Freesurfer November 2006

freesurfer@nmr.mgh.harvard.edu

41 participants
59 discussions

mri_convert 4D
by Shi, Bo 22 Nov '06

22 Nov '06

Hi - I've been using the mri_convert referenced in the email below to convert DICOM to ANALYZE format. Has this feature been included in the new Freesurfer release? Re: [Freesurfer] mri_convert: dicom to nifti 4D Doug Greve Fri, 07 Jul 2006 11:10:27 -0700 Hi Adam, I've created a new version of mri_convert which should hangle multi-frame GE dicom data properly. You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert Run it as you would ordinarily, but add -dicomread2 to the cmd line. I want to stress that this is experimental and that you are practically alpha testing it. Do you have other data sets that you can test it on? It should really be tested on several acquisitions collected with various orientations. The volumes should have fiducials to make sure that we are getting right right, but it might take me a while to drum up such data sets. doug

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Version problems
by Martin Ystad 22 Nov '06

22 Nov '06

Hi, I have currently processed some 100 brains in freesurfer on different machines. Unfortunately, one machine was installed with version 3.0.3 (64 bit version), while the other machines were using version 3.0.1 (32 bit). It now looks like there is a systematic difference in the results from the various versions. I tested my suspicion by processing several identical volumes in both versions. The 3.0.3 version under-estimated the Intra Cranial Volume compared to the 3.0.1 version (around 75% of the 3.0.1-volume). Most other measures were slightly smaller, but no more than between 95-99% of the 3.0.1-volumes. What is the reason for this? How much of the processing stream do I have to re-run? Thanks, Martin Ystad Medical Student University of Bergen, Norway.

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feature wish for tkregister/tkmedit
by Sebastian Moeller 22 Nov '06

22 Nov '06

Hi All, Hi Doug, now since 3.0.4 is out of the door, you might be wondering what to do next ;). In case you are short of ideas, here is my short wish list for new features. It is all about mosaic/slice display in the two programs. Tkmedit does allow a mosaic view of volumes, which is nice. Now it always seems to take 16 slices at fixed interval over the whole volume. Since I am working with small monkey brains this results in almost half of the slices showing nothing. Now it would be great if one could tell tkmedit the start and stop slices (or center point and extent) for the mosiac building, so one can make sure the slices shown actually contain information. The second proposal is actually more of the first, it would be cool, if tkregister2 could also display a mosaic (prefereably at a definable position, like in the tkmedit proposal). Then co registering might profit from this display mode, as this would allow assessment of the effect of changes over the whole volume. I think it would allow a better evaluation about the trade-offs between local fit and global fit. Anyway, thanks for supplying such a nice and powerful package to work with. BTW I dropped one of my speciemens into the ftp drop last week, any idea how to improve the quality of the recon/surface extraction? ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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more than one edit in the same subject
by Gallo, Antonio (NIH/NINDS) [F] 21 Nov '06

21 Nov '06

Dear All, Since I sometimes need to fix more than one output in the same subject (for example, editing the WM, correcting the pial surface, and adding some control points), I was wondering whether 1) I had to run autorecon2 after each correction; 2) If yes (to the above), should I run autorecon2 in any specific order? Thanks, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

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RE: [Freesurfer] mri_convert SC dicom
by Kirk, Gregory 21 Nov '06

21 Nov '06

Once again on this, did not get back from you after my response to this. The dicom spit out by Analyze also crashes spm5, our pacs will eat it and I can display it in pacs. Is there a way to turn off the resampling or do I need to add a tag with the k_ras coords. don't know what to make of WARNING: NumberOfFrames 0 != Found Count of slices 104. I would be glad to dump the files off to you, don't know how interested you are in spending your busy day supporting Analyze software, im getting to find it more trouble than it is worth. but untill I get time to write some ITK thing to do SISCOM studies Im stuck with trying to cooregister the nuclear med hotspots generated in Analyze to FSL diffusion stats. thankx Greg. -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tuesday, November 14, 2006 4:05 PM To: Kirk, Gregory Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert SC dicom What exactly is the problem? Kirk, Gregory wrote: Hi folks, I was trying to convert an dicom MPRAGE with a SISCOM activation( grayscale ) to nii format to use the activation for a seed for probalistic fiber tracking. The siscom is created in Analyze(program not file format) and then exported to dicom , so it is a secondary capture siscom. I know this is not really a freesurfer thing but I guess you guys when possible try to make your tools mutually usefull so I send the error in case you see a simple fix by an option I can apply. set orientation seems to be the issue notice k_ras = (nan, nan, nan) also WARNING: NumberOfFrames 0 != Found Count of slices 104. thanks if you can help Greg. reading from i170927.SCPT.1... 104 DICOM 3.0 files in list Found 104 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 104. reading DICOM image... ------------------------------------------------- DICOM meta-header file name /home/gkirk/tillsis/dicom/i170927.SCPT.1 Date and time study date 20061114 study time 142154 series time 142014.000000 acquisition time 142014.000000 Identification patient name manufacturer SIEMENS NM Dimensions number of rows 256 number of columns 256 number of frames 104 pixel width 1 pixel height 1 slice thickness 2 field of view 256 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 4.7 repetition time 1870 inversion time 1100 echo number 0 flip angle 0.261799 bits allocated 8 Spatial information first image position -132.963 -132.808 -122.125 last image position -132.963 -132.808 -122.125 image orientation 1 -2.05103e-10 0 2.05103e-10 1 0 ------------------------------------------------- TR=1870.00, TE=4.70, TI=1100.00, flip angle=15.00 i_ras = (-1, 2.05103e-10, 0) j_ras = (-2.05103e-10, -1, 0) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): source matrix has zero determinant; matrix is: -1.000 -0.000 nan nan; 0.000 -1.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; [gkirk@Nuit dicom]$ _____ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu 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

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roisummary question
by Cameron Ellis 21 Nov '06

21 Nov '06

Hello, I am trying to interpret the results I receive from roisummary-sess. My analysis models the hrf using spmhrf 1 and I have 3 conditions. However, roisummary-sess generates 6 condition values for each subject. Does this have something to do with the fact that spmhrf 1 calculates both amplitude and latency and is therefore giving me 2 numbers for each condition? If so, which numbers correspond to which calculation? Help from anyone is much appreciated... Thanks, Cameron

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mri_vol2surf puzzle
by Joongnam Yang 21 Nov '06

21 Nov '06

I posted my question to FSL mailing list, but I guess this forum is more appropriate. The question is, I have been using mri_vol2surf to convert FSL output into one that is readable by Freesurfer, like the following. ex) mri_vol2surf --src DPJ/RUN1/djp091306_4_1+.feat/thresh_zstat1.img --src_type analyze --srcreg register.dat --hemi lh --projfrac 0.5 --out DPJ/RUN1/djp091306_4_1+.feat/thresh_zstat1-lh.w --out_type paint However, in the feat directory via the NEW version of FSL, there is no *.img files (such as thresh_zstat1.img), which mri_vol2surf needs. Instead there are *.nii.gz and *.vol files (such as thresh_zstat1.nii.gz or thresh_zstat1.vol). Would someone let me know how to go about this problem? Nam.

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Installation of v3.0.4
by Julia Hamstra 21 Nov '06

21 Nov '06

Hello, I just installed the most recent stable version of freesurfer for Mac Tiger OS. GSL did not install with it and tksurfer and such gives and error like this: dyld: Library not loaded: /usr/pubsw/packages/gsl/1.6/lib/libgsl.0.dylib Referenced from: /Applications/freesurfer/bin/tkmedit.bin Reason: image not found Trace/BPT trap Additionally, FSL GUIs do not run with this error: Application initialization failed: Can't find a usable init.tcl in the following directories: .... This probably means that Tcl wasn't installed properly. Error in startup script: can't find package Tix while executing But the Tcl directories are not empty. X11 is up to date. I ran the set up file. I'm using tcsh. Are these common issues or is there something the matter with my computer? Thanks ~julia -- UC Davis Neuroscience Graduate Group The M.I.N.D. Institute - Amaral Lab (916) 703-0376

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(no subject)
by Richard Bantz 20 Nov '06

20 Nov '06

freesurfer, Control points seem to work for some scans and not others. The enclosed pictures illustrate a case in which cp's are added to wm but when re-run the wm does not take( 12 slices ). I have tried this twice and both times the same results, is there a fix? Thankyou, Richard M Bantz

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pial surface
by Wolf, Ingo 20 Nov '06

20 Nov '06

Dear all, I have 2 question concerning edits to the pial and wm surface. 1) After editing the pial surface in the ventral temporal lobe (parts of the cerebellum were erroneously included), there were no visible changes in the pial surface after rerunning autorecon2. Is it possible that correction of the pial surface by editing/deleting voxels in the brainmask.mgz volume shows an effect in superior parts of the brain (e.g. upper parts of the dura) but not in inferior parts that are adjacent to other tissue? How do I correct errors like that? And how do I extend the pial surface anyways? 2) When deleting those exessive pixels of the cerebellum that were classified as pial surface, I obviously deleted parts of the cerebellum in the brainmask.mgz. Will this have an effect on the cerebellar volume measurements? Thanks a lot! Best, Ingo Wolf

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Freesurfer November 2006