Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

focus in tkmedit
by Michael Harms 03 Jan '08

03 Jan '08

Hello, When using the "Multiple Orientations" display of tkmedit with the 'Select voxels tool' mode of operation, the centering of the images seems to "jump" around as I change the focus (i.e., green outlined quadrant) using a left click, and the cross-hair ends up at a location other than where the mouse cursor was located when the left-click was performed. Consequently, I have a hard time getting the "Multiple Orientations" view to display as I want. Is there a way around these behaviors? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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mri_convert
by HAMID REZA DABIRZADEH 03 Jan '08

03 Jan '08

Hi, I am very new to FMRI and would appreciate your help with my first attempt to use real data. I am trying to convert dicom images produced by a Siemens scanner to nii.gz format to be analysed by FSL FEAT. These BOLD images have 7 digit names without an extension and are in a folder on a CD which also contains a dicomdir file. Below you can see the command I have used and the output. The 001.nii.gz file has only one volume while the study consists of multiple volumes. Is there anything I should do differently. Thanks, Bahman [root@localhost Desktop]# mri_convert -i temp/45516912 -ot nii 001.nii.gz mri_convert -i temp/45516912 -ot nii 001.nii.gz $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from temp/45516912... Getting Series No Scanning Directory INFO: Found 723 files in temp INFO: Scanning for Series Number 80 WARNING: searching dicom file temp/dicomdir for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. WARNING: searching dicom file temp/dicomdir for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. INFO: found 9 files in series INFO: loading series header info. INFO: sorting. RunNo = 79 INFO: (128 128 9), nframes = 1, ismosaic=0 AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName temp/45516912 Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Symphony PatientName **** Date and time StudyDate 20070216 StudyTime 110335.484000 SeriesTime 112105.578000 AcqTime 112059.464999 Acquisition parameters PulseSeq epfid2d1_64 Protocol BOLD 1 (Dec 4) PhEncDir ROW EchoNo 0 FlipAngle 90 EchoTime 40 InversionTime -1 RepetitionTime 2000 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 79 SeriesNo 80 ImageNo 1 NImageRows 128 NImageCols 128 NFrames 1 SliceArraylSize 9 IsMosaic 0 ImgPos 117.6862 129.3817 45.4824 VolRes 1.8750 1.8750 10.0000 VolDim 128 128 9 Vc -1.0000 0.0010 -0.0086 Vr -0.0000 -0.9940 -0.1097 Vs -0.0087 -0.1097 0.9939 VolCenter -2.6996 5.2827 76.0057 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2000.00, TE=40.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999962, 0.000951853, -0.00862145) j_ras = (-2.16616e-10, -0.99396, -0.109738) k_ras = (-0.00867384, -0.109734, 0.993923) writing to 001.nii.gz... _________________________________________________________________ Introducing the City @ Live! Take a tour! http://getyourliveid.ca/?icid=LIVEIDENCA006

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A problem with Deflate compression of tif format
by Jiefeng Jiang 03 Jan '08

03 Jan '08

Hi, I met the problem of "Deflate compression support is not configured. TiffWrite: TIFFWriteScanline returned error" when I used mris_make_template. Currently I use libtiff4 for tiff interface and zlib1g for deflate compression. In addition, I linked libtiff.so.3 to libtiff.so.4. I also tested the two libs by opening and saving a sample tiff image and they worked well. I have no idea how to solve this, maybe I need to establish another link for deflate compression... Could somebody give me some advices? Thank you in advance! Jiefeng Jiang Medical image computing National lab of pattern recognition Institute of automation, CAS Beijing, China +86 10 62659278

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qdec error
by Michael Harms 03 Jan '08

03 Jan '08

Hello, First, ... Happy New Year! When trying to run a basic qdec analysis between two groups (using qdec from FS v4.0.2), I get an error in a pop-up window, which I've screen- captured and attached as a gif. This is a Linux-centos4 installation, and it doesn't have a /usr/pubsw directory, so I'm at a bit of a loss for how to interpret the error message. Do I need to install some other library? The output in the terminal at the point of the error window reads: -------- ... gdfReadHeader: reading /disk/conte_raid1/freesurfer/conte_mprage/qdec/Untitled/y.fsgd INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 classificationProband 2 classificationControl WARNING: Marker for class classificationProband was invalid. WARNING: Color for class classificationProband was invalid. WARNING: Marker for class classificationControl was invalid. WARNING: Color for class classificationControl was invalid. --------- If I click 'Ok', the popup goes away momentarily, and then the same popup window reappears. If I click 'Ok' a second time, I get an inflated surface with p-values in the qdec display, but the popup error message continually re-occurs as I select different analyses under the "Scalars" box. I tried "setenv XLIB_SKIP_ARGB_VISUALS 1" wondering if that might be related, but this had no effect. thanks for any insight, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Re: Freesurfer Digest, Vol 47, Issue 2
by Simon Rushton 02 Jan '08

02 Jan '08

I feel somewhat uneasy simply assuming that the process worked just because it didn't exit with an error. Is my concern misplaced? Should I feel happy about submitting a ms based on freesurfer analyses that have not been independently checked? If it is necessary/advisable to do some independent checking, are there a couple of simple things (later reconstructions) that can be checked that indicate whether all is fine, or whether it is necessary to go back and check systematically each of the various stages documented on the wiki pages? simon > Date: Wed, 2 Jan 2008 07:17:13 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] checking problems > To: Feng-Xian Yan <b9403208(a)stmail.cgu.edu.tw> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <Pine.LNX.4.62.0801020716430.5653(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="big5" > > Hi, > > we don't usually stop and check anymore as things fail pretty > rarely. You > can look at the tutorial on the wiki for examples of the types of > failures > and how to fix them. > > cheers, > Bruce > > On > Wed, 2 Jan 2008, Feng-Xian Yan wrote: > >> Hi, >> I have some confusion. When I completely run the command, recon-all >> ¡Vs x249 ¡Vautorecon1, and I should stop to check for problems with >> intensity normalization, talairach transformation and skull >> stripping. >> How can I do to check these problems? And, which is I must do first? >> >> Thanks. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>

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checking problems
by Feng-Xian Yan 02 Jan '08

02 Jan '08

Hi, I have some confusion. When I completely run the command, recon-all –s x249 –autorecon1, and I should stop to check for problems with intensity normalization, talairach transformation and skull stripping. How can I do to check these problems? And, which is I must do first? Thanks.

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How to generate inflated.H file?
by Jiefeng Jiang 01 Jan '08

01 Jan '08

Hi, Happy New Year everybody! I met a problem when I tried to make a template using "mris_make_template", it needs ?h.inflated.H file. However, I only have ?h.inflated file. Does anyone know how to generate ?h.inflated.H file? Thank you in advance! Jiefeng Jiang Medical image computing National lab of pattern recognition Institute of automation, CAS Beijing, China +86 10 62659278

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Status of the Source ?
by Ivan Blagoev Topolsky 30 Dec '07

30 Dec '07

Hello, I wanted to ask about what's hapenning with the source code, will it be release anytime soon ? The webpages say that it will be available any moment now, but in fact the message has remained such for quite some time : my last question about it on this list was back in summer 2006. Did some unexpected problem arise ? Or will actually the source code be available soon ? Also, another question : Are there developers trying to use GPGPU techniques to accelerate the processing speed ? (using nvidia's CUDA, ATI's Brook or similar technologies ?) Thank you for your help. - Ivan -

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mri_convert --out_orientation with inhomogeneous volumes
by Ray Fix 23 Dec '07

23 Dec '07

Dear FS Listers, mri_convert isn't giving me quite what I expected when I use it to reorient an inhomogeneous volume. I apologize in advance if it is my misunderstanding or something that has been covered before. These orientation issues make my head spin (as they do the subject data ;-). Consider the following example: > % mri_info volume.mgz > : > dimensions: 256 x 256 x 128 > voxel sizes: 1.0000, 1.0000, 1.3300 > : > Orientation : PIL > Primary Slice Direction: sagittal > : > I take this volume and reorient it with mri_convert to LIA orientation. > % mri_convert --out_orientation LIA volume.mgz volume_LIA.mgz But what it gives me back is unexpected. > % mri_info volume_LIA.mgh > : > dimensions: 256 x 256 x 128 > voxel sizes: 1.0000, 1.0000, 1.3300 > : > Orientation : LIA > Primary Slice Direction: coronal I was first surprised first that mri_convert was resorting to trilinear interpolation. It seems like this kind of transformation could be done with 100% fidelity using nearest neighbor. But the bigger concern is I would have also expected the output dimensions to be 128x256x256 with the voxel sizes 1.33, 1.00, 1.00. It seems like if you reorient a non cubic volume with mri_convert, it arbitrarily cuts some of the data out from the posterior and anterior. tkmedit display seems to confirm this. To put it another way, I would expect: > mri_convert --out_orientation PIL volume_LIA.mgz volume_PIL.mgz to generate at volume_PIL.mgz file that was voxel identical to the original volume.mgz. Thanks for your time. Ray

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where is the patient information in the mgz files
by Wang, Xin 23 Dec '07

23 Dec '07

Hello, Group, I have a problem to read patient information in the .mgz files. this information was stored in the header files of dicom files. Could sb. tell me how to read this information from the .mgz files? Thank you in advance, Xin Wang

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Freesurfer