Freesurfer

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30080 discussions

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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structural ROI analysis
by Wiegand, Katrin 16 Oct '08

16 Oct '08

Hi, I'm using freesurfer v4.0.5 and I am trying to do a ROI analysis using func2roi-sess. However, there seems to be some problem with the structural label (created with tkmedit). I.e., when running func2roi-sess only with a structural constraint, the report includes following messages INFO: vol2maskavg: nhits = 0 WARNING: there were no voxels in the input mask > 0.5 (checking the final mask of the output also reveals no voxels being included). Furthermore, when I'm trying to use -raw (instead of averaged data defined by -analysis) I get the following error message: ERROR: no analysis specified Any suggestions how to solve the problems? Thanks, Katrin

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Re: recon-all with voxel sizes other than 1mm^3
by Anderson Winkler 15 Oct '08

15 Oct '08

Hi, I edited the recon-all, omitting the --conform option, and the pipeline failed shortly after. So, is there a way to run the volume processing pipeline (in particular, the subcortical segmentation), without resampling to 1mm^3 voxels, keeping the native format 0.8^3 mm^3? Anderson

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new Freesurfer release v4.1.0
by Nick Schmansky 14 Oct '08

14 Oct '08

Freesurfer users, There is a new release of freesurfer available, v4.1.0. This is a bug- fix release, described on this wiki page: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes The download page is here: https://surfer.nmr.mgh.harvard.edu/fswiki/Download Mainly this release is of interest to those waiting for the updated longitudinal analysis stream. Nick

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