Freesurfer October 2006

freesurfer@nmr.mgh.harvard.edu

41 participants
61 discussions

Converting DICOMs
by Fornito, Alexander 04 Oct '06

04 Oct '06

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 NumarisVer syngo MR 2004V 4VB11D ScannerModel Avanto PatientName Fornito^Alex^^^Mr Date and time StudyDate 20060427 StudyTime 192350.703000 SeriesTime 192556.781000 AcqTime 192554.055005 Acquisition parameters PulseSeq epfid2d1_60 Protocol ep2d_800 PhEncDir COL EchoNo 0 FlipAngle 78 EchoTime 26 InversionTime 26 RepetitionTime 1420 PhEncFOV 206.25 ReadoutFOV 220 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 300 NImageCols 320 NFrames 800 SliceArraylSize 21 IsMosaic 1 ImgPos 106.2426 139.4769 -20.2630 VolRes 3.4375 3.4375 5.0000 VolDim 64 60 21 Vc -0.9981 -0.0053 0.0606 Vr 0.0000 -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: alexander.fornito(a)wh.org.au

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is there any online resource for manual segmentations of subcortical objects...
by Shahabuddin Ansari 03 Oct '06

03 Oct '06

Hello, Is there any online resource for manual segmentations of subcorical objects, e.g. hippocampus, amygdala, caudate etc? I appreciate it. Shahab --------------------------------- Stay in the know. Pulse on the new Yahoo.com. Check it out.

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Missing Dicom Fields (Revisted)
by Niels Bergsland 03 Oct '06

03 Oct '06

Hi again, >From the last time that I asked about this, the project was temporarily put on hold, but now it has started up again... When looking back at the responses from last time, I realized that I am not sure if I made it clear what I was proposing as a solution to the missing fields 0020,0032 (ImagePositionPatient) and 0020,0037 (ImageOrientationPatient). My original question was as follows: Is it possible to 'fake' the 20,37 field by inserting the values: 1\0\0\0\1\0 since we know they are acquired in the axial plane? We also know which way the slices are supposed to be sorted, is it possible to insert values into 20,32 in order to have freesurfer able to 'know' the proper sorting order? To which you said that you didn't have something to allow us to specify the fields ourselves. I realized that you thought I was asking if Freesurfer has the capability. What I actually meant though is if I can manually insert the values using, for example, dcmodify (part of the DCMTK) and then process the scans with Freesurfer. Hopefully this is a bit more clear! Thanks again, Niels Bergsland

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flattened but two surfaces
by Joongnam Yang 03 Oct '06

03 Oct '06

Hi all, I flattened the occipital cortex and viewed it with tksurfer, but there are two flattened surfaces, top and bottom on the tksurfer window. Usually from my experience, there is one flattened surface. Could someone suggest what might have gone wrong? Nam.

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Re: [Freesurfer] mris_flatten missing 4 lib
by Joongnam Yang 03 Oct '06

03 Oct '06

Dear all, I did occipital cortex flattening and when I tried to display it on tksurfer using "tksurfer average lh occip.patch.flat", I got the following error message, which I have never seen. (the error message on memory) surfer: current subjects dir: /home/nam/AVERAGE surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/nam/AVERAGE/average/surf Loading tal xfm file /home/nam/AVERAGE/average/mri/transforms/talairach.xfm surfer: Reading header info from /home/nam/AVERAGE/average/mri/T1.mgz MRISalloc(16711682, 408): could not allocate vertices Cannot allocate memory Would someone hint at a solution? Nam.

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open patch file?
by xingfeng lee 03 Oct '06

03 Oct '06

Dear FreeSurfer Experts, I tested flatten using mris_flatten, it took 8 hours. I want to see the result of the faltten, but i do not know how to open these patch files, rh.patch rh.patch.flat rh.patch.flat.out could you help to give some suggestions? Thanks in advance. Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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how to save segmentation in analyze format by using command line?
by Shahabuddin Ansari 02 Oct '06

02 Oct '06

Hello, I usually open subcortical segmentations in tkmedit and save the segmentations in analyze format. Is there any command line option to do the same? Appreciate it. Shahab --------------------------------- Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business.

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mris_flatten missing 4 lib
by xingfeng lee 02 Oct '06

02 Oct '06

Dear FreeSurfer Experts, Where can I find and install the missing 4 lib for mis_flatten? libtix8.1.8.3.so => not found libtk8.4.so => not found libgsl.so.0 => not found libgslcblas.so.0 => not found [xingfeng@ambrose bin]$ pwd /usr/local/freesurfer/bin [xingfeng@ambrose bin]$ ldd tksurfer linux-gate.so.1 => (0x55000000) libtix8.1.8.3.so => not found libtk8.4.so => not found libtcl8.4.so => /usr/lib/libtcl8.4.so (0x00a69000) libglut.so.3 => /usr/lib/libglut.so.3 (0x5500f000) libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x007e8000) libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x007f2000) libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x00394000) libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x0095b000) libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x009ec000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x006fb000) libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x00965000) libgsl.so.0 => not found libgslcblas.so.0 => not found libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x004a1000) libtiff.so.3 => /usr/lib/libtiff.so.3 (0x074c7000) libz.so.1 => /usr/lib/libz.so.1 (0x007d5000) libm.so.6 => /lib/tls/libm.so.6 (0x006d0000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x07456000) libc.so.6 => /lib/tls/libc.so.6 (0x005b3000) libdl.so.2 => /lib/libdl.so.2 (0x006f5000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x07251000) libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x007c5000) libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x00101000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00560000) libpthread.so.0 => /lib/tls/libpthread.so.0 (0x0088a000) libXxf86vm.so.1 => /usr/X11R6/lib/libXxf86vm.so.1 (0x008de000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x0059a000) [xingfeng@ambrose bin]$ cat /etc/redhat-release Fedora Core release 2 (Tettnang) [xingfeng@ambrose bin]$ uname -m i686 Thanks for the help in advance. All the best, Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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mris_flatten
by xingfeng lee 02 Oct '06

02 Oct '06

Dear FreeSurfer Experts, Could you help for the cortex flatten? I came across the following problem, i do not know how to fix it. [xingfeng@ambrose surf]# ls lh.area lh.defect_labels lh.rh.sphere.reg lh.white rh.defect_chull rh.pial rh.thickness lh.area.pial lh.inflated lh.smoothwm rh.area rh.defect_labels rh.qsphere.nofix rh.white lh.avg_curv lh.inflated.nofix lh.smoothwm.nofix rh.area.pial rh.inflated rh.smoothwm lh.curv lh.orig lh.sphere rh.avg_curv rh.inflated.nofix rh.smoothwm.nofix lh.curv.pial lh.orig.nofix lh.sphere.reg rh.curv rh.lh.sphere.reg rh.sphere lh.defect_borders lh.pial lh.sulc rh.curv.pial rh.orig rh.sphere.reg lh.defect_chull lh.qsphere.nofix lh.thickness rh.defect_borders rh.orig.nofix rh.sulc [xingfeng@ambrose surf]# pwd /usr/local/freesurfer/subjects/frank/surf [xingfeng@ambrose surf]# mris_flatten -w 0 -distances 12 7 lh.patch lh.patch.flat mris_flatten: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory [xingfeng@ambrose surf]# whoami root [xingfeng@ambrose surf]# mris_flatten -w 0 -distances 12 7 lh.patch lh.patch.flat mris_flatten: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory Could you help? All the best, Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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How to get subcortical segmentation for the "average" subject
by jorge luis 02 Oct '06

02 Oct '06

Hello all. How can I get a subcortical segmentation for the average subject (the result of make_average_subject)? There is no aseg.mgz file on the corresponding directory I hope it can be used for VOI analysis of functional data. Any help is welcome. In advance Thank you ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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Freesurfer October 2006