Freesurfer October 2008

freesurfer@nmr.mgh.harvard.edu

71 participants
110 discussions

Re: [martinos-tech] PAR REC Convert to Analyze or Nifti
by Akram Bakkour 20 Oct '08

20 Oct '08

I don't know anything about this, but check out the following: http://iacl.ece.jhu.edu/~bennett/research.shtml under Matlab Philips PAR/REC File Format Toolbox there is a writePARRECtoAVW.m that converts par/rec to analyze. Hope that helps. A On Mon, 20 Oct 2008, aneg(a)nmr.mgh.harvard.edu wrote: > Hi Amy, > It looks like this same question was posed a year ago (7/31/07) on the > FreeSurfer archive, but I dont think anyone answered the question! Anyone > else have some input?! > > thanks > aly > >> Hi all, >> We have par/rec files from a 2005 Phillips scan. Currently we are trying >> to convert the par/rec files to analyze or nifti so to use SPM5 for data >> analysis. We have used r2agui and the resulting nifti and analyze files >> were not readable by SPM or matlab. We are thus looking for a different >> software to perform the conversion. Does anyone know what software is >> capable of this conversion? >> Thanks, >> Amy >> >> >> >> >> >> > > -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org

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rat template, problem MRIstripskull failed
by Mark Bouts 20 Oct '08

20 Oct '08

Hi, I'm trying to set up a rat brain template for analysis using the freesurfer tool. Before setting up the complete template I have to process a representable rat dataset with the available human template. With some much appreciated help I managed to get to the skull strip procedure . But the application ceases its operations at this point with the message: "White matter intensity 0 is lower than CSF intensity 21. Please examine input images. Will terminate ..." Evaluation using tkmedit does not show something really peculiar. It does not show a proper segmentation of the rat brain, however it does show a proper outline of the brain. Since a rat brain and a human brain are very dissimilar would not expect a perfect segmentation of the different structures. It is also known that the WM intensity values in the rat dataset is somewhat reduced to the GM structure. Which is not expected by the freesurfer tool (?), which expects WM to be highest intensity value. My question is: is there a way of circumventing this problem. For instance by defining the mean intensity values of each tissue class or.. Hope someone can help me? Thanks! Mark

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unpacking from CD backup
by jake＠nmr.mgh.harvard.edu 20 Oct '08

20 Oct '08

Hi, Could someone please explain how to unpack an old session saved on a CD? What command line should be used? thank you in advance, Jake

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Re: [Freesurfer] Philips DICOM Files
by ATAE AKHRIF 20 Oct '08

20 Oct '08

thanks a lot PPJ for replying so quickly and for ur hint, next time i ll save my data directly in Nifti format instead of DICOM but just in case where the DICOM format is needed as in the exemple of unpacksdcmdir -src <source> -targ <target> where source must be a directory with DICOM files, is there anything i can do about it or probably i just go another way to unpack my data??. thank you Atae ----- Mensaje original ---- De: Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> Para: ATAE AKHRIF <bonoat(a)yahoo.com> CC: freesurfer(a)nmr.mgh.harvard.edu Enviado: lunes, 20 de octubre, 2008 14:34:02 Asunto: Re: [Freesurfer] Philips DICOM Files Another hint. While you punch the head of your favourite Philips reseller there is a workaround: Use the MRI console go to Administration->Advanced Tools->Research click the first left icon and chose save as Nifti. Best Regards PPJ ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom 2008/10/20 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> Hi, We also have a Philips 3.0T and unfortunately the images from this scanners are not Dicom 3 compliant. We have wrote a patch and we are pressing Philips to fix this. Best Regards PPJ ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom 2008/10/20 ATAE AKHRIF <bonoat(a)yahoo.com> Dear mailinglist, i work with Philips Achieva 3.0T Data. The problem i have, is that every time i use the so obtained DICOM files as an Input argument for any freesurfer command line like unpacksdcmdir -src <source> -targ <target> -scanonly, the files are then not recognized as DICOM. can someone please tell me why is that so and if there s a difference between Philips and Siemens in this regard? Thank you very much Atae __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/

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Philips DICOM Files
by ATAE AKHRIF 20 Oct '08

20 Oct '08

Dear mailinglist, i work with Philips Achieva 3.0T Data. The problem i have, is that every time i use the so obtained DICOM files as an Input argument for any freesurfer command line like unpacksdcmdir -src <source> -targ <target> -scanonly, the files are then not recognized as DICOM. can someone please tell me why is that so and if there s a difference between Philips and Siemens in this regard? Thank you very much Atae __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/

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auto-cropping subcortical structure
by Woo-Suk, Tae 20 Oct '08

20 Oct '08

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Dear FreeSurfer exports.I need the function of auto-cropping the exported binary files (ex. hippocampus or thalamus) from in aseg.mgz by 'mri_binarize'. The cropped hippocampal image may have about 40 x 40 x 50 voxels dimension.Do you have any idea?Woo-Suk, Tae Ph.D.Chuncheon, Korea

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Old scanning sessions, are they gone?
by jake＠nmr.mgh.harvard.edu 17 Oct '08

17 Oct '08

Hi! I am trying to unpack an old scannning session from 2004. In the standard env using findsession, it displays the following: [striatum:OLD_cerv_data] (nmr-std-env) findsession cerv_botox_ctrl1 ======= SUBJECT: cerv_botox_ctrl1 SUBJ ID: cerv_botox_ctrl1 DATE : October 26, 2004 TIME : 13:48:27 XPRMNTR: PATH : /space/archive/29/siemens/Allegra-20401-20041026-134339-796000 However, upon attempting to unpack, the error occurs: ERROR: directory /space/archive/29/siemens/Allegra-20401-20041026-134339-796000 does not exist. I have other old sessions that have shown the same results. Are the data actually there? Thanks in advance for you help, Jake

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Output of selxavg3
by Yigal Agam 17 Oct '08

17 Oct '08

Hi, Of all the files that selxavg3 generates inside the contrast folder, only three are described in the wiki: ces.nii, cesvar.nii, and sig.nii. Does anyone know the other files below represent? Also, which files are used for subsequent group analyses? cesmag.nii fsig.nii minsig.nii cesmagpct.nii cespct.nii cesvarpct.nii iminsig.nii

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converting ROIs to NIFTI
by John Pluta 16 Oct '08

16 Oct '08

I have been trying to use FreeSurfer to automatically generate several ROIs for me. This is easy with the autosegment feature. However, I need to be able to work with them in Analyze or Nifti format. So far, any kind of conversion method has gotten me ROIs that are not the same as the results of autosegmentation. In every case, whether I extract a single roi or try to convert the whole set at once, there is a great deal of noise in the resulting Nifti file. This is obvious just by looking, and you can also see the discrepency by looking at the voxel count of the converted ROI versus the voxel count in the stats file produced by autosegmentation- there is typically a difference of hundreds of voxels. I've tried all of the methods in the tutorials and slides, and everything I could find in the mailing list so far. Everything comes out to this same result. Has anybody else encountered this or had any luck? Also, does anyone know the source of the noise in the converted images? If I could trace where that comes from, maybe I could write some kind of script to repair the ROIs I need. Thank you. -John

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longitudinal processing
by Nicola Hobbs 16 Oct '08

16 Oct '08

Hi there, We would like to do some longitudinal processing. Our baseline scans have been run through v4.0.3, and we spent a long time manually editing the cortical segmentations. Ideally we would like to use these segmentations as the reference for our longitudinal processing (v4.1.0), but we are worried that using different versions for the same study could introduce errors. Could you advise us on whether we need to re-run our baseline data through v4.1.0 before we attempt any longitudinal processing? Many thanks for your help, Nicola -- Nicola Hobbs Dementia Research Centre National Hospital for Neurology and Neurosurgery Queen Square London WC1N 3BG +44 (0)845 155 5000 ext. 723839

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Freesurfer October 2008