Re: [Freesurfer] tkmedit crashes/freezes
Derin, Does the file .xdebug_tkmedit show any error messages after a lock-up occurs? If so, can you send that file to me? Another possibility is that the graphics driver may need to be updated. Do you have an NVIDIA card? Nick I've been experiencing some crashes/freezing using tkmedit lately, and have been able to reproduce it pretty reliably. It occurs when I scroll through the slices of the subject either using the arrows keys or clicking through on the toolbar. It happens when viewing a variety of volumes (brainmask, T1, etc), and from a variety of perspectives (coronal, sagittal, etc); it also happens on different subjects as well. This occurs no matter what workstation I use in the lab (networked environment). My X freezes up as well as the keyboard, but the mouse doesn't. I used to be able to restart my X remotely, but now tkmedit locks up so bad I have to reboot. Any ideas? Dell Precision 670 Workstations CentOS 4.1 (32-bit) freesurfer-Linux-centos4-stable-pub-v3.0.3 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /pkg/brainmap/freesurfer FSFAST_HOME /pkg/brainmap/freesurfer/fsfast SUBJECTS_DIR/disk/k2/freesurfer/neuromorph_v1_flash/ FUNCTIONALS_DIR /pkg/brainmap/freesurfer/sessions MINC_BIN_DIR/pkg/brainmap/freesurfer/mni/bin MINC_LIB_DIR/pkg/brainmap/freesurfer/mni/lib PERL5LIB/pkg/brainmap/freesurfer/mni/lib/perl5/5.8.0 GSL_DIR /pkg/brainmap/freesurfer/lib/gsl QTDIR /usr/lib/qt-3.3 TCLLIBPATH /pkg/brainmap/freesurfer/lib/tcltktixblt/lib FSL_DIR /pkg/brainmap/freesurfer/fsl [EMAIL PROTECTED] ~]$ which tkmedit /pkg/brainmap/freesurfer/bin//tkmedit cd /disk/k2/freesurfer/neuromorph_v1_flash/ Thanks in advance. -Derin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit crashes/freezes
Hm, I can't reproduce this. So, you load up a volume, and repeatedly press an arrow key to scroll through the slices? Or hold the button down? On Mon, Aug 28, 2006 at 11:16:49AM -0500, Derin Cobia wrote: I've been experiencing some crashes/freezing using tkmedit lately, and have been able to reproduce it pretty reliably. It occurs when I scroll through the slices of the subject either using the arrows keys or clicking through on the toolbar. It happens when viewing a variety of volumes (brainmask, T1, etc), and from a variety of perspectives (coronal, sagittal, etc); it also happens on different subjects as well. This occurs no matter what workstation I use in the lab (networked environment). My X freezes up as well as the keyboard, but the mouse doesn't. I used to be able to restart my X remotely, but now tkmedit locks up so bad I have to reboot. Any ideas? Dell Precision 670 Workstations CentOS 4.1 (32-bit) freesurfer-Linux-centos4-stable-pub-v3.0.3 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /pkg/brainmap/freesurfer FSFAST_HOME /pkg/brainmap/freesurfer/fsfast SUBJECTS_DIR/disk/k2/freesurfer/neuromorph_v1_flash/ FUNCTIONALS_DIR /pkg/brainmap/freesurfer/sessions MINC_BIN_DIR/pkg/brainmap/freesurfer/mni/bin MINC_LIB_DIR/pkg/brainmap/freesurfer/mni/lib PERL5LIB/pkg/brainmap/freesurfer/mni/lib/perl5/5.8.0 GSL_DIR /pkg/brainmap/freesurfer/lib/gsl QTDIR /usr/lib/qt-3.3 TCLLIBPATH /pkg/brainmap/freesurfer/lib/tcltktixblt/lib FSL_DIR /pkg/brainmap/freesurfer/fsl [EMAIL PROTECTED] ~]$ which tkmedit /pkg/brainmap/freesurfer/bin//tkmedit cd /disk/k2/freesurfer/neuromorph_v1_flash/ Thanks in advance. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Regarding missing DICOM fields
Which diom tags do you mean? I think we can get away with not having the Patient Orientation (tag 20,20) -- I'm not sure why I required it in the first place. ImagePositionPatient (tag 20,32) is considerably more important as this is one of the ways the slices are sorted and the direction cosines estabilished. Are these for mosaics? doug Niels Bergsland wrote: Hi, We have some old scans that were originally in ACR-NEMA format which we have converted to DICOM. The problem is that they are missing both the ImagePositionPatient and ImageOrientationPatient fields. Is there anyway to use freesurfer without having these two fields? Based on the post by Doug which I found at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03409.html , I am afraid not... Thank you for any help. Regards, Niels Bergsland ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] anonymizing dicom files
sorry about nonstop posting! I'm trying to remove the patient names from dicom files. I was advised to use dcm_modify_elements but it fails on DCM_Openfile. Is there a straight forward way of doing this? Thanks Naj P.S. Doug, I am still looking for the graddir tags :) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] anonymizing dicom files
there is a package for subject deidentification, which contains also DICOM anonymizing. http://www.na-mic.org/Wiki/index.php/MBIRN:BIRNDUP:Distribution or another program for DICOM anonymizing: http://eng.neologica.it/download/downloadDICOMAnonymizer.html Silvester Najmeh Khalili M. wrote: sorry about nonstop posting! I'm trying to remove the patient names from dicom files. I was advised to use dcm_modify_elements but it fails on DCM_Openfile. Is there a straight forward way of doing this? Thanks Naj P.S. Doug, I am still looking for the graddir tags :) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] newbie question event-related
Hi List, hi Doug, for the first time I have now data, that realloy wants event-related analysis (200ms stimulation every 10 seconds). Now, using a TER of 0.2 in the para-file and using -dt event-related in mkanalysis-sess.new (3.0.3 pub x86_64 centos4) was the easy part, but what do I have to specify in mkcontast-sess? Especially thi -ircorr complex (with -deltarang and -taurange) is daunting. Is it necessary to specify anything here to get a real event-related analysis, or does fs-fast already know enough without these parameters (as I specified delta, tau and even taummax in mkanalysis)? So far any nicorr value I used produced errors on the way... I would be delighted for any pointer of how to properly convinve fs-fast to analyse my data ;). Ahoi thanks 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 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] anonymizing dicom files
There's also Osirix on the Mac:http://homepage.mac.com/rossetantoine/osirix/Index2.htmland ImageJ has a plugin:http://rsb.info.nih.gov/ij/plugins/dicom-rewriter.htmlHaven't used the latter, but can vouch for the former!regards,GreigOn 29/08/2006, at 6:16 AM, Russ Poldrack wrote:You can use the LONI deidentification debablet to do this:http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=23cheersrussOn Aug 28, 2006, at 1:07 PM, Doug Greve wrote:Sorry, no clue.Najmeh Khalili M. wrote: sorry about nonstop posting!I'm trying to remove the patient names from dicom files. I was advised to use dcm_modify_elements but it fails on DCM_Openfile.Is there a straight forward way of doing this?ThanksNajP.S. Doug, I am still looking for the graddir tags :)___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D.MGH-NMR Center[EMAIL PROTECTED]Phone Number: 617-724-2358 Fax: 617-726-7422In order to help us help you, please follow the steps in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ---Russell A. Poldrack, Ph.d.Associate ProfessorUCLA Department of PsychologyFranz Hall, Box 951563Los Angeles, CA 90095-1563phone: 310-794-1224fax: 310-206-5895email: [EMAIL PROTECTED]web: www.poldracklab.org ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __Dr Greig de ZubicaraySenior Research FellowfMRI Laboratory, Centre for Magnetic ResonanceUniversity of Queensland, QLD 4072, AustraliaTel: (+617) 3365 4100 (Office) (+617) 3365 4250 (B106, Ritchie Building)Fax: (+617) 3365 3833fMRI Lab Page: http://www.fmrilab.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: newbie question event-related
Hi Sebastian, are you using an FIR or gammafit? doug Sebastian Moeller wrote: Hi List, hi Doug, for the first time I have now data, that realloy wants event-related analysis (200ms stimulation every 10 seconds). Now, using a TER of 0.2 in the para-file and using -dt event-related in mkanalysis-sess.new (3.0.3 pub x86_64 centos4) was the easy part, but what do I have to specify in mkcontast-sess? Especially thi -ircorr complex (with -deltarang and -taurange) is daunting. Is it necessary to specify anything here to get a real event-related analysis, or does fs-fast already know enough without these parameters (as I specified delta, tau and even taummax in mkanalysis)? So far any nicorr value I used produced errors on the way... I would be delighted for any pointer of how to properly convinve fs-fast to analyse my data ;). Ahoi thanks Sebastian -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] anonymizing dicom files
We've had some problems with osirix in that it will strip off all the private fields. For siemens mosaics, these are necessary in order to determine the number of slices and the image positions, etc. Greig de Zubicaray wrote: There's also Osirix on the Mac: http://homepage.mac.com/rossetantoine/osirix/Index2.html and ImageJ has a plugin: http://rsb.info.nih.gov/ij/plugins/dicom-rewriter.html Haven't used the latter, but can vouch for the former! regards, Greig On 29/08/2006, at 6:16 AM, Russ Poldrack wrote: You can use the LONI deidentification debablet to do this: http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=23 cheers russ On Aug 28, 2006, at 1:07 PM, Doug Greve wrote: Sorry, no clue. Najmeh Khalili M. wrote: sorry about nonstop posting! I'm trying to remove the patient names from dicom files. I was advised to use dcm_modify_elements but it fails on DCM_Openfile. Is there a straight forward way of doing this? Thanks Naj P.S. Doug, I am still looking for the graddir tags :) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Russell A. Poldrack, Ph.d. AssociateProfessor UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563 phone: 310-794-1224 fax: 310-206-5895 email: [EMAIL PROTECTED] web: www.poldracklab.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __ Dr Greig de Zubicaray Senior Research Fellow fMRI Laboratory,Centre for Magnetic Resonance University of Queensland, QLD 4072, Australia Tel:(+617) 3365 4100 (Office) (+617) 3365 4250 (B106, Ritchie Building) Fax:(+617) 3365 3833 fMRI Lab Page: http://www.fmrilab.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: newbie question event-related
why don't we have a single MatrixEigenSystem that checks what kind of matrix it is and calls the appropriate one. The time for the check will be negligible compared to the actual calculation On Mon, 28 Aug 2006, Doug Greve wrote: Hi Sebastian, are you using an FIR or gammafit? doug Sebastian Moeller wrote: Hi List, hi Doug, for the first time I have now data, that realloy wants event-related analysis (200ms stimulation every 10 seconds). Now, using a TER of 0.2 in the para-file and using -dt event-related in mkanalysis-sess.new (3.0.3 pub x86_64 centos4) was the easy part, but what do I have to specify in mkcontast-sess? Especially thi -ircorr complex (with -deltarang and -taurange) is daunting. Is it necessary to specify anything here to get a real event-related analysis, or does fs-fast already know enough without these parameters (as I specified delta, tau and even taummax in mkanalysis)? So far any nicorr value I used produced errors on the way... I would be delighted for any pointer of how to properly convinve fs-fast to analyse my data ;). Ahoi thanks Sebastian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] anonymizing dicom files
Can't say we've had this problem when we select only the patient's name field for anonymising in the preferences. Will check again later today!On 29/08/2006, at 7:54 AM, Doug Greve wrote: We've had some problems with osirix in that it will strip off all the private fields. For siemens mosaics, these are necessary in order to determine the number of slices and the image positions, etc. Greig de Zubicaray wrote: There's also Osirix on the Mac: http://homepage.mac.com/rossetantoine/osirix/Index2.html and ImageJ has a plugin: http://rsb.info.nih.gov/ij/plugins/dicom-rewriter.html Haven't used the latter, but can vouch for the former! regards, Greig On 29/08/2006, at 6:16 AM, Russ Poldrack wrote:You can use the LONI deidentification debablet to do this:http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=23cheersrussOn Aug 28, 2006, at 1:07 PM, Doug Greve wrote: Sorry, no clue. Najmeh Khalili M. wrote: sorry about nonstop posting!I'm trying to remove the patient names from dicom files. I was advised to use dcm_modify_elements but it fails on DCM_Openfile.Is there a straight forward way of doing this?ThanksNajP.S. Doug, I am still looking for the graddir tags :)___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ---Russell A. Poldrack, Ph.d.Associate ProfessorUCLA Department of PsychologyFranz Hall, Box 951563Los Angeles, CA 90095-1563phone: 310-794-1224fax: 310-206-5895email: [EMAIL PROTECTED]web: www.poldracklab.org ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __ Dr Greig de Zubicaray Senior Research Fellow fMRI Laboratory, Centre for Magnetic Resonance University of Queensland, QLD 4072, Australia Tel: (+617) 3365 4100 (Office) (+617) 3365 4250 (B106, Ritchie Building) Fax: (+617) 3365 3833 fMRI Lab Page: http://www.fmrilab.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 __Dr Greig de ZubicaraySenior Research FellowfMRI Laboratory, Centre for Magnetic ResonanceUniversity of Queensland, QLD 4072, AustraliaTel: (+617) 3365 4100 (Office) (+617) 3365 4250 (B106, Ritchie Building)Fax: (+617) 3365 3833fMRI Lab Page: http://www.fmrilab.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Freesurfer Digest, Vol 30, Issue 26
Hi Doug, On 28. Aug 2006, at 23:55 Uhr, [EMAIL PROTECTED] wrote: Date: Mon, 28 Aug 2006 17:53:30 -0400 From: Doug Greve [EMAIL PROTECTED] Subject: [Freesurfer] Re: newbie question event-related To: Sebastian Moeller [EMAIL PROTECTED] Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Sebastian, are you using an FIR or gammafit? Gammafit (-gammafit 0 1.25 -gammaexp 2 in union with -taumax 20 and -dt event-related). To illustrate this, I used the same parameters with -dt blocked, but my new paradigm is so sparse (200ms timulation every 16 seconds), that event related analysis seems like a good idea. Since we are at it ;), am I right that I should set the TER to 0.2000 and my stimulation epochs to one, while the only fixation periods are set to zero? Ahoi Thanks Sebastian doug Sebastian Moeller wrote: Hi List, hi Doug, for the first time I have now data, that realloy wants event-related analysis (200ms stimulation every 10 seconds). Now, using a TER of 0.2 in the para-file and using -dt event-related in mkanalysis-sess.new (3.0.3 pub x86_64 centos4) was the easy part, but what do I have to specify in mkcontast-sess? Especially thi -ircorr complex (with -deltarang and -taurange) is daunting. Is it necessary to specify anything here to get a real event-related analysis, or does fs-fast already know enough without these parameters (as I specified delta, tau and even taummax in mkanalysis)? So far any nicorr value I used produced errors on the way... I would be delighted for any pointer of how to properly convinve fs-fast to analyse my data ;). Ahoi thanks Sebastian -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 -- -- 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 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: Freesurfer Digest, Vol 30, Issue 26
Yes, that's fine. But with gammafit, you cannot use the ircor option (it's only meant for FIR). Sebastian Moeller wrote: Hi Doug, On 28. Aug 2006, at 23:55 Uhr, [EMAIL PROTECTED] wrote: Date: Mon, 28 Aug 2006 17:53:30 -0400 From: Doug Greve [EMAIL PROTECTED] Subject: [Freesurfer] Re: newbie question event-related To: Sebastian Moeller [EMAIL PROTECTED] Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Sebastian, are you using an FIR or gammafit? Gammafit (-gammafit 0 1.25 -gammaexp 2 in union with -taumax 20 and -dt event-related). To illustrate this, I used the same parameters with -dt blocked, but my new paradigm is so sparse (200ms timulation every 16 seconds), that event related analysis seems like a good idea. Since we are at it ;), am I right that I should set the TER to 0.2000 and my stimulation epochs to one, while the only fixation periods are set to zero? Ahoi Thanks Sebastian doug Sebastian Moeller wrote: Hi List, hi Doug, for the first time I have now data, that realloy wants event-related analysis (200ms stimulation every 10 seconds). Now, using a TER of 0.2 in the para-file and using -dt event-related in mkanalysis-sess.new (3.0.3 pub x86_64 centos4) was the easy part, but what do I have to specify in mkcontast-sess? Especially thi -ircorr complex (with -deltarang and -taurange) is daunting. Is it necessary to specify anything here to get a real event-related analysis, or does fs-fast already know enough without these parameters (as I specified delta, tau and even taummax in mkanalysis)? So far any nicorr value I used produced errors on the way... I would be delighted for any pointer of how to properly convinve fs-fast to analyse my data ;). Ahoi thanks Sebastian -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 -- -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] anonymizing dicom files
You're absolutely right - the siemens mosaic files return an error in mri_convert after osirix anonymises them, while the single siemens files do not. We've been using mri_convert for siemens DTI data, so weren't playing with mosaics.The dicom-rewriter plugin for ImageJ worked fine.On 29/08/2006, at 7:54 AM, Doug Greve wrote: We've had some problems with osirix in that it will strip off all the private fields. For siemens mosaics, these are necessary in order to determine the number of slices and the image positions, etc. Greig de Zubicaray wrote: There's also Osirix on the Mac: http://homepage.mac.com/rossetantoine/osirix/Index2.html and ImageJ has a plugin: http://rsb.info.nih.gov/ij/plugins/dicom-rewriter.html Haven't used the latter, but can vouch for the former! regards, Greig On 29/08/2006, at 6:16 AM, Russ Poldrack wrote:You can use the LONI deidentification debablet to do this:http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=23cheersrussOn Aug 28, 2006, at 1:07 PM, Doug Greve wrote: Sorry, no clue. Najmeh Khalili M. wrote: sorry about nonstop posting!I'm trying to remove the patient names from dicom files. I was advised to use dcm_modify_elements but it fails on DCM_Openfile.Is there a straight forward way of doing this?ThanksNajP.S. Doug, I am still looking for the graddir tags :)___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ---Russell A. Poldrack, Ph.d.Associate ProfessorUCLA Department of PsychologyFranz Hall, Box 951563Los Angeles, CA 90095-1563phone: 310-794-1224fax: 310-206-5895email: [EMAIL PROTECTED]web: www.poldracklab.org ___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __ Dr Greig de Zubicaray Senior Research Fellow fMRI Laboratory, Centre for Magnetic Resonance University of Queensland, QLD 4072, Australia Tel: (+617) 3365 4100 (Office) (+617) 3365 4250 (B106, Ritchie Building) Fax: (+617) 3365 3833 fMRI Lab Page: http://www.fmrilab.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 __Dr Greig de ZubicaraySenior Research FellowfMRI Laboratory, Centre for Magnetic ResonanceUniversity of Queensland, QLD 4072, AustraliaTel: (+617) 3365 4100 (Office) (+617) 3365 4250 (B106, Ritchie Building)Fax: (+617) 3365 3833fMRI Lab Page: http://www.fmrilab.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
