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Fwd: DICOM unpacking error
by Luc Amdahl 18 Jun '13

18 Jun '13

---------- Forwarded message ---------- From: Luc Amdahl <luc.amdahl(a)gmail.com> Date: Mon, Jun 17, 2013 at 3:45 PM Subject: Re: [Freesurfer] DICOM unpacking error To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi Bruce, Thanks for responding. Here is the command line and screen output: [Sheinberg-Lab-MRI-iMac:~/MRI/Solar_System] lab% unpacksdcmdir -src DICOM -targ subj_4 -fsfast -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii $Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $ /Users/lab/MRI/Solar_System -src DICOM -targ subj_4 -fsfast -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii Fri Jun 14 09:47:20 EDT 2013 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/06/14-13:47:20-GMT BuildTimeStamp: May 13 2013 16:45:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: lab Machine: Sheinberg-Lab-MRI-iMac.local Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40000 Sheinberg-Lab-MRI-iMac.local Darwin Sheinberg-Lab-MRI-iMac.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 Fri Jun 14 09:47:20 EDT 2013 Log File is subj_4/unpack.log INFO: Logfile is subj_4/unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is subj_4/dicomdir.sumfile INFO: status file is subj_4/parse.status Scanning directory Fri Jun 14 09:47:20 EDT 2013 mri_parse_sdcmdir --sortbyrun --d DICOM --o subj_4/dicomdir.sumfile --status subj_4/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 Done scanning Fri Jun 14 09:48:46 EDT 2013 ------------------------------------------ 1 localizer ok 512 512 3 1 59198979 2 T1_MEMPRAGE_freesurfer ok 256 256 176 4 59199008 3 T1_MEMPRAGE_freesurfer ok 256 256 176 4 59187534 4 T1_MEMPRAGE_freesurfer ok 256 256 176 1 59175542 5 ep_TR2500_128 ok 64 64 42 128 59175096 6 ep_TR2500_128 ok 64 64 42 128 59170659 7 ep_TR2500_128 ok 64 64 42 128 59169456 8 ep_TR2500_128 ok 64 64 42 128 59168253 9 ep_TR2500_128 ok 64 64 42 128 59167050 10 ep_TR2500_128 ok 64 64 42 128 59162613 11 ep_TR2500_113 ok 64 64 42 113 59299072 12 t2_3DFLAIR ok 256 240 176 1 59297629 unpacking config ------------------ {5 bold nii f.nii} {6 bold nii f.nii} {7 bold nii f.nii} {8 bold nii f.nii} {9 bold nii f.nii} {10 bold nii f.nii} ----------------------------------- --------------------------------------------------------- Run 5 ----------------------------------------- Fri Jun 14 09:48:46 EDT 2013 5 bold nii f.nii ERROR: reading DICOM/59175096 tag 28 30 Here is the version of FS I'm using: freesurfer-i386-apple-darwin10.8.0-stable5-20130513 What exactly do you mean when you ask where the DICOM's are from? I receive them from Brown's MRF facility, and we've been successful in converting them on other iMac's using the same version of FS. Thanks, Luc On Mon, Jun 17, 2013 at 2:36 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > can you send the complete command line and screen output, and tell us what > version of FS you are using and where the dicoms are from? > > On Mon, 17 Jun 2013, Luc Amdahl wrote: > > Hi Freesurfers, >> I am trying to use Freesurfer to convert DICOM files to nii f.nii files. >> Freesurfer is able to find all the DICOM files but always gives me an >> error: >> "ERROR: reading DICOM/59175096 tag 28 30". >> >> Can anyone help? >> >> Thanks, >> >> Luc >> >> -- >> Luc Amdahl >> Brown University '14 >> Sc.B. Neuroscience >> 69 Brown St., #6137 >> Providence, RI 02912 >> 603.252.4441 >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

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Rejoindre mon réseau sur LinkedIn
by Octavian Lie via LinkedIn 18 Jun '13

18 Jun '13

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Difference b/w White matter hyper-intensities and hypo-intensities
by Akshay 17 Jun '13

17 Jun '13

Hi All, There is a label named White-matter hypo-intensities (77), is it the same as white matter hyper-intensity? If not, can anyone tell me the difference? Thanks in advance, Akshay

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DICOM unpacking error
by Luc Amdahl 17 Jun '13

17 Jun '13

Hi Freesurfers, I am trying to use Freesurfer to convert DICOM files to nii f.nii files. Freesurfer is able to find all the DICOM files but always gives me an error: "ERROR: reading DICOM/59175096 tag 28 30". Can anyone help? Thanks, Luc -- Luc Amdahl Brown University '14 Sc.B. Neuroscience 69 Brown St., #6137 Providence, RI 02912 603.252.4441

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Editing Criterion
by R Duke 17 Jun '13

17 Jun '13

Hello Freesurfer Experts, I am relatively new to FS'r and was wondering if there were any references I could use to establish criteria for editing my results (pial surface, GM, and WM classifications). I am using two MPRAGE files (which gives me great results), but still would like to do some manual editing. Is this just left to the users discretion or would you all recommend a validated method that has been published? Cheers, R. Duke

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correlation analysis
by stdp82＠virgilio.it 17 Jun '13

17 Jun '13

Hi list, I have performed cortical thickness analysis and I have individuated a ROI. Now, I'd like to perform a correlation analysis by qdec (if possible) between cortical thickness in this ROI and neuropsychological test score. I'm reading some previous post such as http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12683.html,but I do not understand the passages that I should do. Please, may you briefly schematize the operation that I should do? Thank you very much, Stefano

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Re: [Freesurfer] SPM ROI to Cortical Thickness
by McMains, Stephanie 17 Jun '13

17 Jun '13

I am wondering why you didn't tell them to go through fsvarege space? I thought that was an easy way to go from SPM MNI to freesurfer land. tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/to/spm/roi/yourfile.img I am wondering because when I look at the segmentation for fsaverage, it seems like it is missing a lot of the gray matter, particularly in the big sulci, most likely from the 'smoothing' that comes with averaging subjects together. And therefore I wonder if this is the best thing to use as an intermediate step. Are you instead suggesting (as it seemed like in this thread), to put the SPM roi into individual subject space and then somehow project it to the surface in free surfer? Thanks, Stephanie +++++++++++++++++++++++++ Stephanie McMains Neuroimaging Staff Scientist Center for Brain Science Harvard University 52 Oxford Street Cambridge, MA 02138 +++++++++++++++++++++++++ For answers to frequently asked questions: http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information…

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Visual Word Form Area and cortical thickness
by Garikoitz Lerma-Usabiaga 17 Jun '13

17 Jun '13

Hi list, I am interested in a Cortical Thickness analysis in the Visual Word Form Area. I have been suggested to use a MNI152 coordinate and make an sphere (circle in this case) of 5mm around it. Has anybody got any experience or any recommendation on how to establish the visual word form area for CT in freesurfer? many thanks in advance, Gari

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20130617 Stelle_postdoc_fMRT_EEG.docx
by Direktion, Institut f. Schlaganfall- und Demenzforschung 17 Jun '13

17 Jun '13

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load annot
by LAOUCHEDI MAKHLOUF 17 Jun '13

17 Jun '13

Hi I loaded an annotation file (that i generated using the command annot2label then label2annot) on a pial surface using tksurfer : tksurfer subj lh pial then i loaded my annotation file (frontal association cortex). is it possible to reload it with a unique color for all the gyri and sulci ? thanks for help

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