Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

(no subject)
by Xie, Hong 28 Aug '08

28 Aug '08

Hello, group, I am running longitudinal process step by step following the wiki page of 12 differences between longitudinal and recon-all process. But some needed files are not generated by these 12 steps, for example, brain.mgz, wm.seg.mgz, wm.asegedit.mgz, aseg.auto_noCCseg.mgz, wm.mgz, fill.mgz, brain.finalsurfers.mgz, ?h.smoothwm, ?h.inflated, ?h.sulc, and ?h.aparc.annot. Should I use recon-all commands to create these files or just copy ( or transform) them from tp1 to tp2? Thank you for help. Hong

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(no subject)
by Xie, Hong 28 Aug '08

28 Aug '08

1 0

how to locate the auditory cortex?
by bin.lv 27 Aug '08

27 Aug '08

Hi all, After getting the cortical surface with Freesurfer,could I identify the location of the auditory cortex in each individual, and further then calculate the surface area , or the volume of it? In the paper of Cerebral Cortex " Cortical Folding Patterns and Predicting Cytoarchitecture", it seems that there is no auditory cortex yet. Thanks in advance, Bin Lv 2008-08-27 bin.lv

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FDR correction
by Manja Lehmann 27 Aug '08

27 Aug '08

Hi, We've noticed that FDR correction produces different p-values for the left and right hemispheres. We found that this issue was observed previously and an email was sent to the mailing list (see below), however, no answer was received. We wondered if anybody has noticed this problem before and if there are any suggestions on how best to deal with it. Thanks Manja Hi, FDR correction for multiple comparisons gives you different p-values for the left and right hemispheres. It seems really weird to report in a paper: a) that you've corrected for the right and left hemispheres separately and b) that the p-value that gave rise to a corrected probability of .05 was different for each. How do people deal with this issue? Take the most stringent p-value and use it for both hemispheres? Just report that FDR adjusted the p- value to .05? Also, correcting for right and left hemispheres separately assumes that they are independent observations. Unless you're studying callosotomy patients (and maybe even if you are) this doesn't seem justified. Are we supposed to be adjusting p-values accordingly? Thanks, Dara -- Manja Lehmann Research Assistant Dementia Research Centre University College London Institute of Neurology Queen Square London WC1N 3BG lehmann(a)drc.ion.ucl.ac.uk Tel: 020 7837 3611 ext. 3962 P Please consider the environment before printing this e-mail

2 1

dPSD in RPER
by Britta Holzel 27 Aug '08

27 Aug '08

For a rapid event-related design, how do I choose my dPSD, i.e. the delay of onset? I have a TR of 2 seconds and 45 trials for one stimulus type. Can I divide 2 seconds by 45 in order to get the maximum fine grained resolution? Or would it be better to have a larger dPSD, to make sure that I can average over several trials? Thanks! Britta -- Dr. Britta Hoelzel Massachusetts General Hospital Psychiatric Neuroscience Program 149 13th Street Charlestown 02129 MA USA https://www.nmr.mgh.harvard.edu/~britta

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Re: [Freesurfer] unpacking dicom
by Adrienne McCallister 27 Aug '08

27 Aug '08

Hello, Below is the unpacklog from the command: the command used was: unpacksdcmdir -src . -targ /autofs/space/jizo_001/users/RR-MBSR/002-ND_post -cfg /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/mycfg I was sitting in the /autofs/space/archive_166/siemens/Avanto-25096-20080621-122038-263000 directory. Thanks!! Log file created by unpacksdcmdir $Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $ /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/unpack.log /autofs/space/archive_166/siemens/Avanto-25096-20080621-122038-263000 Tue Aug 26 16:46:39 EDT 2008 -src . -targ /autofs/space/jizo_001/users/RR-MBSR/002-ND_post -cfg /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/mycfg mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2008/08/26-20:46:39-GMT BuildTimeStamp: Aug 21 2008 19:03:45 CVS: $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ User: adrienne Machine: jizo Platform: Linux PlatformVersion: 2.6.9-67.ELsmp CompilerName: GCC CompilerVersion: 30400 jizo Linux jizo 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:49:06 EST 2007 x86_64 x86_64 x86_64 GNU/Linux SkipMoCo 0 dicomdir . Scanning source directory ... INFO: summary file is /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/dicomdir.sumfile INFO: status file is /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/parse.status mri_parse_sdcmdir --sortbyrun --d . --o /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/dicomdir.sumfile --status /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/parse.status INFO: scanning path to Siemens DICOM DIR: . INFO: Found 1653 files in . INFO: counting Siemens Files $Id: mri_parse_sdcmdir.c,v 1.18 2007/04/27 02:23:42 nicks Exp $ cwd /autofs/space/archive_166/siemens/Avanto-25096-20080621-122038-263000 cmdline --sortbyrun --d . --o /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/dicomdir.sumfile --status /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/parse.status sysname Linux hostname jizo machine x86_64 user adrienne INFO: found 1651 Siemens Files INFO: scanning info from Siemens Files INFO: status file is /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 INFO: found 1651 Siemens files syngo MR B15 Could not parse NUMARIS version string syngo MR B15 found in dicom tag 18,1020 (len = 3 != 6) Sorting Assigning Run Numbers RunNo = 0 RunNo = 1 RunNo = 2 RunNo = 3 RunNo = 4 RunNo = 5 RunNo = 6 RunNo = 7 RunNo = 8 Done scanning Tue Aug 26 16:47:33 EDT 2008 ------------------------------------------ 1 localizer ok 512 512 3 1 263000-000001-000002.dcm 2 AAScout ok 128 128 128 2 263000-000002-000001.dcm 3 T1_MPRAGE_sag ok 256 256 128 1 263000-000003-000001.dcm 4 localizer ok 512 512 3 1 263000-000004-000002.dcm 5 AAScout ok 128 128 128 2 263000-000005-000001.dcm 6 T1_MPRAGE_sag ok 256 256 128 1 263000-000006-000001.dcm 7 T1_MPRAGE_sag ok 256 256 128 1 263000-000007-000001.dcm 8 post_ep2d_t1w ok 64 64 25 1 263000-000008-000001.dcm 9 RRMBSR ok 64 64 25 724 263000-000009-000001.dcm sortmethod fsfast unpacking config ------------------ {6 bold SPM pre_ge_functionals} ----------------------------------- --------------------------------------------------------- Run 6 ----------------------------------------- Tue Aug 26 16:47:33 EDT 2008 6 bold SPM pre_ge_functionals Files In Run: --------------- 263000-000006-000001.dcm 263000-000006-000002.dcm 263000-000006-000003.dcm 263000-000006-000004.dcm 263000-000006-000005.dcm 263000-000006-000006.dcm 263000-000006-000007.dcm 263000-000006-000008.dcm 263000-000006-000009.dcm 263000-000006-000010.dcm 263000-000006-000011.dcm 263000-000006-000012.dcm 263000-000006-000013.dcm 263000-000006-000014.dcm 263000-000006-000015.dcm 263000-000006-000016.dcm 263000-000006-000017.dcm 263000-000006-000018.dcm 263000-000006-000019.dcm 263000-000006-000020.dcm 263000-000006-000021.dcm 263000-000006-000022.dcm 263000-000006-000023.dcm 263000-000006-000024.dcm 263000-000006-000025.dcm 263000-000006-000026.dcm 263000-000006-000027.dcm 263000-000006-000028.dcm 263000-000006-000029.dcm 263000-000006-000030.dcm 263000-000006-000031.dcm 263000-000006-000032.dcm 263000-000006-000033.dcm 263000-000006-000034.dcm 263000-000006-000035.dcm 263000-000006-000036.dcm 263000-000006-000037.dcm 263000-000006-000038.dcm 263000-000006-000039.dcm 263000-000006-000040.dcm 263000-000006-000041.dcm 263000-000006-000042.dcm 263000-000006-000043.dcm 263000-000006-000044.dcm 263000-000006-000045.dcm 263000-000006-000046.dcm 263000-000006-000047.dcm 263000-000006-000048.dcm 263000-000006-000049.dcm 263000-000006-000050.dcm 263000-000006-000051.dcm 263000-000006-000052.dcm 263000-000006-000053.dcm 263000-000006-000054.dcm 263000-000006-000055.dcm 263000-000006-000056.dcm 263000-000006-000057.dcm 263000-000006-000058.dcm 263000-000006-000059.dcm 263000-000006-000060.dcm 263000-000006-000061.dcm 263000-000006-000062.dcm 263000-000006-000063.dcm 263000-000006-000064.dcm 263000-000006-000065.dcm 263000-000006-000066.dcm 263000-000006-000067.dcm 263000-000006-000068.dcm 263000-000006-000069.dcm 263000-000006-000070.dcm 263000-000006-000071.dcm 263000-000006-000072.dcm 263000-000006-000073.dcm 263000-000006-000074.dcm 263000-000006-000075.dcm 263000-000006-000076.dcm 263000-000006-000077.dcm 263000-000006-000078.dcm 263000-000006-000079.dcm 263000-000006-000080.dcm 263000-000006-000081.dcm 263000-000006-000082.dcm 263000-000006-000083.dcm 263000-000006-000084.dcm 263000-000006-000085.dcm 263000-000006-000086.dcm 263000-000006-000087.dcm 263000-000006-000088.dcm 263000-000006-000089.dcm 263000-000006-000090.dcm 263000-000006-000091.dcm 263000-000006-000092.dcm 263000-000006-000093.dcm 263000-000006-000094.dcm 263000-000006-000095.dcm 263000-000006-000096.dcm 263000-000006-000097.dcm 263000-000006-000098.dcm 263000-000006-000099.dcm 263000-000006-000100.dcm 263000-000006-000101.dcm 263000-000006-000102.dcm 263000-000006-000103.dcm 263000-000006-000104.dcm 263000-000006-000105.dcm 263000-000006-000106.dcm 263000-000006-000107.dcm 263000-000006-000108.dcm 263000-000006-000109.dcm 263000-000006-000110.dcm 263000-000006-000111.dcm 263000-000006-000112.dcm 263000-000006-000113.dcm 263000-000006-000114.dcm 263000-000006-000115.dcm 263000-000006-000116.dcm 263000-000006-000117.dcm 263000-000006-000118.dcm 263000-000006-000119.dcm 263000-000006-000120.dcm 263000-000006-000121.dcm 263000-000006-000122.dcm 263000-000006-000123.dcm 263000-000006-000124.dcm 263000-000006-000125.dcm 263000-000006-000126.dcm 263000-000006-000127.dcm 263000-000006-000128.dcm ----------------------------- VolRes: 1 1 1.3300000429153 ------- mri_convert ------------- mri_convert ./263000-000006-000001.dcm /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/pre_ge_functionals --sdcmlist /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/flf -ot spm --nspmzeropad 3 --in_type siemens_dicom ----------------------- mri_convert ./263000-000006-000001.dcm /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/pre_ge_functionals --sdcmlist /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/flf -ot spm --nspmzeropad 3 --in_type siemens_dicom mri_convert ./263000-000006-000001.dcm /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/pre_ge_functionals --sdcmlist /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/flf -ot spm --nspmzeropad 3 --in_type siemens_dicom $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from ./263000-000006-000001.dcm... INFO: found 128 files in list file INFO: loading series header info. RunNo = 5 INFO: sorting. INFO: (256 256 128), nframes = 1, ismosaic=0 AutoAlign matrix detected AutoAlign Matrix --------------------- 0.999 -0.024 0.042 -6.365; 0.029 0.991 -0.128 -13.683; -0.038 0.129 0.991 -2.572; 0.000 0.000 0.000 1.000; FileName ./263000-000006-000001.dcm Identification NumarisVer syngo MR B15 ScannerModel Avanto PatientName 002-ND-post_lazar Date and time StudyDate 20080621 StudyTime 122038.263000 SeriesTime 125014.602000 AcqTime 124127.222500 Acquisition parameters PulseSeq *tfl3d1_ns Protocol T1_MPRAGE_sag PhEncDir ROW EchoNo 1 FlipAngle 7 EchoTime 3.39 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 5 SeriesNo 6 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 85.5418 148.1949 113.2592 VolRes 1.0000 1.0000 1.3300 VolDim 256 256 128 Vc 0.0325 -0.9955 -0.0887 Vr 0.0356 0.0899 -0.9953 Vs -0.9988 -0.0292 -0.0384 VolCenter 9.2392 29.7880 -28.7659 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2730.00, TE=3.39, TI=1000.00, flip angle=7.00 i_ras = (0.0324721, -0.995527, -0.0887199) j_ras = (0.0356403, 0.0898636, -0.995316) k_ras = (-0.998837, -0.029158, -0.038399) writing to /autofs/space/jizo_001/users/RR-MBSR/002-ND_post/bold/006/pre_ge_functionals... Analyze Output Matrix 0.032 0.036 -1.328 86.802; -0.996 0.090 -0.039 149.139; -0.089 -0.995 -0.051 114.394; 0.000 0.000 0.000 1.000; No such orientation specified in Analyze7.5. Set orient to 0 Direction cosines for are: x_r = 0.0325, y_r = 0.0356, z_r = -0.9988, c_r = 9.2392 x_a = -0.9955, y_a = 0.0899, z_a = -0.0292, c_a = 29.7880 x_s = -0.0887, y_s = -0.9953, z_s = -0.0384, c_s = -28.7659 -------------------- INFO: set hdr.hist.orient to 'transverse unflipped' StartTime: Tue Aug 26 16:46:39 EDT 2008 EndTime: Tue Aug 26 16:47:40 EDT 2008 unpacksdcmdir Done On Wed, Aug 27, 2008 at 11:06 AM, Allison Stevens < astevens(a)nmr.mgh.harvard.edu> wrote: > Adrienne, > Please send the exact command line you used to the list. > Allison > > > On Wed, 27 Aug 2008, Adrienne McCallister wrote: > > Hello, >> >> I am trying to unpack dicom files for a specific subject. THese files are >> located at: >> >> /space/archive/166/siemens/Avanto-25096-20080621-122038-263000 >> >> I have tried both the unpacksdcmdir command as well as a dicom import >> directly into SPM. The unpacksdcmdir command did appear to work but there >> was only 1 functional scan unpacked. When I did the SPM import, the >> structurals seemed to import but again the functionals looked really >> strange. They just look like a white diagonal line going through the black >> background. >> >> These files may just be unusable but I wanted to ask if you had any input >> before I give up. Thanks for your help. >> >> Sincerely, >> >> Adrienne McCallister >> >>

2 1

unpacking dicom
by Adrienne McCallister 27 Aug '08

27 Aug '08

Hello, I am trying to unpack dicom files for a specific subject. THese files are located at: /space/archive/166/siemens/Avanto-25096-20080621-122038-263000 I have tried both the unpacksdcmdir command as well as a dicom import directly into SPM. The unpacksdcmdir command did appear to work but there was only 1 functional scan unpacked. When I did the SPM import, the structurals seemed to import but again the functionals looked really strange. They just look like a white diagonal line going through the black background. These files may just be unusable but I wanted to ask if you had any input before I give up. Thanks for your help. Sincerely, Adrienne McCallister

3 2

Compute First level Analysis
by Balaji Goparaju 26 Aug '08

26 Aug '08

Hi Doug and all, When i run selxavg3-sess -analysis LD-analysis -s LD-functional i seem to get errors in some other files, The output is as follows: [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% selxavg3-sess -analysis LD-analysis -s LD-functional -------------------------------------------------------------- selxavg3-sess logfile is /Users/balajigoparaju/Desktop/subjectdata/log/selxavg3-sess-bold-LD-analysis-080728180123.log -------------------------------------------------------------- ------------------------------------------- /Users/balajigoparaju/Desktop/subjectdata/LD-functional Mon Jul 28 18:01:23 EDT 2008 anadir = /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/LD-analysis ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2008 The MathWorks, Inc. Version 7.6.0.324 (R2008a) February 10, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.2 2007/11/27 18:42:09 greve Exp $ outtop = /Users/balajigoparaju/Desktop/subjectdata Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 LD-contrast.mat Loaded /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/emotion.par as a par2 file. ERROR: empty nonpar matrix for mcextreg ??? Attempt to reference field of non-structure array. Error in ==> flac_taskregind at 37 nev = length(flac.ev); Error in ==> flac_customize at 267 flacnew.indtask = flac_taskregind(flacnew); Error in ==> fast_selxavg3 at 97 flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thank you for the help you have been providing!

1 0

mgz into BRIK
by Deniz KATIRCIOGLU 26 Aug '08

26 Aug '08

Hi, When converting an AFNI .BRIK file to .mgz file, we are using the command "mri_convert" with the proper arguments supplied. So far, we do not have any problems and we can continue with the .mgz file quite fine. But, when the opposite operation is intended (converting the same .mgz file back into .BRIK), a "volume type 7" error appears saying that AFNI .BRIK format is not supported etc. We are desperately in need of using AFNI for several substantial purposes, how can we achieve that?? Thanks.. Deniz KATIRCIOGLU

3 2

Preproc-sess: Spatial smoothing and brain masking
by N. Eiji Nawa 26 Aug '08

26 Aug '08

Hi, I have just installed Freesurfer and I am now following the steps in the preprocessing tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/ FsFastTutorial) but for some reason preproc-sess is not generating (1) the motion corrected & smoothed volume fmcsm5.nii, and (2) the brain mask masks/brain.nii volume, as it should. Inspecting the terminal output, I couldn't see any potential source of problems apart from a warning generated by Matlab which says: Warning: Duplicate directory name: /Users/eiji/matlab. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Warning: Executing startup failed in matlabrc. This indicates a potentially serious problem in your MATLAB setup, which should be resolved as soon as possible. Error detected was: MATLAB:UndefinedFunction Undefined command/function 'setenv'. > In matlabrc at 224 >> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------ In spite of that, preproc-sess seems to exit without errors, later displaying 'spatiallysmooth-sess Done' and 'mkbrainmask-sess done'. So it looks that technically there wasn't an error? Checking the mailing lists archives, I found a recent thread discussing a similar problem but it is not very clear to me how it was solved in the end (Balaji? Doug?). Directory permissions looks fine (755). Could anyone help? (Link to the thread: http://www.mail-archive.com/ freesurfer(a)nmr.mgh.harvard.edu/msg07826.html. I am using the same subject line in this post...) I am attaching as a text file the terminal output of the command I am executing (' preproc-sess -s mgh-101.1 -fwhm 5 ' ). I also installed AFNI and FSL as I tried to advance in the tutorial. This is surely not a bug report, but for the record the description of my platform is as follows: --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v4.0.5 Kernel info: Darwin 8.11.0 Power Macintosh --------------------------------------------------------------------- Please include the following additional information in your report: 1) subject name -> mgh-101.1 (I suppose) 2) the entire command-line executed -> preproc-sess -s mgh-101.1 - fwhm 5 3) the error message generated -> No obvious error message, but fmcsm5.nii and masks/brain.nii are not generated 4) optionally include the subject's /script/recon-all.log -> (OK, now you got me, I see there are several recon-all.log's but none in the vicinity of the preproc tutorial directory...) ---- Any help will be greatly appreciated! If there is anything unclear, please, let me know. Thank you very much in advance. Eiji

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