Freesurfer April 2005

freesurfer@nmr.mgh.harvard.edu

25 participants
35 discussions

Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

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RE: [Freesurfer] Problem converting IMA files
by Kristine Beate Walhovd 19 May '05

19 May '05

Hi Bruce I tried -it siemens too (based on some list question) and that did't work either, but I see now that hey are named .IMA not .ima Sorry, the FW-disk I got them from likely caused the problem. Thanks, Kristine -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 4/19/2005 12:00 AM To: Kristine Beate Walhovd Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem converting IMA files Hi Kristine, mri_convert should handle ima files. Have you tried -it siemens? Are they named .ima? cheers, Bruce On Tue, 19 Apr 2005, Kristine Beate Walhovd wrote: > Hi > > I've tried converting IMA files (taken directly from the Siemens scanner) in Freesurfer with the command > > mri_convert -ot cor <one filename in the sequence> <output file> > > but it doesn't work. Gives an error message "cannot parse..." (see attached error message). > > I'd be grateful for any suggestions. > > Thanks, > > Kristine > >

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Brodman areas on cortical sheet
by Darren Weber 30 Apr '05

30 Apr '05

Hi Bruce et al., do you have Brodmann regions defined for the surface template (average7)? If so, how are they defined and what is the practical implementation? Best, Darren -- Darren L. Weber, Ph.D. Visiting Postdoctoral Scholar Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." --Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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Re: [Freesurfer] Dicom
by Joongnam Yang 29 Apr '05

29 Apr '05

Thanks Doug, When I used mri_convert to convert *.dcm to *.hdr, the resulting *.hdr has anterior and posterior reversed. The top was posterior and the bottom was anterior. Is there any way to change, so that the top is anterior and the bottom is posterior? Nam. >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 04/28/05 6:09 PM >>> It will transform all of them that belong to the same series into one file. If they don't all belong to the same series, then you're on your own. doug Joongnam Yang wrote: > > Thanks Doug, > > Is there a way of transforming all the *.dcm files into one-volume > {img,hdr,mat} file? > > Nam. > > >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 04/28/05 2:56 PM >>> > > Try > > mri_convert file.dcm f -ot spm > > where file.dcm is a dicom file in the series you want to convert (there > is no special naming requirements -- in fact the file names can be > random). The output will be > > f001.{img,hdr,mat} > f002.{img,hdr,mat} > > doug > > Joongnam Yang wrote: > > > > Hi all, > > > > I am sorry, since I might have missed the answer. > > My question is, the following question by Mr. Ajay Pillai has been > answered? > > If yes, would someone forward me the answer please? > > > > Thanks. > > Nam. > > > > >>> Ajay Pillai <pillai(a)ccs.fau.edu> 04/27/05 2:26 PM >>> > > Hi, > > I am trying to convert my dicom funcional scan images into SPM analyze > > (or even AFNI BRIK) format. > > > > I have about 320 functional volumes of 30 slices each. So basically I > > have 9600 .dcm files which I have renamed sequentially for each > > subject.The first 30 constitute one volume the next 30 next volume and > > so on. > > > > Can mri_convert do this? If so could some one please tell me how? > > > > Thank you > > > > Ajay > > > > _______________________________________________ > > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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MNI install
by 윤종철 29 Apr '05

29 Apr '05

Dear. I installed freesurfer-2004-2-18 version, recently. I have trouble in installing MNI packages as install guideline. [root@kphe pubsw]# ls bin packages ln -s usr/lib/perl5 perl and then, unpacked mni packages under mni directory When I start mritotal, permission error was occured. [root@kphe freesurfer]# mritotal /usr/pubsw/packages/mni/current/bin/mritotal: Permission denied. But, all files in usr directory was already changed to root permission. -rwxrwxrwx 1 root root 87070 Aug 10 2001 mritotal Except perl script, binary files like xfmri was working. I use Redhat Linux 9.0. I don't know what is the problem. Could you help me? Jong Chul , Youn M.D. Kunggi Provincial Hospital for the elderly 17 Sangha-Ri Koosung-Eup Yongin-City, Kyunggi-Do Republic of Korea (449-769) Tel. 82-31-288-0417 Fax. 82-31-288-0405 e-mail: <BLOCKED::mailto:yjc0811@snu.ac.kr> yjc0811(a)snu.ac.kr

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Re: [Freesurfer] Dicom
by Joongnam Yang 28 Apr '05

28 Apr '05

Thanks Doug, Is there a way of transforming all the *.dcm files into one-volume {img,hdr,mat} file? Nam. >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> 04/28/05 2:56 PM >>> Try mri_convert file.dcm f -ot spm where file.dcm is a dicom file in the series you want to convert (there is no special naming requirements -- in fact the file names can be random). The output will be f001.{img,hdr,mat} f002.{img,hdr,mat} doug Joongnam Yang wrote: > > Hi all, > > I am sorry, since I might have missed the answer. > My question is, the following question by Mr. Ajay Pillai has been answered? > If yes, would someone forward me the answer please? > > Thanks. > Nam. > > >>> Ajay Pillai <pillai(a)ccs.fau.edu> 04/27/05 2:26 PM >>> > Hi, > I am trying to convert my dicom funcional scan images into SPM analyze > (or even AFNI BRIK) format. > > I have about 320 functional volumes of 30 slices each. So basically I > have 9600 .dcm files which I have renamed sequentially for each > subject.The first 30 constitute one volume the next 30 next volume and > so on. > > Can mri_convert do this? If so could some one please tell me how? > > Thank you > > Ajay > > _______________________________________________ > 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

2 1

Re: [Freesurfer] Dicom
by Joongnam Yang 28 Apr '05

28 Apr '05

Hi all, I am sorry, since I might have missed the answer. My question is, the following question by Mr. Ajay Pillai has been answered? If yes, would someone forward me the answer please? Thanks. Nam. >>> Ajay Pillai <pillai(a)ccs.fau.edu> 04/27/05 2:26 PM >>> Hi, I am trying to convert my dicom funcional scan images into SPM analyze (or even AFNI BRIK) format. I have about 320 functional volumes of 30 slices each. So basically I have 9600 .dcm files which I have renamed sequentially for each subject.The first 30 constitute one volume the next 30 next volume and so on. Can mri_convert do this? If so could some one please tell me how? Thank you Ajay _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Dicom
by Ajay Pillai 27 Apr '05

27 Apr '05

Hi, I am trying to convert my dicom funcional scan images into SPM analyze (or even AFNI BRIK) format. I have about 320 functional volumes of 30 slices each. So basically I have 9600 .dcm files which I have renamed sequentially for each subject.The first 30 constitute one volume the next 30 next volume and so on. Can mri_convert do this? If so could some one please tell me how? Thank you Ajay

1 0

where to download freesurfer-Linux-rh9-20050415.tar.gz
by JLH 26 Apr '05

26 Apr '05

Dear freesurfer expert, I jsut wonder where to download the freesurfer-Linux-rh9-20050415.tar.gz. Is this program release ? or someone can tell me where to download it. thanks sincerely JLH

2 1

problems generating the filled volume
by wilms 26 Apr '05

26 Apr '05

Dear freesurfers, when I check my mri_converted data after running (1) using <csurf> I find my data shifted relative to the voxel space center (volume index at [128 128 128]) as can be seen in the attached screenshots. The subsequent generation of the "filled" images leaves the cerebellum always attached. I tried to manually set the cutting planes as described in the FreeSurfer Manual (pp. 32-36) but the whole cerebellum is still connected to the brain and always attributed to the left hemisphere. In addition to that I think the bert "orig" data set is smoothed, right? In comparison to bert does my data look much more grainy. Do I have to smooth my data first? Any suggestions in how I can proceed in trying to successfully set the cutting planes are most welcome! Marcus (1) mri_convert -ot cor -it siemens_dicom $SUBJECTS_DIR/7481/mri/orig/3D/<some file.ima> $SUBJECTS_DIR/7481/mri/orig/

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Freesurfer April 2005