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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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recon-all did not complete
by Abi Gopal 20 Nov '06

20 Nov '06

Hello all Below is my information: rhinal cat $FREESURFER_HOME/build-stamp.txt source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/rhinal/2/users/gopal/lynch_data which recon-all cd /space/rhinal/2/users/gopal/lynch_data I am not having an error per se, but recon-all keeps crashing before it is complete. If i look at the files that were created in order of date modified, the last file created in the surf folder (before it crashed) is rh_defect labels. files such as rh.sphere and rh.thickness were not created (although the corresponding lh files were). Do I have to run the entire recon-all program again? Or can I just run recon-all -s lynch -autorecon3? I am just trying to figure out if there is a quicker way to create the remaining files other than running the entire recon-all process, which will take another 30 hrs. I appreciate any suggestions. Thanks very much Abi

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WG: [Freesurfer] recon-all with more than one subject
by Juergen Haenggi 20 Nov '06

20 Nov '06

Dear Freesurfer users I tried to run a loop for the recon-all command over subjects in order to use computational resources optimally. But the following error occured: I used the following command: foreach s (Patient01 Patient02 Patient03) recon-all $s -all end The error message is: s: undefined variable Any idea what is wrong in the command? Thanks a lot in advance Best regards Juergen > > Dear Avram > > thanks for your advise. I had try it, but there is an error message. > > I used the following command: > > foreach s (Patient01 Patient02 Patient03) recon-all $s -all end > > The error message is: > > s: undefined variable > > Any idea what is wrong in the command? > > Thanks a lot in advance > Best regards > Juergen > > ---------------------------------------------- > Juergen Haenggi, Ph.D. student > Neuropsychology and Imaging > Division of Psychiatry Research > Psychiatric University Hospital > University of Zurich, Switzerland > P.O. Box 1931 > Lenggstrasse 31, 8032 Zurich > 0041 44 384 26 10 (office phone) > 0041 76 445 86 84 (mobile phone) > 0041 44 384 26 86 (fax) > H 115 (office room number) > juergen.haenggi(a)bli.unizh.ch (division email) > http://www.dpr.unizh.ch/ (division website) > http://www.juergenhaenggi.ch (private website) > ---------------------------------------------- > > > > -----Ursprüngliche Nachricht----- > > Von: Avram Holmes [mailto:holmes@fas.harvard.edu] > > Gesendet: Donnerstag, 19. Oktober 2006 15:10 > > An: Juergen Haenggi > > Betreff: Re: [Freesurfer] recon-all with more than one subject > > > > Juergen, > > > > You could use a 'foreach' loop > > > > e.g., "foreach s (subject1 subject2)" then enter your recon-all > > command with a "$s" in the place of the subject name. Then > type "end". > > > > This makes a loop that will run through each of the subjects > > individually. > > > > Avram > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Avram Holmes > > Department of Psychology > > Harvard University > > 1210 William James Hall Phone:(617) 495-0790 > > 33 Kirkland Street Fax:(617) 495-3728 > > Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > > > > > > On Thu, 19 Oct 2006, Bruce Fischl wrote: > > > > > Hi Juergen, > > > > > > why would you want to do such a thing? Just run recon-all > multiple > > > times with different subjects. > > > > > > cheers > > > Bruce > > > On Thu, 19 Oct 2006, Juergen Haenggi wrote: > > > > > >> Dear Freesurfer users > > >> > > >> is there any possibility to run recon-all with more than > > one subject? > > >> what is the option to use several subjects within one > > recon-all command? > > >> can one use more than one -s option in one recon-all command? > > >> > > >> thanks in advance > > >> best regards > > >> Juergen > > >> > > >> ---------------------------------------------- > > >> Juergen Haenggi, Ph.D. student > > >> Neuropsychology and Imaging > > >> Division of Psychiatry Research > > >> Psychiatric University Hospital > > >> University of Zurich, Switzerland > > >> P.O. Box 1931 > > >> Lenggstrasse 31, 8032 Zurich > > >> 0041 44 384 26 10 (office phone) > > >> 0041 76 445 86 84 (mobile phone) > > >> 0041 44 384 26 86 (fax) > > >> H 115 (office room number) > > >> juergen.haenggi(a)bli.unizh.ch (division email) > > >> http://www.dpr.unizh.ch/ (division website) > > >> http://www.juergenhaenggi.ch (private website) > > >> ---------------------------------------------- > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer(a)nmr.mgh.harvard.edu > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> > > >> > > >> > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >

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func2sph-sess registration question - where should individual subject's register.dat files be?
by raij＠nmr.mgh.harvard.edu 17 Nov '06

17 Nov '06

Hi, I did not see this documented anywhere so I figured it would be best to double check. Any group analysis relies on that the individual functional and structural data have first been aligned, and there is therefore a register.dat file in the individual subject's directory. This is usually saved at $STUDY_DIR/$SESSION_DIR/bold/register.dat Now, when I run a group analysis, the functional (or structural) space of each individual subject is re-mapped onto the structural space of the target brain. This process must have access to the correct subject-specific register.dat files for each individual subject. In the case of a spherical surface group analysis, I would do this re-mapping by func2sph-sess that I run inside the $STUDY_DIR. The command would have the format func2sph-sess -analysis <analysisname> -sf sessid -df sesspar -trgsubject fsaverage -projfrac 0.3 where the contents of the "sessid" file would list all my $SESSION_DIRs (i.e., different subjects). Question: Where does func2sph-sess look for the individual level register.dat files? I assume it will automatically find them at $STUDY_DIR/$SESSION_DIR/bold/register.dat Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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GM segmentation
by Gallo, Antonio (NIH/NINDS) [F] 17 Nov '06

17 Nov '06

Dear All, I have a question regarding the pial surface in medial temporal lobes since segmentation fails to catch up some GM. Do you have any suggestions (do control point to add GM exist?) to fix this underextimation of GM ? Many 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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