcal depth)? Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 11:29 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth I think they are volume RAS coords, with 0,0,0 at the center of the volume. I think we distribute a read_label.m or load_label.m that can read it into matlab. On Fri, 23 Dec 2005, Fornito, Alexander wrote: Famous last words, but seems simple enough. Will give it a try. Would just like to clarify what the columns represent in curvature files after converting to ascii: The first volumn is the vertx id. The next three columns are the xyz co-ords. The rightmost column is the actual 'curvature value', e.g., in thickness file, it's the thickness associated with that vertex, in the sulc file, it's the integrated the distnace the node moves during inflation, etc.. In which case, for extracting sulcal and gyral regions separately, I'd need to split vertices based on the sign of the final column in the sulc file. Another question: are the xyz coords talairach or native coords? They're not surface coords are they? I would've thought surface coords would be in 2D (although I have been known to get it completely wrong form time to time!). Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 10:36 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth sure, just sum them separately. Would be easy to do in matlab (we did it in our PNAS thickness paper) On Fri, 23 Dec 2005, Fornito, Alexander wrote: What it require a lot of work? What would be the odds of somehting like that happening in the near future? :) On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral regions separately? I remember seeing a posting about this some time ago, bu can't seem to find it again. Thanks again. Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth not all that easily, although I guess we could write out something from mris_inflate that has the units of mm. On Fri, 23 Dec 2005, Fornito, Alexander wrote: Hi all, From my understanding, ?h.sulc can be used to measure sulcal depth. I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ 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] Defining one's own atlas in FreeSurfer
Hi Bruce,
I;d like to take up your offer of sending a subject with the annot file, as I'm
quite stuck.
Where can I upload it to? I can't seem to find the link on the wiki.
Also, I only retained the mri, surf, and label subdirectories, although the tar
is still quite big (~125 MB). Are there specific files that you need?
Cheers,
Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 16/12/2005 12:25 PM
To: Fornito, Alexander
Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer
yes, sulc represents large scale structure of the folding patterns and
preferences deep folds over shallow ones, while curv is a differential
measure (mean curvature) and is much noiser. The sulc alignment comes
first and aligns the major folds, then the curv alignment moves secondary
folds such as the hand area into alignment where they are consistent.
Don't know why you can't create a .annot file. I'm waiting for Kevin to
respond. You could try sending us the subject with the .annot file and we
can take a look, or maybe the .xdebug_tksurfer file has some clue?
cheers,
Bruce
On
Fri, 16 Dec 2005, Fornito, Alexander wrote:
Hi Bruce,
Is there a reason why use sulc and curv together would be better than one
alone?
Also, any ideas as to why I can't create my annotations?
Thanks again for your help,
Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 16/12/2005 11:34 AM
To: Fornito, Alexander
Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer
-n 2 tells it to use 2 feature dimensions (sulc and curv)
-t fname tells it to use the color LUT in fname
On Fri, 16 Dec
2005, Fornito, Alexander wrote:
Hi,
I'm also trying to create my own custom atlas, but can't seem to create an
annotation file.
I load my files in tksurfer, than click the Export annotation option and
save the file.
When I then try to re-import the annotation, nothing appears, and I get the
message:
% surfer: WARNING: no labels imported; annotation was empty
Any help is much appreciated!
PS - Greg, I noticed that you used -n and -t in your command line. What do
these flags refer to? I can't seem to get options in the usage.
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
-Original Message-
From: [EMAIL PROTECTED] on behalf of Greg Harris
Sent: Thu 15/12/2005 4:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Defining one's own atlas in FreeSurfer
By snooping in the log files in scripts/ and considering the instruction
to train and then label with commands such as
mris_ca_train -n 2 -t ./iowa_gross_fs_colors.txt rh sphere.reg
iowa_gross_hand_parc ${SUBJECT_LIST} ./rh.iowa_gross_cort_parc.gcs
which prepares the way for
mris_ca_label ${SUBJECT} rh sphere.reg
/opt/freesurfer/average/rh.iowa_gross_cort_parc.gcs
it becomes evident that the -autorecon3 step applies the MGH standard
parcellation atlas from
/opt/freesurfer/average/[lr]h.curvature.buckner40.filled.desikan_killiany.gcs
and thus, the standard atlas is known as
curvature.buckner40.filled.desikan_killiany.
When we evaluate our own atlas, we compare hand-traced labels
with the labels produced by mris_ca_label.
Now my question: Is there a way we could access the training data
for curvature.buckner40.filled.desikan_killiany,
so we can compare how mris_ca_label approximates the MGH atlas's
gold standard with how it approximates the Iowa atlas's gold standard?
We are curious how many subjects went into the standard atlas at
mris_ca_train, too. Is there a paper (a pdf?) where this is reported?
Greg Harris
University of Iowa
Psychiatry Brain Imaging Lab
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RE: [Freesurfer] Defining one's own atlas in FreeSurfer
Hi Bruce,
Is there a reason why use sulc and curv together would be better than one alone?
Also, any ideas as to why I can't create my annotations?
Thanks again for your help,
Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 16/12/2005 11:34 AM
To: Fornito, Alexander
Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer
-n 2 tells it to use 2 feature dimensions (sulc and curv)
-t fname tells it to use the color LUT in fname
On Fri, 16 Dec
2005, Fornito, Alexander wrote:
Hi,
I'm also trying to create my own custom atlas, but can't seem to create an
annotation file.
I load my files in tksurfer, than click the Export annotation option and
save the file.
When I then try to re-import the annotation, nothing appears, and I get the
message:
% surfer: WARNING: no labels imported; annotation was empty
Any help is much appreciated!
PS - Greg, I noticed that you used -n and -t in your command line. What do
these flags refer to? I can't seem to get options in the usage.
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
-Original Message-
From: [EMAIL PROTECTED] on behalf of Greg Harris
Sent: Thu 15/12/2005 4:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Defining one's own atlas in FreeSurfer
By snooping in the log files in scripts/ and considering the instruction
to train and then label with commands such as
mris_ca_train -n 2 -t ./iowa_gross_fs_colors.txt rh sphere.reg
iowa_gross_hand_parc ${SUBJECT_LIST} ./rh.iowa_gross_cort_parc.gcs
which prepares the way for
mris_ca_label ${SUBJECT} rh sphere.reg
/opt/freesurfer/average/rh.iowa_gross_cort_parc.gcs
it becomes evident that the -autorecon3 step applies the MGH standard
parcellation atlas from
/opt/freesurfer/average/[lr]h.curvature.buckner40.filled.desikan_killiany.gcs
and thus, the standard atlas is known as
curvature.buckner40.filled.desikan_killiany.
When we evaluate our own atlas, we compare hand-traced labels
with the labels produced by mris_ca_label.
Now my question: Is there a way we could access the training data
for curvature.buckner40.filled.desikan_killiany,
so we can compare how mris_ca_label approximates the MGH atlas's
gold standard with how it approximates the Iowa atlas's gold standard?
We are curious how many subjects went into the standard atlas at
mris_ca_train, too. Is there a paper (a pdf?) where this is reported?
Greg Harris
University of Iowa
Psychiatry Brain Imaging Lab
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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RE: [Freesurfer] Defining one's own atlas in FreeSurfer
There doesn't seem to be a .xdebug file. How do you create one?
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 16/12/2005 12:25 PM
To: Fornito, Alexander
Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer
yes, sulc represents large scale structure of the folding patterns and
preferences deep folds over shallow ones, while curv is a differential
measure (mean curvature) and is much noiser. The sulc alignment comes
first and aligns the major folds, then the curv alignment moves secondary
folds such as the hand area into alignment where they are consistent.
Don't know why you can't create a .annot file. I'm waiting for Kevin to
respond. You could try sending us the subject with the .annot file and we
can take a look, or maybe the .xdebug_tksurfer file has some clue?
cheers,
Bruce
On
Fri, 16 Dec 2005, Fornito, Alexander wrote:
Hi Bruce,
Is there a reason why use sulc and curv together would be better than one
alone?
Also, any ideas as to why I can't create my annotations?
Thanks again for your help,
Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 16/12/2005 11:34 AM
To: Fornito, Alexander
Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer
-n 2 tells it to use 2 feature dimensions (sulc and curv)
-t fname tells it to use the color LUT in fname
On Fri, 16 Dec
2005, Fornito, Alexander wrote:
Hi,
I'm also trying to create my own custom atlas, but can't seem to create an
annotation file.
I load my files in tksurfer, than click the Export annotation option and
save the file.
When I then try to re-import the annotation, nothing appears, and I get the
message:
% surfer: WARNING: no labels imported; annotation was empty
Any help is much appreciated!
PS - Greg, I noticed that you used -n and -t in your command line. What do
these flags refer to? I can't seem to get options in the usage.
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
-Original Message-
From: [EMAIL PROTECTED] on behalf of Greg Harris
Sent: Thu 15/12/2005 4:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Defining one's own atlas in FreeSurfer
By snooping in the log files in scripts/ and considering the instruction
to train and then label with commands such as
mris_ca_train -n 2 -t ./iowa_gross_fs_colors.txt rh sphere.reg
iowa_gross_hand_parc ${SUBJECT_LIST} ./rh.iowa_gross_cort_parc.gcs
which prepares the way for
mris_ca_label ${SUBJECT} rh sphere.reg
/opt/freesurfer/average/rh.iowa_gross_cort_parc.gcs
it becomes evident that the -autorecon3 step applies the MGH standard
parcellation atlas from
/opt/freesurfer/average/[lr]h.curvature.buckner40.filled.desikan_killiany.gcs
and thus, the standard atlas is known as
curvature.buckner40.filled.desikan_killiany.
When we evaluate our own atlas, we compare hand-traced labels
with the labels produced by mris_ca_label.
Now my question: Is there a way we could access the training data
for curvature.buckner40.filled.desikan_killiany,
so we can compare how mris_ca_label approximates the MGH atlas's
gold standard with how it approximates the Iowa atlas's gold standard?
We are curious how many subjects went into the standard atlas at
mris_ca_train, too. Is there a paper (a pdf?) where this is reported?
Greg Harris
University of Iowa
Psychiatry Brain Imaging Lab
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RE: [Freesurfer] autorecon2-wm
That did the trick. Thanks! Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] on behalf of Nick Schmansky Sent: Thu 15/12/2005 9:46 AM To: Fornito, Alexander Cc: Freesurfer Mailing List; Marin Richardson; Sasha Wolosin Subject: RE: [Freesurfer] autorecon2-wm Alex, The file is actually called 'recon-all', so try: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all After that is copied to your $FREESURFER_HOME/bin directory, be sure to make it executable: chmod a+x $FREESURFER_HOME/bin/recon-all Nick On Thu, 2005-12-15 at 09:24 +1100, Fornito, Alexander wrote: Hi Doug, I tried to download this but get a No such file `recon-all-nmr' message. Cheers, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] on behalf of Doug Greve Sent: Wed 14/12/2005 6:02 AM To: Sasha Wolosin Cc: freesurfer@nmr.mgh.harvard.edu; Marin Richardson Subject: Re: [Freesurfer] autorecon2-wm I only recently (ie, last weekish) added a flag to keep the edits when wm is edited with aseg. You can get a new copy of recon all from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all-nmr dogu Sasha Wolosin wrote: Dear all, When we run autorecon2-wm it doesn't seem to be reading the editing done in the Edit WM With ASeg step. Looking at wm.mgz, none of the filling that we see after autorecon2 is present after autorecon2-wm. What's going wrong? Thanks, Marin Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ 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] Custom parcellation atlas
sorry, do you mean 1 annot per subject in the training set? I noticed that there is an 'export annotation' option in tksurfer. I figured it would be a matter of drawing my labels on each subject, then, while they're all loaded, clicking the 'export annotation' option and saving the file. However, if I do this and then try to load the annotation again, nothing appears. Am i missing something? Thanks again, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Sun 11/12/2005 12:34 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Custom parcellation atlas you need 1 annot/training subjects. The canonical surface is the ?h.sphere.reg. The annots can be created by drawing in tksurfer. cheers, Bruce On Sat, 10 Dec 2005, Fornito, Alexander wrote: Hi all, I would like to create my own custom parcellation atlas for the frontal lobes using labels that I have traced on the surfaces. From what I can gather from the mailing list, I need to use mris_ca_train to do this. The usage states indicates I need to specify a canonical surface and an annotation file, but I don't know how to create these. Also, I would have thought I would need to input one annotation file per subject, rather than the single one that is implied in the usage. Do need to do something else before I start using mris_ca_train? Any help is much appreciated. Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ 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_label2vol
From memory, the space between the two surface seems to have holes in it. UnfortunatelyI'm out of state atm, but aybe I can send you a pick when I get back next week to show you what I mean? Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 6/12/2005 9:50 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol Hmmm, when you say it looks splotch do you mean that it just looks pixelated? or that there are wholes in it? I would expect that the ribbon would fill in all the space between the two surfaces with some voxels jutting out beyond the surface. Your interpretation of delta is correct doug Fornito, Alexander wrote: Hi Doug, I tried lowering delta to really low values, eg., .001, but it doesn't seem change things much. Under ideal circumstances, would I expect the space between the white and pial surfaces to be completely filled? Also, I noted the -help states that delta is relative to the thickness at each vertex if -frac is used, but am a bit unsure of what this means. Does it mean that, for eg., if the vertex thickness is 3mm, then start = 0, stop = 1, delta = 0.5 will fill the entire 3mm space in increments of 1.5mm? Whereas if -abs is specified, start = 0, stop = 1, delta = 0.5 means that the space between 0 and 1mm from the specified surface will be filled, in increments of 0.5mm? Hope this makes sense and thanks again for your help, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 6/12/2005 6:10 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol From --help on mri_label2vol: --proj type start stop delta Project the label along the surface normal. type can be abs or frac. abs means that the start, stop, and delta are measured in mm. frac means that start, stop, and delta are relative to the thickness at each vertex. The label definition is changed to fill in label points in increments of delta from start to stop. Requires subject and hemi in order to load in a surface and thickness. Uses the white surface. The label MUST have been defined on the surface. Not sure why it's splotchy. Can you lower the delta? doug Fornito, Alexander wrote: I see. The ribbon actually looks like the result I got when i used mri_label2vol. So would I be correct in saying that a that using the flag -proj frac 0, 1, .1 will extract that protion of ?h.ribbon.mgz that is associated with the label? What exactly does delta (eg., .1) correspond to? How come the ribbon.mgz appears 'splotchy' (ie., the space between the white and pial surfaces is not completely filled.) Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Sat 3/12/2005 9:43 AM To: Fornito, Alexander Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2vol This is done in the newer versions of recon all. It creates subject/mri/?h.ribbon.mgz using mri_surf2vol. Here's what recon-all does: set cmd = (mri_surf2vol --mkmask --hemi $hemi) set cmd = ($cmd --fillribbon --template orig$MGZ) set cmd = ($cmd --volregidentity $subjid --outvol $hemi.ribbon.mgz) doug On Sat, 3 Dec 2005, Fornito, Alexander wrote: Hi, I'm wandering if its possible to convert a label into a volume so that it fills the space between the white and pial surfaces used in calculating thickness. That is, if the label is drawn on the wm surface, is is possible to determine what points on the pial surface are used to calculate the thickness of that label? I've been playing with the --proj option in mr_label2vol. The --help states that --proj frac means that start, stop, and delta are relative to the thickness at each vertex. I tried using the start, stop and delta values provided in the example (0, 1 .1), but it doesn't seem to completely fill the area between the two surfaces. I've also tried plugging in other values and can't seem to get it right.Is there soemthing I'm missing? Thanks, Alex Alex Fornito
[Freesurfer] mri_label2vol
Hi, I'm wandering if its possible to convert a label into a volume so that it fills the space between the white and pial surfaces used in calculating thickness. That is, if the label is drawn on the wm surface, is is possible to determine what points on the pial surface are used to calculate the thickness of that label? I've been playing with the --proj option in mr_label2vol. The --help states that --proj frac means that start, stop, and delta are relative to the thickness at each vertex. I tried using the start, stop and delta values provided in the example (0, 1 .1), but it doesn't seem to completely fill the area between the two surfaces. I've also tried plugging in other values and can't seem to get it right.Is there soemthing I'm missing? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Normalization problem
Hi, I've encountered similar problems. Do you know if it's specific to the autorecon2 flag? I'm wondering if running each process separately and sequentially get around it, e.g, running recon-all -normalization2, then recon-all -segmentation, then recon-all -fill, etc... Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] on behalf of Bruce Fischl Sent: Mon 21/11/2005 11:03 PM To: Martin Ystad Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Normalization problem Hi Martin, we're looking into it - it's probably a bug in recon-all. Bruce On Mon, 21 Nov 2005, Martin Ystad wrote: I'm working on the latest developmental release for Rh. 9. and I'm having problems with the normalization procedures on my datasets. My datasets have large intensity inhomogeneities due to their acquisition with a surface coil (8-ch. GE). To fix this problem I have resorted to the use of control points. This works if I add enough points across the brain ( over 200), and I get a better normalization result after running recon-all -normalization -usecontrolpoints and another skull-stripping on the new T1-volume. To test whether or not this produces a good segmentaition of white matter, I run mri_segment on my brain.mgz -volume. If I'm satisfied with the segmentation result, I move on to the surface processing stage, and run the -autorecon2 -script. The problem is that after running the -autorecon2, the normalization is completely wrong again, looking more like the first normalization done without control points, and the wm.mgz -volume is also bad. So are the surfaces. How do I make freesurfer produce the same good results as I got during the first normalization? Do I need to specify the use of control points again, even though the brain.mgz volume looks ok? Thanks, Martin Ystad Medical Student University of Bergen Institute of Biomedicine Jonas Lies vei 91, 5009 Bergen, Norway. ___ 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] labels in tksurfer
HI, Just wandering if there's any way to adjust the opacity of labels as displayed in tksurfer? I'd like to display a label on the inflate surface and still see the curvature underneath. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Control point problems
Hi, The orig (white matter) surface misses some spots in some of my images, particularly around the anterior temporal lobes. I've tried using control points, and although this segments the strands in the wm.mgz volume, the surface still does not capture the true grey/white interface. I've tried using a few control points as well as completely saturating the area with little change in results. Any tips would be much appreciated !! Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Control points
Hi, I was just after some more pointers on using control points. Some gyri are missed in some of my images, and using control points recovers them, but it also tends to make the wm surface eat into the grey matter in some regions. Just wandering if there's anyway to prevent this from happening? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] area file
Hi, I was just wandering what determines the area value assigned to a given vertex. Is it the average area of the faces of the triangles to which it is attached? If so, what determines the area of the traingle faces? Do the values in the ?.area file reflect regional variations in surface area? I'm wandering whether using the ?.area file in mris_glm would produce meaningful results (eg., a difference between groups would represent regional differences in surface area), or whether the area is determined by some feature of the surface reconstruction process rather than an intrinsic neuroanatomical variation, and areas for labels would be the only valid way of looking at surface area. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] From: [EMAIL PROTECTED] on behalf of Marie Schaer Sent: Thu 3/11/2005 6:01 AM To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] area file http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrievedb=pubmeddopt=Abstractlist_uids=9278543query_hl=1 I got it, thank you very much! Marie Quoting Bruce Fischl [EMAIL PROTECTED]: Hi Marie, the folding indices are taken from one of the original Van Essen and Drury papers. Sorry I don't have the ref handy. Bruce On Wed, 2 Nov 2005, Marie Schaer wrote: I tried with mris_anatomical_stats from freesurfer-Linux-rh9-v2.1 and I obtained exactly the same result for total surface area as in matlab with the sum of all the triangles, thanks for the advice! In the mean time I was just wondering how folding index returned by mris_anatomical_stats is calculated? Thank you! Marie Schaer Quoting Doug Greve [EMAIL PROTECTED]: We found a problem with this computation about a year ago (11/12/2004 to be specific). I think I sent an email about it to the list. Any releases prior to that date will have this error in the area computations. Can you try it with a more recent release? Marie Schaer wrote: Hello everybody! I have one question about how surface areas are calculated by mris_anatomical stats (release2004). I noticed that the ?h.area file may contain the portion of area corresponding to each different vertex. Actually, the sum of all these areas is around 7'500mm^2 for one hemisphere, which is approximately (but not exactely) the result given by mris_anatomical_stats. However, when I converted the pial surface in matlab, and calculated the sum of the area of each triangle using the following equation http://mathworld.wolfram.com/TriangleArea.html, I obtained a very higher result (~10'000mm^2). Perhaps because the triangles are too big to calculate an accurate area at this stage? So my question was, on which basis is calculated the information contained in lh.area? Does the first row of ?h.area correspond to the piece of area attributable to the first vertice, and so on? Thank you very much for your response! Marie Schaer ___ 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 ___ 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] .sulc and .curv
Hi, I was just wanting to know more about the .curv and .sulc files. Specifically, I had three questions: 1 - What exactly does the value assigned to each vertex represent (eg., is it the curvature of the vertex in the .cuv file?) 2 - How are they derived/calculated? 3 - What do they mean neuroanatomically (eg., does .sulc correspond to the depth of a sulcus?). Many thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] .sulc and .curv
So if I wanted to derive some kind of measure of the complexity of cortical folding, would .curv be the way to go? Would it be safe to say regions of higher curvature have greater cortical folding? Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 25/10/2005 10:57 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] .sulc and .curv 1. This is the smoothed mean curvature - the average of the two principal curvatures smoothed spatially. 2. sulc is the integrated dot product of the movement vector with the surface normal over the inflation process. Things that move consistently outwards thus get a positive sign (sulci) and inwards a negative sign (gyri). 3. curv highlights secondary and tertiary folds as much as primary ones, whereas sulc highlights the primary, deep folds. Bruce On Tue, 25 Oct 2005, Fornito, Alexander wrote: Hi, I was just wanting to know more about the .curv and .sulc files. Specifically, I had three questions: 1 - What exactly does the value assigned to each vertex represent (eg., is it the curvature of the vertex in the .cuv file?) 2 - How are they derived/calculated? 3 - What do they mean neuroanatomically (eg., does .sulc correspond to the depth of a sulcus?). Many thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ 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] PDs?
Hi, We're about to start a longitudinal study and are keen to get accurate measures of structural change. Currently we are planning to acquire a T1 and T2, and have some spare time for another acuqisition. I've noticed in a recent paper (Fischl, et al (2004) Neuroimage,23, S69-S84) you discuss the benefits of combining T1 and PD images to aid segmentation. Just wandering if there are any plans to incorporate multichannel segmentation into freesurfer, and if so, would you recommed acquiring two T1s and averaging, or a single T1 and PD? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Surface edits
Hi, When editing the wm, is it better to fill sections (eg., when thickening temporal lobe strands) using a brush with intensity at 255, or 110? I've noticed that if I fill using 110 and run autorecon2-cp with -keepwmedits the fill is basically ignored when the wm is re-segmented. Just wandering why 255 would be better than 110? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Surface edits
And would placing control points in the filled part work? Or maybe at the base of the strand, before the filled part? Also, It seems that if I run autorecon2-cp after making pial edits to brain volume, the edits are ignored, and a new brain volume is generated, ie., my edits to the brain volume are no longer there. Does autorecon2-pial have to be run as a separate process, after autorecon2-cp? Thanks again, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 14/10/2005 9:13 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface edits you need to fill the wm with 255 so we know it's an edit. Bruce On Fri, 14 Oct 2005, Fornito, Alexander wrote: Hi, When editing the wm, is it better to fill sections (eg., when thickening temporal lobe strands) using a brush with intensity at 255, or 110? I've noticed that if I fill using 110 and run autorecon2-cp with -keepwmedits the fill is basically ignored when the wm is re-segmented. Just wandering why 255 would be better than 110? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ 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] Subcortical questions
Hi, Just wandering if there are any options for improving the results of the subcortical segmentation. It seems to label to large an area for many structures (eg., white matter gets included in the thalamus label). Also, are the surfaces through the midline of the subcortex (ie., the portion labelled as 'medial wall' bu the parcellation step) used during ther spherical registration for the cortex? I'm wandering if I need to pay attention to how the surfaces look in these areas or not. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Keeping edits
HI, I've been running autorecon2-wm or -cp after making edits to the brain volume as well, but it seems that the brain edits are not retaned in the final output. Is there a flag I'm missing? Also, to confim, If I run autorecon2-cp with the -keepwmedits flag, this will retain any edits made to the wm volume won't it? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Pial surface errors
Hi, I've been having some problems with some of my images where the pial surface misses some parts of some gyri. Just wandering what the best way to fix this is. I've experimented changing the intensities using the configure volume brush tool in tkmedit with some success, but was wandering if there are any rules that might be useful to this end, or whether there is an alternative to fixing this problem? Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] anatomical stats
HI, I'm finishing a study I completed using an older version of freesurfer (20040218), and have noticed that I get different values for surface area and grey matter volume when using mris_anatomical_stats for my labels depending on whether I use the mris_anatomical_stats that it is part of this older distribution, or the one packaged as part of the newer dev release (20050905). I noticed on a previous posting that Doug Greve identified an error with respect to how surface area was calculated (I've included it below) and was wandering if this is the reason for the discrepancy. Should I believe the figures calculated using the newer version, or will this also be associated with errors, since the surfaces were generated using the older version? Thanks, Alex I have just fixed a bug in FreeSurfer that involves computing the area of some surface structures. For those of you who care, this was a bug that emerged after converting our surface meshes from quadralaterals to triangles. This change was made a few years ago. This change should have little effect on the reconstruction. It will have an effect on programs that report the area of subsections of cortex (but not total cortical area). At least three such programs that are affected are: mris_compute_overlap, mris_label_area, and mri_surfcluster. The bug causes the reported area to appear to be 1.5 times what it really is. For example, in mri_surfcluster, a cluster threshold of 300 mm^2 would actually be a threshold of 200 mm^2. For those in the NMR center, these three programs have been updated. For those outside, you can get these programs from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve New versions of freesurfer will, of course, have the update. Sorry for any inconvenience. doug ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] anatomical stats
I can create a log file, but in the output, the numbers are out of alignment, so you can't easily figure out what each number refers to. Is there some preferable output format or suffix that I can add to the log file name to adjust this? Also, I can't seem to use the -f flag to create a table. mris_anatomical_stats runs, but there is no table file output at the end. Is this only for the annotation table (I'm using custom labels)? An example command I've tried is: mris_anatomical_stats -mgz -l roi.label -f roi_table 101 lh white -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 9/16/2005 9:51 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] anatomical stats p.s. the flags should always come before the mandatory command line args. On Fri, 16 Sep 2005, Fornito, Alexander wrote: Hi, I'm using the 20050905 distribution and it seems like mris_anatomical_stats is trying to look for cor files, when I've run my analyses using mgz. Is there a way to change this, or have I got it wrong?. Here is the output mris_anatomical_stats 101 lh white reading volume /data/flanders/work/alex/freesurfer/subjects_fe/101/mri/wm... corRead(): can't open file /data/flanders/work/alex/freesurfer/subjects_fe/101/mri/wm/COR-.info mris_anatomical_stats: could not read input volume /data/flanders/work/alex/freesurfer/subjects_fe/101/mri/w Also, I've been having trouble using the -f and -log options (the program runs, but I can't seem to create an output file) with some other surfaces (that I have used cor with). Could you pls give me an example of how to use these flags in the command line? I tried: mris_anatomical_stats 127 lh white -l 127/label/127_roi.label -f roi_stats.log (and I also tried putting the options right after mris_anatomical_stats). Thanks, Alex ___ 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] intensity normalization failure
Hi, Just had a couple of questions re: the -pvvol flag in mri_segstats: How does it take account of partial voluming? Is there anyway to visualize what the partial volume-corrected volume would look like? Would you recmmoned using this falg routinely to obtain subcortical volumes? Finally, on a completely unrelated question, is there any reason to think that surfaces created using the same freesurfer distribution on a Mac would be incompatible with those created using a Linux machine (ie., would you be able to pool them for one study without any problems, and could you start creating surfaces on one, and then re-run afdter manual edits on the other?) Thanks, Alex -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 9/15/2005 10:11 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu; Tracy Wang Subject:RE: [Freesurfer] intensity normalization failure You should be able to use mri_segstats somehow. You'll need a segmentation, though. You could tell it to report on the aseg wm values. You could also use the fill volume (127 and 255?). Check out the --help doug On Wed, 14 Sep 2005, Bruce Fischl wrote: should be easy enough to do in matlab. Just load the wm volume, then find all the T1 voxels that are nonzero in it. Bruce On Thu, 15 Sep 2005, Fornito, Alexander wrote: Is it possible to obtain and intensity histogram of the wm voxels, or descriptive stats (eg., Mean, SD) as a quick check? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thursday, September 15, 2005 3:33 AM To: Tracy Wang Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] intensity normalization failure if it succeeds then the intensity in the wm should be exactly 110 over much of the brain, and 90wm120 pretty much everywhere Bruce On Wed, 14 Sep 2005, Tracy Wang wrote: Hi What is a typical example of when the intensity normalization process fails? Does the over-all image seem brighter? What is a good indicator of success or failure? Thanks, Tracy Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 [EMAIL PROTECTED] ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] intensity normalization failure
Is it possible to obtain and intensity histogram of the wm voxels, or descriptive stats (eg., Mean, SD) as a quick check? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thursday, September 15, 2005 3:33 AM To: Tracy Wang Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] intensity normalization failure if it succeeds then the intensity in the wm should be exactly 110 over much of the brain, and 90wm120 pretty much everywhere Bruce On Wed, 14 Sep 2005, Tracy Wang wrote: Hi What is a typical example of when the intensity normalization process fails? Does the over-all image seem brighter? What is a good indicator of success or failure? Thanks, Tracy Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 [EMAIL PROTECTED] ___ 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] large radius
Hi Bruce and Florent, Your comments re: isoptropic voxels raised a question for me. How is mgz different to cor format? Does mri_convert not interpolate to 1mm3 for mgz? The imaging parameters are: IR prep time, 500 ms; TE minimum, 2.8 ms; TR 13.9 ms; bandwidth, 15.63 kHz; 1 NEX; 20° flip angle; 2 mm contiguous slices; FOV 24 cm; up to 128 volumes for full brain coverage; 512 (frequency, SI) by 256 (phase) matrix, zipped to 512 in phase direction with extended dynamic range. -Original Message- From: florent segonne [mailto:[EMAIL PROTECTED] Sent: Wed 14/09/2005 6:29 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] large radius Hi Alex, I think that mri_watershed is 'incorrectly' assuming 1*1*1mmm isotropic voxels. We'll update the code so that it won't stop there. Florent - Florent Segonne PhD Candidate Stata Center 32-D430 CSAIL MIT 1 617 253 2986 http://people.csail.mit.edu/~fsegonne - On Tue, 13 Sep 2005, Bruce Fischl wrote: Hi Alex, the 2mm slice thickness could be trouble. Usually we don't recommend trying to recon cortical models with any dimension greater than 1.5mm. Why do anisotropic? Can you describe the rest of the acquisition parameters? Bruce On Tue, 13 Sep 2005, Fornito, Alexander wrote: HI, I've got some 3T SPGR data (512 x 512 x 104, vox dim. 0.488 x 0.488 x 2). I seem to be able to convert them to .mgz ok, but when I run mri_watershed I get an error saying main radius too high (output below). Any ideas as to what's happening? Thanks, Alex mri_watershed 1001670.mgz 1001670_brain.mgz The input file is 1001670.mgz The output file is 1001670_brain.mgz If this is incorrect, please exit quickly the program (Ctl-C) *WATERSHED** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=253 y=50 z=235 r=135 first estimation of the main basin volume: 10415397 voxels Error main radius too high ___ 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] subcortical segmentation
I thought the recent version, eg., freesurfer-Linux-rh7.3-dev20050912-full.tar.gz did the subcortical segmentation. I've run it on a couplde of brains so far and it seems to be ok. Are there still some bugs with it? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 9/13/2005 5:45 AM To: Bosky Ravindranath Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] subcortical segmentation not quite, sorry. We *really* don't want to release a version with major problems, so we've been going through everything repeatedly trying to catch everything. We're getting there. Bruce On Mon, 12 Sep 2005, Bosky Ravindranath wrote: To Bruce Fischl and List, I just wanted to know if the subcortical segmentation feature has been released. Thanks, Bosky ___ 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] large radius
HI, I've got some 3T SPGR data (512 x 512 x 104, vox dim. 0.488 x 0.488 x 2). I seem to be able to convert them to .mgz ok, but when I run mri_watershed I get an error saying main radius too high (output below). Any ideas as to what's happening? Thanks, Alex mri_watershed 1001670.mgz 1001670_brain.mgz The input file is 1001670.mgz The output file is 1001670_brain.mgz If this is incorrect, please exit quickly the program (Ctl-C) *WATERSHED** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=253 y=50 z=235 r=135 first estimation of the main basin volume: 10415397 voxels Error main radius too high ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Skull stripping
Hi all, Couple of questions re: failures of skull stripping - If you edit the brain volume after autorecon1, do you need to re-run autorecon1 again, or van you just continue on to autorecon2? - Is it a major problem if the strip removes the cerebellum, since it's excluded by the cuttting planes anyway, or does this interfere with finding the cutting planes later on? Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Skull stripping
Does it affect the aseg with respect to the GCA registration? Is so, how perfect does the strip need to be to avoid biasing the aeg results, eg., are small portions of the meninges or skull around the top of the cortex going to affect the results much? I now they can affect the pial surface, but I'd prefer to edit that after the surfaces are created. Thanks again! Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Sat 9/10/2005 10:56 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] Skull stripping Hi Alex, if the strip removes the cerebellum, then the aseg stuff will fail (if you're using it). If you aren't it doesn't really matter. cheers, Bruce On Sat, 10 Sep 2005, Fornito, Alexander wrote: Hi all, Couple of questions re: failures of skull stripping - If you edit the brain volume after autorecon1, do you need to re-run autorecon1 again, or van you just continue on to autorecon2? - Is it a major problem if the strip removes the cerebellum, since it's excluded by the cuttting planes anyway, or does this interfere with finding the cutting planes later on? Thanks, Alex ___ 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] Intstallation problems on new dev?
Do you mean you're not sure if it will work? -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 9/9/2005 9:28 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intstallation problems on new dev? You should be able to run it with -autorecon-all -rerun. Having said that, I don't know that we've actually run it that way. doug Fornito, Alexander wrote: Hi Bruce and Doug, When you say it can be done automatically,does that mean it wouldn't require additional editing? Does it use edits that are already performed (eg., in creating surfaces with the dev version)? If so, do you know how long it would roughly take to re-create them in this way? Thanks again, Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 9/8/2005 10:45 PM To: Fornito, Alexander Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] Intstallation problems on new dev? Hi Alex, you probably want to regenerate everything. Note that this can be done automatically through recon-all (Doug can tell you the switches). cheers, Bruce On Thu, 8 Sep 2005, Fornito, Alexander wrote: Seems to be working now. Thanks Doug, you're a lifesaver!! As an aside, will surfaces created using the 20050509 dev version be compatible with those created using the upcoming stable release? -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 9/8/2005 1:43 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intstallation problems on new dev? That's due to a problem I created a few days ago. Fixes are at: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve doug On Thu, 8 Sep 2005, Fornito, Alexander wrote: Hi, We've recently installed the freesurfer-Linux-rh9-dev20050905-full.tar.gz distribution on our systems, which run Debian 3.1. I noticed that unpacking the distribution did not place the perl5 directory in $FREESURFER_HOME/lib/mni/lib,as the readme file says it should. I then downloaded the mni-Linux2-2.3-i386.tar.gz and copied the perl5 in to the $FREESURFER_HOME/lib/mni/lib directory, and set the environment appropriately. When I source the environment, I get: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer-dev20050905 FSFAST_HOME /usr/local/freesurfer-dev20050905/fsfast SUBJECTS_DIR /data/flanders/work/alex/freesurfer/subjects FUNCTIONALS_DIR /usr/local/freesurfer-dev20050905/sessions MINC_BIN_DIR /usr/local/freesurfer-dev20050905/lib/mni/bin MINC_LIB_DIR /usr/local/freesurfer-dev20050905/lib/mni/lib PERL5LIB /usr/local/freesurfer-dev20050905/lib/mni/lib/perl5/5.8.5 GSL_DIR /usr/local/freesurfer-dev20050905/lib/gsl QTDIR /usr/local/freesurfer-dev20050905/lib/qt TCLLIBPATH /usr/local/freesurfer-dev20050905/lib/tcltktixblt/lib FSL_DIR /usr/local/fsl However, when I try to run autorecon, I get a message saying cmd: Undefined variable. I get this whether the environment is set to link to perl5 in $FREESURFER_HOME/lib/mni/lib/ or in /usr/pubsw/packages/mni/current/lib/. I don't even know if it's
RE: [Freesurfer] Intstallation problems on new dev?
I understand. Good to hear I wouldn't have to do all the manual editing again. Would it still take about 24 hours from start to finish, or is much quicker on the re-run? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 9/9/2005 9:31 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Intstallation problems on new dev? we just have to test it. We've run the equivalent process many times, just not in the recon-all env yet. On Fri, 9 Sep 2005, Fornito, Alexander wrote: Do you mean you're not sure if it will work? -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 9/9/2005 9:28 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intstallation problems on new dev? You should be able to run it with -autorecon-all -rerun. Having said that, I don't know that we've actually run it that way. doug Fornito, Alexander wrote: Hi Bruce and Doug, When you say it can be done automatically,does that mean it wouldn't require additional editing? Does it use edits that are already performed (eg., in creating surfaces with the dev version)? If so, do you know how long it would roughly take to re-create them in this way? Thanks again, Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 9/8/2005 10:45 PM To: Fornito, Alexander Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] Intstallation problems on new dev? Hi Alex, you probably want to regenerate everything. Note that this can be done automatically through recon-all (Doug can tell you the switches). cheers, Bruce On Thu, 8 Sep 2005, Fornito, Alexander wrote: Seems to be working now. Thanks Doug, you're a lifesaver!! As an aside, will surfaces created using the 20050509 dev version be compatible with those created using the upcoming stable release? -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 9/8/2005 1:43 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intstallation problems on new dev? That's due to a problem I created a few days ago. Fixes are at: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve doug On Thu, 8 Sep 2005, Fornito, Alexander wrote: Hi, We've recently installed the freesurfer-Linux-rh9-dev20050905-full.tar.gz distribution on our systems, which run Debian 3.1. I noticed that unpacking the distribution did not place the perl5 directory in $FREESURFER_HOME/lib/mni/lib,as the readme file says it should. I then downloaded the mni-Linux2-2.3-i386.tar.gz and copied the perl5 in to the $FREESURFER_HOME/lib/mni/lib directory, and set the environment appropriately. When I source the environment, I get: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer-dev20050905 FSFAST_HOME /usr/local/freesurfer-dev20050905/fsfast SUBJECTS_DIR /data/flanders/work/alex/freesurfer/subjects FUNCTIONALS_DIR /usr/local/freesurfer-dev20050905/sessions MINC_BIN_DIR /usr/local/freesurfer-dev20050905/lib/mni/bin MINC_LIB_DIR /usr/local/freesurfer-dev20050905/lib/mni
[Freesurfer] Intstallation problems on new dev?
Hi, We've recently installed the freesurfer-Linux-rh9-dev20050905-full.tar.gz distribution on our systems, which run Debian 3.1. I noticed that unpacking the distribution did not place the perl5 directory in $FREESURFER_HOME/lib/mni/lib,as the readme file says it should. I then downloaded the mni-Linux2-2.3-i386.tar.gz and copied the perl5 in to the $FREESURFER_HOME/lib/mni/lib directory, and set the environment appropriately. When I source the environment, I get: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer-dev20050905 FSFAST_HOME /usr/local/freesurfer-dev20050905/fsfast SUBJECTS_DIR/data/flanders/work/alex/freesurfer/subjects FUNCTIONALS_DIR /usr/local/freesurfer-dev20050905/sessions MINC_BIN_DIR/usr/local/freesurfer-dev20050905/lib/mni/bin MINC_LIB_DIR/usr/local/freesurfer-dev20050905/lib/mni/lib PERL5LIB/usr/local/freesurfer-dev20050905/lib/mni/lib/perl5/5.8.5 GSL_DIR /usr/local/freesurfer-dev20050905/lib/gsl QTDIR /usr/local/freesurfer-dev20050905/lib/qt TCLLIBPATH /usr/local/freesurfer-dev20050905/lib/tcltktixblt/lib FSL_DIR /usr/local/fsl However, when I try to run autorecon, I get a message saying cmd: Undefined variable. I get this whether the environment is set to link to perl5 in $FREESURFER_HOME/lib/mni/lib/ or in /usr/pubsw/packages/mni/current/lib/. I don't even know if it's the perl library that's the problem. Could someone please help out? As far as we're aware, all the environments are set correctly, so we're not sure what Undefined variable is referring to. The entire output is below: recon-all -autorecon1 -subjid 27_new -hemi lh INFO: SUBJECTS_DIR is /data/flanders/work/alex/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer-dev20050905 Linux flanders 2.4.26 #2 SMP Tue Dec 14 03:07:23 EST 2004 i686 GNU/Linux program versions used $Id: recon-all-nmr,v 1.102 2005/09/02 18:03:58 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve 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 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED] (i686-pc-linux-gnu) on 2005-08-29 at 19:41:40 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_fill.c,v 1.94 2005/08/15 14:30:08 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/08-01:59:54-GMT CVS:
[Freesurfer] Lib prob?
Hi, We've recently installed the freesurfer-Linux-rh9-dev20050729.tar.gz distribution along with fs_supportlibs.tar.gz. csurf works ok, but if i try to run tksurfer, I get the error message below. We'd appreciate any help as we've been stuck for a while. Thanks! tksurfer 127 rh white surfer: current subjects dir: /data/flanders/work/alex/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/flanders/work/alex/freesurfer/subjects surfer: Reading header info from /data/flanders/work/alex/freesurfer/subjects/127/mri/T1/COR-.info INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. surfer: vertices=152190, faces=304376 surfer: single buffered window Xlib: extension XFree86-DRI missing on display :0.0. Tix_Init failed: version conflict for package Tcl: have 8.3, need 8.4 surfer: using interface /usr/local/freesurfer-linux9/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer-linux9/lib/tcl/fsgdfPlot.tcl couldn't load file /usr/lib/libtix8.1.8.4.so: /usr/lib/libtix8.1.8.4.so: cannot open shared object file: No such file or directorysurfer: Error sending tcl command UpdateUndoItemLabel Nothing to Undo: invalid command name UpdateUndoItemLabel surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_OriginalVSetLoaded 1: can't read glMenuGroups(mg_OriginalVSetLoaded): no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_InflatedVSetLoaded 0: can't read glMenuGroups(mg_InflatedVSetLoaded): no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_WhiteVSetLoaded 0: can't read glMenuGroups(mg_WhiteVSetLoaded): no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_PialVSetLoaded 0: can't read glMenuGroups(mg_PialVSetLoaded): no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_TimeCourseLoaded 0: can't read glMenuGroups(mg_TimeCourseLoaded): no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_OverlayLoaded 0: can't read glMenuGroups(mg_OverlayLoaded): no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_CurvatureLoaded 0: can't read glMenuGroups(mg_CurvatureLoaded): no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_LabelLoaded 0: can't read glMenuGroups(mg_LabelLoaded): no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldSignLoaded 0: can't read glMenuGroups(mg_FieldSignLoaded): no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: can't read glMenuGroups(mg_FieldMaskLoaded): no such variable % surfer: Error sending tcl command MoveToolWindow 663 670: invalid command name MoveToolWindow surfer: Error sending tcl command MoveToolWindow 663 670: invalid command name MoveToolWindow surfer: Error sending tcl command MoveToolWindow 663 670: invalid command name MoveToolWindow ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Label colours
Hi, Can labels be loaded in different colours in tkmedit? Alexander Fornito M.psych (Clin. Neuro.)/PhD candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Editing labels
Hi Kevin, Apologies for the delay. The output is below.Is it not assiging enough vertices to the label after it has been saved in tkmedit? tksurfer 127 lh smoothwm surfer: current subjects dir: /data/flanders/work/alex/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/flanders/work/alex/freesurfer/subjects surfer: /data/flanders/work/alex/freesurfer/subjects/127/mri/T1/COR-.info INFO: Src volume /tmp/mritotal_17663/orig_8_dxyz.mnc INFO: Target volume /usr/local/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. DimSizes: 3, 86, 110, 68, 1 DataType: 1 MINC Linear Transform 2. 0. 0. -86.0950 0. 2. 0. -126.5100 0. 0. 2. -58.2500 0. 0. 0. 1. Done reading minc surfer: vertices=148018, faces=296032 surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Using /usr/local/freesurfer/lib/Linux/libtclfsgdf.so Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Read /usr/local/freesurfer/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % 1199 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... -Original Message- From: Kevin Teich [mailto:[EMAIL PROTECTED] Sent: Fri 8/12/2005 7:56 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] Editing labels The internal representation of the label format is treated differently between tkmedit and tksurfer. Labels are lists of RAS coords. When you load one into tkmedit, it converts each RAS coord to a voxel index for its internal data structure. When you save it out, it converts the voxel index to an RAS coord, but this can be different than the original RAS coord because it is always the corner of the voxel, where as the original point can be anywhere inside the voxel. However, when tksurfer loads the label, even though the RAS coords in the label don't match exactly with the RAS coords of the surface vertices, it should find the closest vertex coord for each RAS coord, and add that to the label. Can you send the output that tksurfer makes to the shell when you load a label that becomes fragmented like this? On Thu, 11 Aug 2005, Fornito, Alexander wrote: Hi Kevin, It shouldn't. I created the labels by the doing the following: 1 - manully raced an ROI using another program (Analyze) in volume space and saved the ROI as a greyscale mask in analyze format 2 - used mri_convert to convert both the original T1 and ROI to COR format. 3 - Generated the surface of the T1 and loaded the ROI as an overlay in tksurfer 4 - Filled the overlay using custom fill and saved it as a label. I'm not sure how I would check the image dimensions of the label, but I assume step 2 would have put it into 1mm3, which would then convert to 1mm2 when projected onto the surface (?). -Original Message- From: Kevin Teich [mailto:[EMAIL PROTECTED] Sent: Thu 8/11/2005 5:18 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Editing labels I've been trying to edit some labels in tkmedit and have noticed that if I save a label in tkmedit and then project it back onto the surface in tksurfer, it appears fragmented (ie., speckled). This happens even if I save a label that was created in tksurfer in tkmedit without even editing it (ie., create label in tksurfer, load it in tkmedit, save it in tkmedit (without editing), and then load it back in tksurfer). I don't understand why this should happen, particulalry in the latter case, as the label should remain unchanged. Can anyone explain why this might happen? Thanks, Alex Does your data have a voxel resolution different than 1mm squared? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Editing labels
Hi Kevin, It shouldn't. I created the labels by the doing the following: 1 - manully raced an ROI using another program (Analyze) in volume space and saved the ROI as a greyscale mask in analyze format 2 - used mri_convert to convert both the original T1 and ROI to COR format. 3 - Generated the surface of the T1 and loaded the ROI as an overlay in tksurfer 4 - Filled the overlay using custom fill and saved it as a label. I'm not sure how I would check the image dimensions of the label, but I assume step 2 would have put it into 1mm3, which would then convert to 1mm2 when projected onto the surface (?). -Original Message- From: Kevin Teich [mailto:[EMAIL PROTECTED] Sent: Thu 8/11/2005 5:18 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] Editing labels I've been trying to edit some labels in tkmedit and have noticed that if I save a label in tkmedit and then project it back onto the surface in tksurfer, it appears fragmented (ie., speckled). This happens even if I save a label that was created in tksurfer in tkmedit without even editing it (ie., create label in tksurfer, load it in tkmedit, save it in tkmedit (without editing), and then load it back in tksurfer). I don't understand why this should happen, particulalry in the latter case, as the label should remain unchanged. Can anyone explain why this might happen? Thanks, Alex Does your data have a voxel resolution different than 1mm squared? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_vol2surf help
Hi, I'm trying to resample a volume (representing a subregion of the subjects T1) onto the surface using mri_vol2surf. When I try to load the output as an overlay in tksurfer, nothing appears. The output is below. Any help would be appreciated (note, I;ve also tried to output in analyze format with no success) Thanks, Alex mri_vol2surf --src 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg --src_type analyze --srcreg register.dat --fwhm 3 --trgsubject 127 --hemi lh --surf white --surfreg 127/surf/lh.white --out test/test --out_type cor srcvol = 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = 127 surfreg = 127/surf/lh.white interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg - INFO: could not find 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg.mat file - INFO: analyzeRead(): min = 0, max = 63 INFO: chaning type to float Done loading volume INFO: smoothing volume at fwhm = 3 mm (std = 1.27398) Reading surface /data/flanders/work/alex/freesurfer/subjects/127/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface vol2surf_linear: nhits = 148018/148018 Done mapping volume to surface Number of source voxels hit = 92960 Reshaping 2 (nvertices = 148018) Writing non-standard value for imnr1 (2, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (74009, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] mri_vol2surf help
That worked thanks. Wandering if I could get your advice on the best way to proceed. I'm resampling manually traced ROIs onto the surface and using custom fill to convert them to labels to obtain regional thickness. As I see it, I can do this in 2 ways: 1 - convert the ROI (which is saved as a greyscale mask in analyze format) to cor format (which puts the ROI in the same space as the orig, and therefor the surface), and load it as an overlay in tksurfer 2 - use mri_vol2surf to resample the mask to the surface Both approaches produce a pretty good result (ie., the ROI is where it should be), but there appears to be slight differences in the exact locations of the marked vertices around the ROI borders. I was wandering if there's any reason why I should prefer on approach over the other? Also, the borders of the labels are somewhat jagged when overlaid on the surface, which I presume is because the overlays are at voxel resolution, whereas the surface is smoothed at subvoxel resolution. Is there any way to correct the overlays for this discrepancy? Would it be a sin not to? Thanks for your help, Alex -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 8/11/2005 1:42 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] mri_vol2surf help Definitely do not use cor as the output. Use paint format (also known as .w). See the examples. doug On Thu, 11 Aug 2005, Fornito, Alexander wrote: Hi, I'm trying to resample a volume (representing a subregion of the subjects T1) onto the surface using mri_vol2surf. When I try to load the output as an overlay in tksurfer, nothing appears. The output is below. Any help would be appreciated (note, I;ve also tried to output in analyze format with no success) Thanks, Alex mri_vol2surf --src 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg --src_type analyze --srcreg register.dat --fwhm 3 --trgsubject 127 --hemi lh --surf white --surfreg 127/surf/lh.white --out test/test --out_type cor srcvol = 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = 127 surfreg = 127/surf/lh.white interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg - INFO: could not find 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in 127/mri/orig/001/reg_objects/127_lh_cog_limbic_surfreg.mat file - INFO: analyzeRead(): min = 0, max = 63 INFO: chaning type to float Done loading volume INFO: smoothing volume at fwhm = 3 mm (std = 1.27398) Reading surface /data/flanders/work/alex/freesurfer/subjects/127/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface vol2surf_linear: nhits = 148018/148018 Done mapping volume to surface Number of source voxels hit = 92960 Reshaping 2 (nvertices = 148018) Writing non-standard value for imnr1 (2, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (74009, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] anatomical_stats
Hi Brian, I tried the -f flag and got the following. Is there a newer version of anatomical_stats that runs the -f option? mris_anatomical_stats -f ./lh_aff_limbic.txt -l 127/label/127_lh_aff_limbic.label 127 lh pial unknown option -f -Original Message- From: Brian T. Quinn [mailto:[EMAIL PROTECTED] Sent: Sat 7/30/2005 4:27 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] anatomical_stats sure: cd $SUBJECTS_DIR mris_anatomical_stats -f file.txt -b -a subjid/label/hemi.aparc.annot subjid hemi On Sat, 30 Jul 2005, Fornito, Alexander wrote: Hi, Is there anyway to print the output of mri_anatomical_stats to a text file? Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Editing labels
Hi, I've been trying to edit some labels in tkmedit and have noticed that if I save a label in tkmedit and then project it back onto the surface in tksurfer, it appears fragmented (ie., speckled). This happens even if I save a label that was created in tksurfer in tkmedit without even editing it (ie., create label in tksurfer, load it in tkmedit, save it in tkmedit (without editing), and then load it back in tksurfer). I don't understand why this should happen, particulalry in the latter case, as the label should remain unchanged. Can anyone explain why this might happen? Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] stage1
Hi, The new version of recon-all certainly sounds exciting. Any dates for Linux release planned? I'm looking at starting processing on a large set of images and wouldn't want to begin and then re-do some of the processing because a superior method came out. Regards, Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 7/19/2005 11:32 AM To: Ray Fix Cc: FreeSurfer Mailing List Subject: Re: [Freesurfer] stage1 Hi Ray, you shouldn't compare across datasets that use the subcortical segmentation (aseg) and those that don't. The aseg fills the entire ventricle, and thus changes the effective folding pattern on the medial wall, requiring a different atlas and parcellation targets. The advantage is that it is quite a bit more robust and fully automated in 90-95% of the cases we've tested (including elderly and AD), plus you get the whole subcortical segmentation for either structural or functional analysis. cheers, Bruce p.s. the subcortical does take a long (15 hours) time, but reduces person time as most datasets go through without any manual fixing. On Mon, 18 Jul 2005, Ray Fix wrote: Hello Doug, Thanks for the info. I tried out the Tiger install a couple of weeks ago and was very impressed but when I tried to process bert, it took so long that I finally gave up. What is the advantage of doing this subcortical segmentation step? For example, will it potentially improve the results of later stages? In the README file in freesurfer/subjects it states that the sample should be processed with recon-all-nmr -all -subjid bert Do you recommend adding -nosubcortseg to the recon-all-nmr script? Previously, I used to use recon-all. It looks like it that is a grepped / stripped subset of the -nmr version. Is recon-all deprecated? When I run recon-all with bert I get an error about DoCANormalize not being defined. Will I be able to correctly compare samples that I have run in previously releases using recon-all? Thank you. Yours confused, Ray Fix On Jul 18, 2005, at 10:26 AM, Doug Greve wrote: That one now automatically does subcortical segmentation, which will take about 24 hours. Add -nosubcortseg to the command-line (AFTER -stage1) to disable it. doug Timothy O'Keefe wrote: Also, I am using the OSX Tiger snapshot of FreeSurfer with a new recon-all script courtesy of Doug Greve. On Jul 18, 2005, at 10:03 AM, Timothy O'Keefe wrote: I ran recon-all stage1 and it took a very long time. Well, at least longer than people document. I didn't time it, but it must have taken close to 10 hours. Also I received this error during mri_fill(): ... using +/- offset search region where offset is 39. using +/- offset search region where offset is 42. using +/- offset search region where offset is 45. using +/- offset search region where offset is 48. mri_fill: could not find pons No such file or directory INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (0.90, -7.51, 23.75) INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... find_cutting_plane:seed point not in structure! Searching neighborhood... ERROR: mri_fill exited with non-zero status recon-all exited with errors at Sat Jul 16 01:13:52 EDT 2005 Are there any suggestions? I am using a single T1 (1x1x1) image acquired from a Siemens 1.5T machine. I realize I should use multiple images for averaging, however I am just trying to get a feel for the software. -T ___ 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
[Freesurfer] Skull stripping
Hi, recon-all stage1 overstrips some of my images during the skull-stripping stage. I've played with the different options, but they don't seem to make any difference at all. Any suggestions? I've tried feeding in a pre-stripped brain (stripped using BET), but the intensity normalization doesn't seem to do to well (ie., although it finishes without error, the wm values are not very uniform, and the segmentation misses large portions of wm). Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] mri_vol2surf
Ok, I feel I am tantalizingly close...
It seems my confusion stemmed from the belief that the mask needed to be in
label format, but I've since worked out that it can be loaded in tksurfer in
analyze format as an overlay.
Now that I can view my mask on the surface, the question is how can I obtain
the thickness for the region under the overlay?
I thought I could use the -t option in mris_anatomical stats with the mask, but
it doesn't seem to read the file and results in 0 thickness (see below).
Is a label the only way to obtain thickenss for an ROI?
I tried mri_vol2roi and obtained an ROI in bfloat format, but am unsure how to
display this in tksurfer, or convert this into a label (it didn't work with the
-t command either). The --label argument seems to require a label to already be
in place.
Thanks for your help!
A.
mris_anatomical_stats -t ./186_corconv_native_testmask_binary_y.img 1000186 lh
pial
using thickness file ./186_corconv_native_testmask_binary_y.img.
reading volume /data/flanders/work/alex/freesurfer/subjects/1000186/mri/wm...
reading input surface
/data/flanders/work/alex/freesurfer/subjects/1000186/surf/lh.pial...
MRISreadCurvature: could not open ./186_corconv_native_testmask_binary_y.img
No such file or directory
Computing inter-vertex distance
computing second fundamental form...done.
total white matter volume = 659946 mm^3
total surface area = 123477 mm^2
total gray matter volume= 0 mm^3
average cortical thickness = 0.000 mm +- 0.000 mm
integrated rectified mean curvature = 30613.737
integrated rectified Gaussian curvature = 7478.872
folding index = 3110.626
intrinsic curvature index = 338.606
avg inter-vertex dist (mm) = 1.00548 +/- 0.427572
avg vertex radius (mm) = 61.0534 +/- 17.1529
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Tue 7/5/2005 1:40 AM
To: Bruce Fischl
Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu
Subject:RE: [Freesurfer] mri_vol2surf
Something like this should work:
vertex_coords = read_surf('lh.white')
[w,v] = read_wfile(wfilename);
lindex = v;
lxyz = vertex_coords(lindex);
lvals = zeros(size(lindex));
write_label(lindex, lxyz, lvals, labelfile, subjid);
On Mon, 4 Jul 2005, Bruce Fischl wrote:
Hi Alex,
I think Doug has a .m file to do this in matlab. We'll put an mri_vol2label
on the to-do list, or maybe extend vol2roi to do it.
Bruce
On Mon, 4 Jul 2005, Fornito, Alexander wrote:
Never mind about the differences between tkmedit and tkregister - I
retained --regheader in the command line, even though the mask and the
volume were already correctly aligned, which caused them to move out of
alignment. However, I'm still unsure of what the correct file format is for
me to apply the image as an ROI to the surface to get regional anatomical
info.
Thanks,
Alex
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Mon 7/4/2005 11:25 AM
To: Fornito, Alexander
Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] mri_vol2surf
Hi Alex,
no, label files are text files with the extension .label that
usually
reside in the subject's label directory. .w files are weight files
(from EEG/MEG inverse solutions), and more generally, are a sparse
set of
floating point values. You can load them in tksurfer with file-load
overlay, and leave the register field blank. but they probably aren't
the
right format for a label, which is just a list of voxels. Maybe Doug
can
point you in the right direction for that (mri_vol2roi?)
cheers,
Bruce
On Mon, 4 Jul 2005, Fornito, Alexander wrote:
Hi,
I've managed to get the mask to a point where it's in the correct
position if I load it through tkmedit (as a binary in analyze format). I
then run mri_vol2surf, which seems to work (output below). However, If I
try to load the mask (now saved as a .w file) though tksurfer as file
label load, nothing happens (nothing happens if I try to load it as an
overlay with the register.dat file either). If I try to load it as a label
in tkmedit, I get the following:
Couldn't load the label.
Tkmedit couldn't read the label you specified. This could be
because the format wasn't valid or the file wasn't found.
Am I missing something? I though .w was the correct format for
labels of this type.
Here's the mri_vol2surf output. Thanks again!
mri_vol2surf --src 186_corconv_native_testmask_binary_y --src_type
analyze --srcreg register.dat --hemi lh --out
./186_native_flip_y_mask_surf.w --out_type paint
INFO: output format is paint
srcvol = 186_corconv_native_testmask_binary_y
srctype = analyze
srcreg
RE: [Freesurfer] mri_vol2surf
Aahh... that would explain it. I assumed that because you saved labels from the parcellation to get ROI thickness stats, label was the correct format for a manually delineated ROI. I'm probably wrong, but from understanding of the mri_vol2roi --help, it allows me to create a binary ROI from the volume, which is what I already have (albeit mine is in analyze format). What I'm trying to do is apply this ROI to the surface as a mask to get regionally specific anatomical stats (ie., thickness, curvature, etc. info for the manually delineated ROI only). Should I try to obtain the mri_vol2surf output in some other format that would allow me to do this? I'm not sure which would do the trick... Also, another source of confusion is that when I overlay the mask in tkmedit, I get a good fit, but it's in the wrong position when I load it in tkregister2. Why does this happen? Thanks again, A. -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Mon 7/4/2005 11:25 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] mri_vol2surf Hi Alex, no, label files are text files with the extension .label that usually reside in the subject's label directory. .w files are weight files (from EEG/MEG inverse solutions), and more generally, are a sparse set of floating point values. You can load them in tksurfer with file-load overlay, and leave the register field blank. but they probably aren't the right format for a label, which is just a list of voxels. Maybe Doug can point you in the right direction for that (mri_vol2roi?) cheers, Bruce On Mon, 4 Jul 2005, Fornito, Alexander wrote: Hi, I've managed to get the mask to a point where it's in the correct position if I load it through tkmedit (as a binary in analyze format). I then run mri_vol2surf, which seems to work (output below). However, If I try to load the mask (now saved as a .w file) though tksurfer as file label load, nothing happens (nothing happens if I try to load it as an overlay with the register.dat file either). If I try to load it as a label in tkmedit, I get the following: Couldn't load the label. Tkmedit couldn't read the label you specified. This could be because the format wasn't valid or the file wasn't found. Am I missing something? I though .w was the correct format for labels of this type. Here's the mri_vol2surf output. Thanks again! mri_vol2surf --src 186_corconv_native_testmask_binary_y --src_type analyze --srcreg register.dat --hemi lh --out ./186_native_flip_y_mask_surf.w --out_type paint INFO: output format is paint srcvol = 186_corconv_native_testmask_binary_y srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for /data/flanders/work/alex/freesurfer/subjects/186_corconv_native_testmask_binary_y - INFO: could not find /data/flanders/work/alex/freesurfer/subjects/186_corconv_native_testmask_binary_y.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /data/flanders/work/alex/freesurfer/subjects/186_corconv_native_testmask_binary_y.mat file - INFO: analyzeRead(): min = 0, max = 1 INFO: chaning type to float Done loading volume Reading surface /data/flanders/work/alex/freesurfer/subjects/1000186/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface vol2surf_linear: nhits = 152789/152789 Done mapping volume to surface Number of source voxels hit = 96553 avg = 1.000, stdev = 0.000, min = 1.000, max = 1.000 -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 7/1/2005 10:11 PM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Sorry, I gave you a slightly wrong tkmedit command-line, it should have been -overlay-reg ... As for tkmedit, the mask is probably too dark. Click in the window and hit 'i'. This will turn on intensity normalization, which will probably fix the problem. You may want to load in the volume that you traced the mask on instead of the mask itself. doug Fornito, Alexander wrote: Hi Doug, I tried the tkmedit command and it loaded the volume with the mask, although I got a message saying: Error: Parsing command line options Option -reg not recognized This option was not recognized and ignored. Not sure why this occurred, as I loaded it from scratch through the GUI (File Load Overlay Data, with the mask as the volume and register.dat as the registration file) and it produced the same with no error. In any case, I
RE: [Freesurfer] mri_vol2surf
Never mind about the differences between tkmedit and tkregister - I retained --regheader in the command line, even though the mask and the volume were already correctly aligned, which caused them to move out of alignment. However, I'm still unsure of what the correct file format is for me to apply the image as an ROI to the surface to get regional anatomical info. Thanks, Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Mon 7/4/2005 11:25 AM To: Fornito, Alexander Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] mri_vol2surf Hi Alex, no, label files are text files with the extension .label that usually reside in the subject's label directory. .w files are weight files (from EEG/MEG inverse solutions), and more generally, are a sparse set of floating point values. You can load them in tksurfer with file-load overlay, and leave the register field blank. but they probably aren't the right format for a label, which is just a list of voxels. Maybe Doug can point you in the right direction for that (mri_vol2roi?) cheers, Bruce On Mon, 4 Jul 2005, Fornito, Alexander wrote: Hi, I've managed to get the mask to a point where it's in the correct position if I load it through tkmedit (as a binary in analyze format). I then run mri_vol2surf, which seems to work (output below). However, If I try to load the mask (now saved as a .w file) though tksurfer as file label load, nothing happens (nothing happens if I try to load it as an overlay with the register.dat file either). If I try to load it as a label in tkmedit, I get the following: Couldn't load the label. Tkmedit couldn't read the label you specified. This could be because the format wasn't valid or the file wasn't found. Am I missing something? I though .w was the correct format for labels of this type. Here's the mri_vol2surf output. Thanks again! mri_vol2surf --src 186_corconv_native_testmask_binary_y --src_type analyze --srcreg register.dat --hemi lh --out ./186_native_flip_y_mask_surf.w --out_type paint INFO: output format is paint srcvol = 186_corconv_native_testmask_binary_y srctype = analyze srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh interp = nearest float2int = round INFO: float2int code = 0 INFO: analyzeRead(): found 1 files for /data/flanders/work/alex/freesurfer/subjects/186_corconv_native_testmask_binary_y - INFO: could not find /data/flanders/work/alex/freesurfer/subjects/186_corconv_native_testmask_binary_y.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /data/flanders/work/alex/freesurfer/subjects/186_corconv_native_testmask_binary_y.mat file - INFO: analyzeRead(): min = 0, max = 1 INFO: chaning type to float Done loading volume Reading surface /data/flanders/work/alex/freesurfer/subjects/1000186/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface vol2surf_linear: nhits = 152789/152789 Done mapping volume to surface Number of source voxels hit = 96553 avg = 1.000, stdev = 0.000, min = 1.000, max = 1.000 -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 7/1/2005 10:11 PM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Sorry, I gave you a slightly wrong tkmedit command-line, it should have been -overlay-reg ... As for tkmedit, the mask is probably too dark. Click in the window and hit 'i'. This will turn on intensity normalization, which will probably fix the problem. You may want to load in the volume that you traced the mask on instead of the mask itself. doug Fornito, Alexander wrote: Hi Doug, I tried the tkmedit command and it loaded the volume with the mask, although I got a message saying: Error: Parsing command line options Option -reg not recognized This option was not recognized and ignored. Not sure why this occurred, as I loaded it from scratch
[Freesurfer] mri_vol2surf
Hi, I'm trying apply ROI masks that I've manually traced in volume space to the same image's surface using mri_vol2surf. mri_vol2surf seems to requires a register.dat file, and I'm unsure what needs to be registered, since the volume that I traced the masks on is exactly the same as the one that I began with to create the surface (so presumably they are in the same space?) . Any hints would be appreciated. Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] mri_vol2surf
Hi Doug,
I tried the tkmedit command and it loaded the volume with the mask, although I
got a message saying:
Error: Parsing command line options
Option -reg not recognized
This option was not recognized and ignored.
Not sure why this occurred, as I loaded it from scratch through the GUI (File
Load Overlay Data, with the mask as the volume and register.dat as the
registration file) and it produced the same with no error.
In any case, I can see from tkmedit that the mask is not where it should be
(It's in the neck, where it should be in the cingulate, above the corpus
callosum).
However, I tried running tkregister as you suggested to me, and although the
GUI pops up, I'm unable to see the movable volume (ie., the mask). This has
happened to me before when i tried something else in tkregister, and am not
sure if I'm doing anything wrong. The output is below.
Thanks for your help,
Alex.
tkregister2 --s ./1000186 --mov ./186_corconv_mask.img --reg ./register.dat
--regheader
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume ./186_corconv_mask.img
reg file ./register.dat
LoadVol1
$Id: tkregister2.c,v 1.22 2003/11/05 21:30:50 greve Exp $
Diagnostic Level -1
INFO: analyzeRead(): found 1 files for ./186_corconv_mask.img
-
INFO: could not find ./186_corconv_mask.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in ./186_corconv_mask.mat
file
-
INFO: loading target
/data/flanders/work/alex/freesurfer/subjects/./1000186/mri/orig
INFO: changing target type to float
Ttarg:
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable ./186_corconv_mask.img
INFO: analyzeRead(): found 1 files for ./186_corconv_mask.img
-
INFO: could not find ./186_corconv_mask.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in ./186_corconv_mask.mat
file
-
INFO: analyzeRead(): min = 0, max = 1
INFO: changing move type to float
Tmov:
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 1, float2int = 0
Input registration matrix (computed)
1.000 0.000 0.000 0.000;
0.000 0.000 1.000 -0.000;
0.000 -1.000 0.000 0.000;
0.000 0.000 0.000 1.000;
---
subject = ./1000186
Zoom Factor = 2
Input registration matrix
1.000 0.000 0.000 0.000;
0.000 0.000 1.000 -0.000;
0.000 -1.000 0.000 0.000;
0.000 0.000 0.000 1.000;
Opening window ./1000186
Setting scale
tkregister2: interface: /usr/local/freesurfer/lib/tcl/tkregister2.tcl
tkregister.tcl: startup done
tkregister.tcl: default macro interface (to change: macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Fri 7/1/2005 12:47 PM
To: Fornito, Alexander
Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu
Subject:RE: [Freesurfer] mri_vol2surf
The first thing that you should do is load your mask as an overlay in
tkmedit to make sure that it is actually falling where you think it
is:
tkmedit yoursubject orig -overlay ./mask.img -reg ./register.dat \
-fthresh 0.5
The fthresh is set assuming your mask is 0 or 1. You can even load
the surface to see if it actually inersects.
If this fails, then you need a new registration file. You can
create this with:
tkregiser2 --s yoursubject --mov mask.img --reg reg.dat --regheader
tkregiser2 allows you to interactively change the registration. Note
that you only use --regheader the first time you run it (ie, before
you have a reg.dat).
doug
On Fri, 1 Jul 2005, Fornito, Alexander wrote:
Sorry, I forgot to mention, I have the mask in analyze format (I traced it in
another program). I ran mri_vol2surf using the register.dat file format that
Doug provided, and got the output below. Although it creates a .w file,
nothing happens when I load it in tksurfer, I'm gessing because the vertex
values are zero (?). Have I done something wrong?
mri_vol2surf --src 186_corconv_mask --src_type analyze --srcreg register.dat
--hemi lh --out ./186_mask_surf.w --out_type paint
INFO: output format is paint
srcvol = 186_corconv_mask
srctype = analyze
srcreg = register.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi
RE: [Freesurfer] mris_glm
Hi again, I've been playing around with the other segmentation fault I was getting (stage 1 recon-all with the 3T images). I've noticed that my 1.5T images (with which I have no problems) are coronally acquired, 256 x 256 x 123 (x, y, z) , voxel size 0.9 x 0.9 x 1.5, 16 bit. My 3Ts are 512 x 512 x 124, coronally acquired, voxel size 0.6 x 0.6 x 1.7, 16 bit. It seems the FOV is too big, since mri_convert ends up producing a COR image with 330 slices instead of 256. I registered and resmapled the 3T to one of my 1.5Ts using a 6 parameter rigid body registration in AIR so that the 3T took on the properties of the 1.5T (ie., it became 256 x 256 x 123, 0.9 x 0.9 x 1.5). recon-all -stage1 only worked if I converted the resampled image to 8 bit. If I tried to run it on the 16bit image, the intensity normalization failed. The relevant output is below. Do images need to be in a certain format before mri_convert can convert them to COR format successfully? Thanks again for all your help, Alex Intensity Normalization Tue Jun 28 14:40:54 EST 2005 /data/flanders/work/alex/freesurfer/subjects/mw_3T_2_186/mri mri_normalize orig T1 reading from orig... normalizing image... talairach transform 1.051 0.565 0.381 -29.026; -0.317 1.126 -0.797 -10.790; -0.719 0.586 1.113 -42.660; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks No such file or directory mri_normalize: normalization failed No such file or directory ERROR: mri_normalize exited with non-zero status -- Filesystem 1k-blocks Used Available Use% Mounted on /dev/hda9130282400 12379432 111284996 11% /data/flanders -- recon-all exited with errors at Tue Jun 28 14:41:03 EST 2005 -Original Message- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Wed 6/29/2005 2:26 AM To: Fornito, Alexander Cc: Itamar Kahn; Freesurfer Mailing List Subject:RE: [Freesurfer] mris_glm Alex, I'm trying to track down the source of the segmentation fault. In the meantime, can you re-run the script with the parameter --echo just after 'make_average_surface' (and before the --subjects)? This will give me a better idea on where its faulting. I don't think the subject naming is the problem, but I am wondering about the two warnings about not being able to open the .avg_curv files. Thanks, Itamar, for pointing out the problem with the script. I'm not sure how the file got converted to DOS format (as we use Linux), maybe a mail system, but I hadn't seen that error before. I've posted a gzip'd make_average_surface on the ftp site (same as sent prior), in case others want the script. At: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/make_average_surface.gz Copy it to $FREESURFER_HOME/bin, and remember to make it executable by typing 'chmod 755 make_average_surface' after gunzip'ing it. Nick On Tue, 2005-06-28 at 13:11 +1000, Fornito, Alexander wrote: Thanks - that got it working! I tried running it on a small sample of 8 subjects, and got a segmentation fault (below). I've noticed that make_average_surface requires subject names to start with a letter. My subjects were coded as numbers, so I just added an 's' to the beginning to get it going. I'm not sure if this has anything to do with the problem. Any help is appreciated. Alex make_average_surface --subjects s1000186 s1000187 s1000188 s1000189 s1000190 s1000191 s1000192 s1000194 make_average_surface input subjects: s1000186 s1000187 s1000188 s1000189 s1000190 s1000191 s1000192 s1000194 output subject: average mris_average_curvature... processing subject s1000186... processing subject s1000187... processing subject s1000188... processing subject s1000189... processing subject s1000190... processing subject s1000191... processing subject s1000192... processing subject s1000194... MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc No such file or directory mris_average_curvature... processing subject s1000186... processing subject s1000187... processing subject s1000188... processing subject s1000189... processing subject s1000190... processing subject s1000191... processing subject s1000192... processing subject s1000194... MRISwriteCurvature: could not open ../average/surf/lh.avg_curv No such file or directory mris_make_average_surface... reading vertex positions from orig... processing subject s1000186... The following must be revisited** Segmentation fault -Original Message- From: Itamar Kahn [mailto:[EMAIL PROTECTED] Sent: Tue 6/28/2005 9:51 AM To: Fornito, Alexander Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] mris_glm The 'make_average_surface' script is in Dos format. You can use the 'dos2unix
RE: [Freesurfer] mris_glm
Thanks - that got it working! I tried running it on a small sample of 8 subjects, and got a segmentation fault (below). I've noticed that make_average_surface requires subject names to start with a letter. My subjects were coded as numbers, so I just added an 's' to the beginning to get it going. I'm not sure if this has anything to do with the problem. Any help is appreciated. Alex make_average_surface --subjects s1000186 s1000187 s1000188 s1000189 s1000190 s1000191 s1000192 s1000194 make_average_surface input subjects: s1000186 s1000187 s1000188 s1000189 s1000190 s1000191 s1000192 s1000194 output subject: average mris_average_curvature... processing subject s1000186... processing subject s1000187... processing subject s1000188... processing subject s1000189... processing subject s1000190... processing subject s1000191... processing subject s1000192... processing subject s1000194... MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc No such file or directory mris_average_curvature... processing subject s1000186... processing subject s1000187... processing subject s1000188... processing subject s1000189... processing subject s1000190... processing subject s1000191... processing subject s1000192... processing subject s1000194... MRISwriteCurvature: could not open ../average/surf/lh.avg_curv No such file or directory mris_make_average_surface... reading vertex positions from orig... processing subject s1000186... The following must be revisited** Segmentation fault -Original Message- From: Itamar Kahn [mailto:[EMAIL PROTECTED] Sent: Tue 6/28/2005 9:51 AM To: Fornito, Alexander Cc: Freesurfer Mailing List Subject:Re: [Freesurfer] mris_glm The 'make_average_surface' script is in Dos format. You can use the 'dos2unix' application to remove the offending characters from it (dos2unix comes with all linux dist and you can use fink to download it for mac os x). Cheers, Itamar - [EMAIL PROTECTED] kahn]$ dos2unix --help dos2unix Copyright (c) 1994-1995 Benjamin Lin Copyright (c) 1998 Bernd Johannes Wuebben (Version 3.0) Copyright (c) 1998 Christian Wurll (Version 3.1) Usage: dos2unix [-hkqV] [-c convmode] [-o file ...] [-n infile outfile ...] -h --helpgive this help -k --keepdatekeep output file date -q --quiet quiet mode, suppress all warnings always on in stdin-stdout mode -V --version display version number -c --convmodeconversion mode convmode ASCII, 7bit, ISO, Mac, default to ASCII -l --newline add additional newline in all but Mac convmode -o --oldfile write to old file file ... files to convert in old file mode -n --newfile write to new file infile original file in new file mode outfile output file in new file mode On Jun 27, 2005, at 4:39 PM, Fornito, Alexander wrote: Hi Nick, I copied the script into the bin dir, but when I type make_average_surface, I get the following: make_average_surface 'nknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. Is this normal? Thanks, Alex -Original Message- From:Nick Schmansky [mailto:[EMAIL PROTECTED] Sent:Tue 6/21/2005 11:00 PM To:Fornito, Alexander Cc:Freesurfer Mailing List; Bruce Fischl Subject:RE: [Freesurfer] mris_glm Alex, Attached is the make_average_surface script. Copy it to the freesurfer/bin directory, and be sure to make it executable (run 'chmod 755 make_average_surface' in the freesurfer/bin directory). Type 'make_average_surface' to get help. Basically, just the subject names are required. By default, a 'subject' named 'average' will be created from your set of subjects (a name instead of 'average' can be specified on the command line). Nick ps. I am working on the mris_surface seg-fault problem using the rh.orig file that you sent. On Tue, 2005-06-21 at 08:23 -0400, Bruce Fischl wrote: Hi Alex, you're better off using the make_average_surfaces.csh script to make an average of your subjects. Nick: can you send Alex a copy? thanks, Bruce On Tue, 21 Jun 2005, Fornito, Alexander wrote: Def. sounds worth doing then! I'll give it a try. My other question is, where can I get my hands on the average7? It's used as the target in the mris_glm examples, but I haven't been able to find the actual average7 surface in any of the freesurfer directories. Am I missing something? Thanks again, Alex -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tuesday, June 21, 2005 4:11 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_glm You can run with just the design matrix, but you won't be able to use the cool fsgdf stuff in tksurfer (Load-FSGDF). The fsgdf is a way to specify how to build
[Freesurfer] mris_make_average_surface
Hi, I'm having a little trouble interpreting the mris_make_average_surface usage and was hpoing for some help: usage: mris_make_average_surface [options] hemi output surf name canon surface output subject name subject ... output subject name this program will generate an average of the orig surfaces of all the subjects specified (unless the -s surface name flag is used) the transform defaults to talairach.xfm in the subject's mri/transforms directory, but can be changed using the -x xform name switch What does the canon surface refer to? Why is there an ouput subject name for each subject? Why does it avarege the orig, and not final surfaces? Could you please give me an example of a command line? Thanks, Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 6/22/2005 10:02 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] vertex correspondance they are in correspondence, but there may be shear in the pial deformation, so the link will overestimate the thickness. Easy to compute though, just the distance between the same vertex on the 2 surfaces On Wed, 22 Jun 2005, Fornito, Alexander wrote: Is there some kind of correspondance between them that is specified in any of the files? I'm thinking of trying to use something like the link method (desrcibed in the Lerch Evans, 2005 paper) for estimating thickness, but as I understand it, there needs to be some kind of established link between the points on each surface. -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 6/22/2005 9:20 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] vertex correspondance Hi Alex, yes, all the surfaces of a hemisphere (except qsphere) have the same # of vertices/edges and faces. I think Doug has something that will sample the mask. mri_vol2label or something like that? Bruce On Wed, 22 Jun 2005, Fornito, Alexander wrote: Hi again, So many questions!! Is there some sort of correspondence between vertices on the inner (wm) and outer (pial) surfaces? Ie., for every vertex on the inner surface, is there a point on the outer surface, and if so, does Freesurfer retain this information in any of the files? Also, I have some binary masks that I have manually traced using another program that I would like to apply to the surfaces to get regional measures of thickness. The mask images are in analyze format. Is there any way that I can do this? Thanks as always, Alex Alexander Fornito M.psych (Clin. Neuro.)/PhD candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] vertex correspondance
Hi again, So many questions!! Is there some sort of correspondence between vertices on the inner (wm) and outer (pial) surfaces? Ie., for every vertex on the inner surface, is there a point on the outer surface, and if so, does Freesurfer retain this information in any of the files? Also, I have some binary masks that I have manually traced using another program that I would like to apply to the surfaces to get regional measures of thickness. The mask images are in analyze format. Is there any way that I can do this? Thanks as always, Alex Alexander Fornito M.psych (Clin. Neuro.)/PhD candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] vertex correspondance
Is there some kind of correspondance between them that is specified in any of the files? I'm thinking of trying to use something like the link method (desrcibed in the Lerch Evans, 2005 paper) for estimating thickness, but as I understand it, there needs to be some kind of established link between the points on each surface. -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 6/22/2005 9:20 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] vertex correspondance Hi Alex, yes, all the surfaces of a hemisphere (except qsphere) have the same # of vertices/edges and faces. I think Doug has something that will sample the mask. mri_vol2label or something like that? Bruce On Wed, 22 Jun 2005, Fornito, Alexander wrote: Hi again, So many questions!! Is there some sort of correspondence between vertices on the inner (wm) and outer (pial) surfaces? Ie., for every vertex on the inner surface, is there a point on the outer surface, and if so, does Freesurfer retain this information in any of the files? Also, I have some binary masks that I have manually traced using another program that I would like to apply to the surfaces to get regional measures of thickness. The mask images are in analyze format. Is there any way that I can do this? Thanks as always, Alex Alexander Fornito M.psych (Clin. Neuro.)/PhD candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mris_glm
Hi, I was seeking some clarification re: the relationship between the fsgdf and design matrix file for use with mris_glm. It seems to me that the two contain very similar info, the examples in the help dont use the fsdf at all. Is it necessary to create one, or can you just run an analysis with the desmtx? Thanks, Alex Alexander Fornito M.psych (Clin. Neuro.)/PhD candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problems in pial surface?
Hi, I've been using freesurfer with only one run (image) pers subject and have generally been obtaining good results. I've just noticed a few quirks in the estimation of the pial surface that I was seeking some clarification. 1 - the algorithm consistently misses portions of grey matter in the medial temporal lobes (amygdala/hippocampus). I've noticed that this missed area becomes part of the medial wall region when parcellate_subject is run. Does the algorithm intentionally avoid estimatiung the grey/csf surface in the medial temporal lobes? 2 - Sometimes a portion of the other hemisphere gets included in estimates of the pial surface. Any tips for dealing with this? I was thinking of manually deleting a thin line of voxels through the midline of the T1 to emphasise the medial surface in areas where the algorithm has trouble? As an aside, where can I find the average7? I thought it would be in /usr/local/freesurfer/average/, but all I have is .gcs, .tif, and .txt files. Thanks as always, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] recon-all stage3
I'll keep an eye one it. As an aside, I tried to run freesurfer on an image acquired at 3T (I converted it to 8 bit first), and got an error during stage1 of recon-all. I've included the relevant bits below. Any ideas? Transforming slices:...Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:..Done mri_convert nu/nu4.mnc nu mri_convert nu/nu4.mnc nu reading from nu/nu4.mnc... DimSizes: 3, 330, 330, 330, 1 DataType: 1 MINC Linear Transform -1. 0. 0. 165. 0. 0. 1. -165. 0. -1. 0. 165. 0. 0. 0. 1. Done reading minc TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (330, 330, 330) voxels. Data is conformed to 1 mm size and 330 voxels for all directions writing to nu... non-standard value for imnr1 (330, usually 256) in volume structure non-standard value for width (330, usually 256) in volume structure non-standard value for height (330, usually 256) in volume structure ... #it then seems to proceed as normal until I get this: - Tessellate rh Tue Jun 14 18:34:47 EST 2005 mri_tessellate /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled 127 /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.orig /data/flanders/work/alex/freesurfer/subjects/mw_3T/scripts warning: non-standard value for imnr1 (330, usually 256) in file /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled/COR-.info warning: non-standard value for x (330, usually 256) in file /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled/COR-.info warning: non-standard value for y (330, usually 256) in file /data/flanders/work/alex/freesurfer/subjects/mw_3T/mri/filled/COR-.info slice 80: 25 vertices, 35 faces slice 90: 2235 vertices, 2414 faces slice 100: 7950 vertices, 8225 faces slice 110: 14980 vertices, 15343 faces slice 120: 24760 vertices, 25210 faces slice 130: 35948 vertices, 36485 faces slice 140: 47251 vertices, 47791 faces slice 150: 59398 vertices, 59994 faces slice 160: 69840 vertices, 70396 faces slice 170: 79968 vertices, 80513 faces slice 180: 89126 vertices, 89647 faces slice 190: 97517 vertices, 98045 faces slice 200: 104180 vertices, 104653 faces slice 210: 110417 vertices, 110849 faces slice 220: 115639 vertices, 116067 faces slice 230: 120291 vertices, 120699 faces slice 240: 123600 vertices, 123982 faces slice 250: 125319 vertices, 125574 faces slice 260: 125319 vertices, 125574 faces slice 270: 125319 vertices, 125574 faces slice 280: 125319 vertices, 125574 faces slice 290: 125319 vertices, 125574 faces slice 300: 125319 vertices, 125574 faces slice 310: 125319 vertices, 125574 faces slice 320: 125319 vertices, 125574 faces slice 330: 125319 vertices, 125574 faces using the conformed surface RAS to save vertex points... writing /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.orig - Smooth1 rh Tue Jun 14 18:35:32 EST 2005 mris_smooth /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.orig /data/flanders/work/alex/freesurfer/subjects/mw_3T/surf/rh.smoothwm /data/flanders/work/alex/freesurfer/subjects/mw_3T/scripts Segmentation fault -- Filesystem 1k-blocks Used Available Use% Mounted on /dev/hda9130282400 12524220 40208 11% /data/flanders -- recon-all exited with errors at Tue Jun 14 18:35:33 EST 2005 -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 6/15/2005 12:33 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject:RE: [Freesurfer] recon-all stage3 then you should just run the rest of the analysis I guess and see if it works. In general all the surfaces of a hemisphere should have the same # of edges/faces/vertices *except* the ?h.qsphere surface. They should have all have an euler number of 2. cheers, Bruce On Wed, 15 Jun 2005, Fornito, Alexander wrote: Hi Bruce, I ran the topology fixer again and it seemed to work. Unfortunately, silly me just wrote over the original files, so all I have is the euler number from the orig surface that is output in the recon-all log. Euler Number lh Sat Jun 11 04:20:04 EST 2005 /data/flanders/work/alex/freesurfer/subjects/1000192 mris_euler_number /data/flanders/work
[Freesurfer] recon-all stage3
Hi, I got an error when running recon-all -stage3.I've included the relevant part of the log below. Any ideas as to what went wrong? Thanks, alex writing spherical brain to /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere spherical transformation took 0.91 hours navgs=32 and tol=1.000e-01 integrating with navgs=32 and tol=1.000e-01 integrating with navgs=8 and tol=1.000e-01 taking momentum steps... integrating with navgs=8 and tol=1.000e-01 integrating with navgs=8 and tol=1.000e-01 integrating with navgs=2 and tol=1.000e-01 taking momentum steps... integrating with navgs=2 and tol=1.000e-01 integrating with navgs=2 and tol=1.000e-01 integrating with navgs=0 and tol=1.000e-01 pass 1 complete, delta sse/iter = 0.16/60 = 0.00 final distance error %31.34 optimization complete. unfolding took 0.81 hours - Fix Topology lh Sat Jun 11 04:24:54 EST 2005 /data/flanders/work/alex/freesurfer/subjects/1000192/scripts mris_fix_topology 1000192 lh reading input surface /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere... before topology correction, eno=-301 (nv=188932, nf=378516, ne=567749, g=151) mrisReadTriangleFile(/data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.orig): surface doesn't match /data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_fix_topology: could not read original surface orig No such file or directory reading T1 volume from T1... reading wm segmentation from wm... recon-all exited with errors at Sat Jun 11 04:24:58 EST 2005 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Strip and register check
Hi, A couple of questions; 1 - The skull stripping feature has overstripped some of my brains, and using -wsmore doesn't completely fix the problem. Are there any other options? 2 - I'd like to check my registrations by mapping labels from the average back onto the individual's brain. What's the best way to do this? Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] recon-all-nmr -disable-autoseg
I can't find any usage or help for parcellate_subject, and if I simply run parcellate_subject [subjname], I get the following message: CSURF_DIR: Undefined variable. Any clues? Thanks, A. -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 6/9/2005 1:10 AM To: Bruce Fischl Cc: Fornito, Alexander; Elizabeth Fenstermacher; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all-nmr -disable-autoseg I think it looks in the average7 directory for a few labels (central sulc, calc, ...), then maps them to your subject through the registration. The intent was that you could then look at these labels to make sure they were in about the right place. doug Bruce Fischl wrote: the labels are deprecated since we have the cortical parcellation. And yes, run parcellate_subject and it will create *.annot files in the label dir. cheers, Bruce On Wed, 8 Jun 2005, Fornito, Alexander wrote: That worked, thanks, Doug. To expand on the labels issue, from my understanding, the labels are used to check that the registration worked, and that these are automatically created. I don't have any files in my labels directory. Do you need to run parcellate_subject to get them? Is there any documentation on parcellate_subject? I tried to run it and got the message: CSURF_DIR: Undefined variable. as an aside, where is the average7 surface. I though it might be in /usr/local/freesurfer/average/, but I don't seem to be able to open any of the files in there with tksurfer. Thanks again, Alex -Original Message- From:Doug Greve [mailto:[EMAIL PROTECTED] Sent:Wed 6/8/2005 11:08 AM To:Elizabeth Fenstermacher Cc:freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] recon-all-nmr -disable-autoseg use the one in dev not std env Elizabeth Fenstermacher wrote: Hello All, I have a number of jobs that I will be running through recon-all-nmr -stage1 in the next few days. I tried using the -disable-autoseg flag, but it seems not to work as the jobs I submitted this morning have now run for 50 minutes. The command line as I typed it was pbsubmit -c recon-all-nmr -stage1 -subjid $s -nuintensitycor -usenuintensitycor -disable-autoseg perhaps I've misplaced the flag? If anyone has any insight as to why it seems to be persitting in running the autoseg I would appreciate it. Thanks! Eliz ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all stage4b error
Hi all, I've created my the fional surface for some people and am trying to register them using recon-all -stage4b.However, I get an error message saying that I needed to do average labels (see output below). I've noticed that I get the same message if I try to morph_subject, except morph_subject actually creates sphere.reg files. Am I missing something? Thanks for your patience! Alex recon-all -subjid 186 -stage4b 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 $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ### INFO: SUBJECTS_DIR is /data/flanders/work/alex/freesurfer/subjects ERROR: cannot subject average7, needed to do average labels. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] recon-all-nmr -disable-autoseg
That worked, thanks, Doug. To expand on the labels issue, from my understanding, the labels are used to check that the registration worked, and that these are automatically created. I don't have any files in my labels directory. Do you need to run parcellate_subject to get them? Is there any documentation on parcellate_subject? I tried to run it and got the message: CSURF_DIR: Undefined variable. as an aside, where is the average7 surface. I though it might be in /usr/local/freesurfer/average/, but I don't seem to be able to open any of the files in there with tksurfer. Thanks again, Alex -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Wed 6/8/2005 11:08 AM To: Elizabeth Fenstermacher Cc: freesurfer@nmr.mgh.harvard.edu Subject:Re: [Freesurfer] recon-all-nmr -disable-autoseg use the one in dev not std env Elizabeth Fenstermacher wrote: Hello All, I have a number of jobs that I will be running through recon-all-nmr -stage1 in the next few days. I tried using the -disable-autoseg flag, but it seems not to work as the jobs I submitted this morning have now run for 50 minutes. The command line as I typed it was pbsubmit -c recon-all-nmr -stage1 -subjid $s -nuintensitycor -usenuintensitycor -disable-autoseg perhaps I've misplaced the flag? If anyone has any insight as to why it seems to be persitting in running the autoseg I would appreciate it. Thanks! Eliz ___ 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 ___ 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] Missing libraries?
:.Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 3 CV of field change: 0.000802066 [EMAIL PROTECTED]:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:05:49] running: /usr/local/mni/bin/make_template -quiet -shrink 3 nu/nu2.mnc /var/tmp/nu_correct_15089//template.mnc Transforming slices:..Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:Done nu_correct -clobber nu/nu3.mnc nu/nu4.mnc [EMAIL PROTECTED]:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:06:01] running: /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_15162/ nu/nu3.mnc nu/nu4.imp Processing:.Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 3 CV of field change: 0.000831802 [EMAIL PROTECTED]:/data/flanders/work/alex/freesurfer/subjects/186_good/mri/] [2005-06-07 12:06:13] running: /usr/local/mni/bin/make_template -quiet -shrink 3 nu/nu3.mnc /var/tmp/nu_correct_15162//template.mnc Transforming slices:..Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:Done mri_convert nu/nu4.mnc nu mri_convert nu/nu4.mnc nu reading from nu/nu4.mnc... DimSizes: 3, 256, 256, 256, 1 DataType: 1 MINC Linear Transform -1. 0. 0. 128. 0. 0. 1. -128. 0. -1. 0. 128. 0. 0. 0. 1. Done reading minc TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to nu... -Original Message- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Sat 6/4/2005 7:41 AM To: Fornito, Alexander Cc: Freesurfer Mailing List Subject:Re: [Freesurfer] Missing libraries? Alex, I've just posted a source code bundle of most of the MNI-BIC tools, along with a Makefile for building/installing/testing this software. The README file is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README and the gzip file is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz Although the README says the ideal place to install is at /usr/pubsw/packages/mni/current, I've installed the set in a local home directory, and the segment_subject works for me (on Mac OS X, and Linux CENTOS 4) However, you may be able to get your existing install working by just adding the environment var DYLD_LIBRARY_PATH. See the README for an example. Your error (not finding a .so file) is indicative of this problem. Let me know how things go. Nick On Fri, 2005-05-27 at 14:38 +1000, Fornito, Alexander wrote: Hi, We're really stuck on this one... We are running a linux kernel 2.4.26 debian 3.0 (woody). We've installed the freesurfer and the packaged MINC tools in the apporpriate directories and set the appropriate environment variables. We can't get the MNI tools to work through freesurfer, and only some limited MINC tools work if we try to run them on their own (eg., we can use MINC display, but can't do anyting with the images). It seems like
RE: [Freesurfer] Missing libraries?
Thanks Nick, We'll give it a try and keep you posted. A. -Original Message- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Sat 6/4/2005 7:41 AM To: Fornito, Alexander Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Missing libraries? Alex, I've just posted a source code bundle of most of the MNI-BIC tools, along with a Makefile for building/installing/testing this software. The README file is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README and the gzip file is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz Although the README says the ideal place to install is at /usr/pubsw/packages/mni/current, I've installed the set in a local home directory, and the segment_subject works for me (on Mac OS X, and Linux CENTOS 4) However, you may be able to get your existing install working by just adding the environment var DYLD_LIBRARY_PATH. See the README for an example. Your error (not finding a .so file) is indicative of this problem. Let me know how things go. Nick On Fri, 2005-05-27 at 14:38 +1000, Fornito, Alexander wrote: Hi, We're really stuck on this one... We are running a linux kernel 2.4.26 debian 3.0 (woody). We've installed the freesurfer and the packaged MINC tools in the apporpriate directories and set the appropriate environment variables. We can't get the MNI tools to work through freesurfer, and only some limited MINC tools work if we try to run them on their own (eg., we can use MINC display, but can't do anyting with the images). It seems like there are some libraries missing (see below). Can you tell us why the MINC tools that came packaged with fressurfer aren't working? Is there something else that needs to be installed? If I try to run mri_convert from the GUI after checking the MNI Linear Register option in expert preferences, I get a message saying MNI align not yet implemented. If I run segment_subject I get : segment_subject 190 cp: cannot stat `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' : No such file or directory /data/flanders/work/alex/freesurfer/subjects/190/scripts /data/flanders/work/ale x/freesurfer/subjects registering 190 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory Error executing mincinfo on orig/orig.mnc Error: could not open file /data/flanders/work/alex/freesurfer/subjects/190/mr i/transforms/talairach.xfm. System message: No such file or directory mri_add_xform_to_header: could not read xform file '/data/flanders/work/alex/fre esurfer/subjects/190/mri/transforms/talairach.xfm' Any help would be much appreciated!!! Thanks, Alex ___ 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] skull stripping
Hi all, The page about using FSL with freesurfer on the FSL website recommends using BET to skull strip the images before feeding them into freeusrfer. I've had a bit of play with this, and have noticed some marginal improvements. Would you generally recommed this practice? Are there any reasons not to? Also, what exactly does the -atlas option do? Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] morph_subject error
Hi, I've come across some problems when I run morph_subject. It seems to work fine until near the end. I've included the final bit of the log below. The problem seems to occur after it calls MNI programs. I've been having trouble using the MNI tools through freesurfer, so I created the talairach.xfm separately and placed it in the transforms directory. Is this problem due to the trouble with the MNI tools? What are the MNI tools used for in morph_subject, and are they necessary at this step? Thanks again for your help, Alex registration took 1.70 hours writing registered surface to ../surf/lh.rh.sphere.reg... /data/flanders/work/alex/freesurfer/subjects/1000186_mni /data/flanders/work/alex/freesurfer/subjects/1000186_mni/scripts /data/flanders/work/alex/freesurfer/subjects/1000186_mni/scripts - /data/flanders/work/alex/freesurfer/subjects/1000186_mni/scripts mris2rgb -o 1000186_mni.reg -both -c /data/flanders/work/alex/freesurfer/subjects/1000186_mni/surf/lh.sulc -canon /data/flanders/work/alex/freesurfer/subjects/1000186_mni/surf/lh.sphere.reg /data/flanders/work/alex/freesurfer/subjects/1000186_mni/surf/lh.sphere.reg /data/flanders/work/alex/freesurfer/subjects/1000186_mni/rgb - using 1000186_mni.reg as output stem reading canonical coordinates from /data/flanders/work/alex/freesurfer/subjects/1000186_mni/surf/lh.sphere.reg. writing rgb file /data/flanders/work/alex/freesurfer/subjects/1000186_mni/rgb/lateral.lh.1000186_mni.reg.rgb writing rgb file /data/flanders/work/alex/freesurfer/subjects/1000186_mni/rgb/medial.lh.1000186_mni.reg.rgb morph_rgb-lh completed SUCCESSUFLLY 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/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.13 2004/02/02 18:24:58 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.12 2003/09/18 15:01:33 bert Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.4 2001/04/24 13:38:42 neelin Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ### INFO: SUBJECTS_DIR is /data/flanders/work/alex/freesurfer/subjects ERROR: cannot subject average7, needed to do average labels. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Missing libraries?
Hi, We're really stuck on this one... We are running a linux kernel 2.4.26 debian 3.0 (woody). We've installed the freesurfer and the packaged MINC tools in the apporpriate directories and set the appropriate environment variables. We can't get the MNI tools to work through freesurfer, and only some limited MINC tools work if we try to run them on their own (eg., we can use MINC display, but can't do anyting with the images). It seems like there are some libraries missing (see below). Can you tell us why the MINC tools that came packaged with fressurfer aren't working? Is there something else that needs to be installed? If I try to run mri_convert from the GUI after checking the MNI Linear Register option in expert preferences, I get a message saying MNI align not yet implemented. If I run segment_subject I get : segment_subject 190 cp: cannot stat `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' : No such file or directory /data/flanders/work/alex/freesurfer/subjects/190/scripts /data/flanders/work/ale x/freesurfer/subjects registering 190 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory Error executing mincinfo on orig/orig.mnc Error: could not open file /data/flanders/work/alex/freesurfer/subjects/190/mr i/transforms/talairach.xfm. System message: No such file or directory mri_add_xform_to_header: could not read xform file '/data/flanders/work/alex/fre esurfer/subjects/190/mri/transforms/talairach.xfm' Any help would be much appreciated!!! Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Talairach help!!
Hi all, Sorry to labour this point, but I'm stuck with the MNI tools and am having trouble progressing through my freesurfer analyses. I can't create the talairach.xfm and was hoping for some help. If I run mri_convert in the command line, I get the following: mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ reading from 190/mri/orig/001/1000190_wbc... INFO: analyzeRead(): found 1 files for 190/mri/orig/001/1000190_wbc - INFO: could not find 190/mri/orig/001/1000190_wbc.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default).INFO: if not valid, please provide the information in 190/mri/orig/001/1000190_wbc.mat file - INFO: analyzeRead(): min = 0, max = 211 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) Original Data has (1, 1, 1) mm size and (250, 250, 250) voxels. Data is conformed to 1 mm size and 256 voxels for all directions Reslicing using trilinear interpolation writing to 190/mri/orig/... Alternatively, if I run it from the GUI after checking the MNI Linear Register option in expert preferences, I get a message saying MNI align not yet implemented. Then, when I run segment_subject, it begins with the following messages: segment_subject 190 cp: cannot stat `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' : No such file or directory /data/flanders/work/alex/freesurfer/subjects/190/scripts /data/flanders/work/ale x/freesurfer/subjects registering 190 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory Error executing mincinfo on orig/orig.mnc Error: could not open file /data/flanders/work/alex/freesurfer/subjects/190/mr i/transforms/talairach.xfm. System message: No such file or directory mri_add_xform_to_header: could not read xform file '/data/flanders/work/alex/fre esurfer/subjects/190/mri/transforms/talairach.xfm' As far as I'm aware, all the MNI tools packaged with Freesurfer have been installed correctly, and the appopriate enviornment variables have been set in the default settings and in my own. Any tips? Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] MNI problems
Hi, I've been having some problems with the MNI tools (I can't create the talairach.xfm) and was hoping for some help. If I run mri_convert in the command line, I get the following: mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ reading from 190/mri/orig/001/1000190_wbc... INFO: analyzeRead(): found 1 files for 190/mri/orig/001/1000190_wbc - INFO: could not find 190/mri/orig/001/1000190_wbc.mat file for direction cosine info. INFO: use Analyze 7.5 hdr-hist.orient value: 0, transverse unflipped (default).INFO: if not valid, please provide the information in 190/mri/orig/001/1000190_wbc.mat file - INFO: analyzeRead(): min = 0, max = 211 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) Original Data has (1, 1, 1) mm size and (250, 250, 250) voxels. Data is conformed to 1 mm size and 256 voxels for all directions Reslicing using trilinear interpolation writing to 190/mri/orig/... Alternatively, if I run it from the GUI after checking the MNI Linear Register option in expert preferences, I get a message saying MNI align not yet implemented. Then, when I run segment_subject, it begins with the following messages: segment_subject 190 cp: cannot stat `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' : No such file or directory /data/flanders/work/alex/freesurfer/subjects/190/scripts /data/flanders/work/ale x/freesurfer/subjects registering 190 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory Error executing mincinfo on orig/orig.mnc Error: could not open file /data/flanders/work/alex/freesurfer/subjects/190/mr i/transforms/talairach.xfm. System message: No such file or directory mri_add_xform_to_header: could not read xform file '/data/flanders/work/alex/fre esurfer/subjects/190/mri/transforms/talairach.xfm' I'm guessing the mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory is the culprit, but can't figure out what it is since, as far as I'm aware, all the MNI tools packaged with Freesurfer have been installed correctly, and the appopriate enviornment variables have been set in the default settings and in my own. Any tips? Thanks, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] WMFilll and talairach coordinates
Other than that though, should there be any problem if I align my images prior to starting with freesurfer? Provided I align to the MNI 152 brain, it should still be in talaraich space... -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 5/18/2005 10:55 AM To: Fornito, Alexander Cc: peggy christidis; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates 1. to report talairach coords. 2. To get cutting planes to separate the hemispheres when the head is at an angle. 3. To find the callosum if other heuristics fail. 4. To pick some control points in the white matter for intensity normalization. cheers, Bruce On Wed, 18 May 2005, Fornito, Alexander wrote: Hi, Just to toss my hat into the ring, can I ask why the transform is kept. Is it used later on? I've also been having trouble with the MNI tools, and was thinking of using FLIRT or AIR to align the images first. What is th point of having the .xfm? Thanks, Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 5/18/2005 6:00 AM To: peggy christidis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WMFilll and talairach coordinates Hi Peggy, we don't apply the transform, just keep it around, so blurring isn't a problem. I don't know if AFNI knows how to write out .xfm files (the mni transform format), but that would be the best solution. Bruce On Tue, 17 May 2005, peggy christidis wrote: Hello, I'm having a bit of trouble with the Create Surface step in FreeSurfer. I have a single mprage scan that creates a decent first pass surface, but there's still some brainstem and cerebellum attached to it. I followed the troubleshooting guidelines in the FreeSurfer manual regarding Failure of Automatic Cutting Planes. I went to Expert Preferences -- WMFill, and inputed the appropriate coordinates to separate the brainstem and cerebellum. The coordinates I used were not in Talairach space, but I assumed this was okay because the manual says to use original coordinates if you don't have Talairach coordinates. However, when I re-ran Create Surface, nothing happened (i.e., filled volume and surface both still show the pons/cerebellum/brainstem attached). I read through the FreeSurfer mailing list archives and read that Talairach coordinates are indeed needed. Here's my question: The volume I'm using shows a head that's slightly tilted about 10 degrees to the left, so I should probably do the Taliarach transformation anyway. However, I don't have the mni_tools installed on my computer (I had major installation problems with them). Anyway, could I do a taliarach transformation outside of Freesurfer (like in AFNI) and then tranfer that talairached volume to FreeSurfer? My concern is that the transformation will blur the volume, making segmentation difficult. What should I do? Thanks, Peggy ___ 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] WMFilll and talairach coordinates
Wouldn't that occur by using the MNI tools anyway? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 5/18/2005 9:39 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates just that you have sacrificed resolution. On Wed, 18 May 2005, Fornito, Alexander wrote: Other than that though, should there be any problem if I align my images prior to starting with freesurfer? Provided I align to the MNI 152 brain, it should still be in talaraich space... -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 5/18/2005 10:55 AM To: Fornito, Alexander Cc: peggy christidis; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates 1. to report talairach coords. 2. To get cutting planes to separate the hemispheres when the head is at an angle. 3. To find the callosum if other heuristics fail. 4. To pick some control points in the white matter for intensity normalization. cheers, Bruce On Wed, 18 May 2005, Fornito, Alexander wrote: Hi, Just to toss my hat into the ring, can I ask why the transform is kept. Is it used later on? I've also been having trouble with the MNI tools, and was thinking of using FLIRT or AIR to align the images first. What is th point of having the .xfm? Thanks, Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 5/18/2005 6:00 AM To: peggy christidis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WMFilll and talairach coordinates Hi Peggy, we don't apply the transform, just keep it around, so blurring isn't a problem. I don't know if AFNI knows how to write out .xfm files (the mni transform format), but that would be the best solution. Bruce On Tue, 17 May 2005, peggy christidis wrote: Hello, I'm having a bit of trouble with the Create Surface step in FreeSurfer. I have a single mprage scan that creates a decent first pass surface, but there's still some brainstem and cerebellum attached to it. I followed the troubleshooting guidelines in the FreeSurfer manual regarding Failure of Automatic Cutting Planes. I went to Expert Preferences -- WMFill, and inputed the appropriate coordinates to separate the brainstem and cerebellum. The coordinates I used were not in Talairach space, but I assumed this was okay because the manual says to use original coordinates if you don't have Talairach coordinates. However, when I re-ran Create Surface, nothing happened (i.e., filled volume and surface both still show the pons/cerebellum/brainstem attached). I read through the FreeSurfer mailing list archives and read that Talairach coordinates are indeed needed. Here's my question: The volume I'm using shows a head that's slightly tilted about 10 degrees to the left, so I should probably do the Taliarach transformation anyway. However, I don't have the mni_tools installed on my computer (I had major installation problems with them). Anyway, could I do a taliarach transformation outside of Freesurfer (like in AFNI) and then tranfer that talairached volume to FreeSurfer? My concern is that the transformation will blur the volume, making segmentation difficult. What should I do? Thanks, Peggy ___ Freesurfer mailing list Freesurfer
RE: [Freesurfer] WMFilll and talairach coordinates
-Original Message- From: Fornito, Alexander Sent: Thu 5/19/2005 10:27 AM To: Bruce Fischl Cc: Subject: RE: [Freesurfer] WMFilll and talairach coordinates Now I understand. And this information has to be in .xfm format? It can't be in .mat (FLIRT) or .tfn (AIR) format? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thu 5/19/2005 10:25 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates no, because we just keep the transform around, but only apply it for either reporting purposes, or apply the inverse to find anatomical features (e.g. the callosum) On Thu, 19 May 2005, Fornito, Alexander wrote: Wouldn't that occur by using the MNI tools anyway? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 5/18/2005 9:39 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates just that you have sacrificed resolution. On Wed, 18 May 2005, Fornito, Alexander wrote: Other than that though, should there be any problem if I align my images prior to starting with freesurfer? Provided I align to the MNI 152 brain, it should still be in talaraich space... -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 5/18/2005 10:55 AM To: Fornito, Alexander Cc: peggy christidis; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] WMFilll and talairach coordinates 1. to report talairach coords. 2. To get cutting planes to separate the hemispheres when the head is at an angle. 3. To find the callosum if other heuristics fail. 4. To pick some control points in the white matter for intensity normalization. cheers, Bruce On Wed, 18 May 2005, Fornito, Alexander wrote: Hi, Just to toss my hat into the ring, can I ask why the transform is kept. Is it used later on? I've also been having trouble with the MNI tools, and was thinking of using FLIRT or AIR to align the images first. What is th point of having the .xfm? Thanks, Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wed 5/18/2005 6:00 AM To: peggy christidis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WMFilll and talairach coordinates Hi Peggy, we don't apply the transform, just keep it around, so blurring isn't a problem. I don't know if AFNI knows how to write out .xfm files (the mni transform format), but that would be the best solution. Bruce On Tue, 17 May 2005, peggy christidis wrote: Hello, I'm having a bit of trouble with the Create
RE: [Freesurfer] Segmentation error
Great. Thanks!! -Original Message- From: florent segonne [mailto:[EMAIL PROTECTED] Sent: Wed 5/18/2005 1:22 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation error Hello Alex, This warning message appears during the watershed segmentation process. The final brain shape is compared to a statistical atlas and the correctness of the segmentation (of the shape) is evaluated. It turns out that the validation is often too restrictive and often generates a useless warning message. As a consequence, you should most often ignore this message. If the skull stripping appears to be incorrect, this message might then become of interest. In any case, we'll shortly fix this. Best, Florent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
