Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

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

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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

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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

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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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Binary locations--new linux distro
by Brian Schweinsburg, Ph.D. 25 Apr '05

25 Apr '05

Hi, After installing the freesurfer-Linux-rh9-20050415.tar.gz and setting up the SetUpFreeSurfer and FreesurferEnv, I get an error message when csurf loads. It states that it cannot find numerous binaries in /usr/local/freesurfer/beta/bin. This issue seemed to resolve by symbollically linking the my $FREESURFER_HOME/bin directory to previously mentioned one. Is there a place to change where csurf expects to find the binaries? Did I miss it in the FreesurferEnv setup? Thanks for your time, Brian

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static version for tksurfer
by 유우경 22 Apr '05

22 Apr '05

Hi ! I have the same problem with tksurfer as they detail in the mail (see link). http://www.mail-archive.com/freesurfer@mail.nmr.mgh.harvard.edu/msg00642.ht… I installed last version of freesurfer (20040218) wich doesn't have tksurfer.static. Perhaps it's in an earlier version... Can somebody send it to me ? Thanks

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"consider relinking" warnings
by wilms 21 Apr '05

21 Apr '05

Please help a freesurfer beginner: I am just trying to get the FreeSurfer software running on my local (and later on the cluster) machine (debian sarge, P4). When running > recon-all -stage1 -s bert on the bert example data, the script runs smoothly except for lots of "consider relinking" warnings (see below). I sense this might be related to compiler version issues? My question: Are these errors harmful?- If yes, what can I do? - Build the minc-tools on my machine? Help is greatly appreciated, Marcus ########### snip: Nu Intensity Correction Wed Apr 20 16:49:30 CEST 2005 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, -0) j_ras = (0, 0, -1) k_ras = (-0, 1, -0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc [wilms@medpc32:/data/Wilms/projects/freesurfer_data/newbert/mri/] [2005-04-20 16:49:39] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_2638/ nu/nu0.mnc nu/nu1.imp /usr/pubsw/packages/mni/current/bin/volume_stats: Symbol `__vt_8iostream.3ios' has different size in shared object, consider re-linking /usr/pubsw/packages/mni/current/bin/volume_stats: Symbol `__vt_3ios' has different size in shared object, consider re-linking /usr/pubsw/packages/mni/current/bin/volume_stats: Symbol `__vt_7istream.3ios' has different size in shared object, consider re-linking /usr/pubsw/packages/mni/current/bin/volume_stats: Symbol `__vt_7fstream.3ios' has different size in shared object, consider re-linking (...) ############ snip. -- ------------------------------- Dr. Marcus Wilms Cognitive Neurology Group Institute of Medicine Forschungszentrum Juelich 52425 Juelich, Germany Phone: +49 (02461) 61-6184 E-Mail: ma.wilms(a)fz-juelich.de Home: http://www.netwilms.net ----------------------------><>

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RE: [Freesurfer] Problem converting IMA files
by Kristine Beate Walhovd 20 Apr '05

20 Apr '05

Hi Someone told me that using mri_convert -it siemens_dicom <first IMA file> <destination directory> had worked, and I tried that. The files were then converted, but even though I don't get any error messages, there is serious conversion error. In the coronal view, I see black stripes and a quarter of the head is cut off and placed at the other side of the image. When I go through the slices sagitally, I see that it jumps from slice 13 to 56, and there also appears to be some slices of very different (darker) intensities in between. The scans looked excellent when I looked at them at the hospital work station, so this must be a conversion, not quality problem. These are GRAPPA series, could that have anything to do with the problems? Thanks, Kristine -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 4/19/2005 2:42 AM To: Kristine Beate Walhovd Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem converting IMA files What was your exact command-line? Did you try adding "-it siemens"? Also, I could not read the attachment. Is it in text/ascii format? doug 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 > > ------------------------------------------------------------------------ > Name: IMA_error.sxw > IMA_error.sxw Type: unspecified type (application/octet-stream) > Encoding: base64 > Description: IMA_error.sxw > > ------------------------------------------------------------------------ > _______________________________________________ > 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

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RE: [Freesurfer] Problem converting IMA files
by Kristine Beate Walhovd 20 Apr '05

20 Apr '05

Hi Doug Here it is: [brain@hippocampus ~/freesurfer]$ cd ../../../var/lab-data/barn [brain@hippocampus barn]$ cd 005 [brain@hippocampus 005]$ mri_convert -ot cor 005.MR.2.4.2005.04.12.14.16.43.31250.31756010.IMA ../fp005/mri/orig/001 mri_convert -ot cor 005.MR.2.4.2005.04.12.14.16.43.31250.31756010.IMA ../fp005/mri/orig/001 reading from 005.MR.2.4.2005.04.12.14.16.43.31250.31756010.IMA... ERROR: could not parse /var/lab-data/barn/005/005.MR.2.4.2005.04.12.14.16.43.31250.31756010.IMA ERROR: siemensRead(): /var/lab-data/barn/005/005.MR.2.4.2005.04.12.14.16.43.31250.31756010.IMA When I do -it siemens instead of -ot cor it does the same thing. Thanks, Kristine -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 4/19/2005 2:42 AM To: Kristine Beate Walhovd Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem converting IMA files What was your exact command-line? Did you try adding "-it siemens"? Also, I could not read the attachment. Is it in text/ascii format? doug 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 > > ------------------------------------------------------------------------ > Name: IMA_error.sxw > IMA_error.sxw Type: unspecified type (application/octet-stream) > Encoding: base64 > Description: IMA_error.sxw > > ------------------------------------------------------------------------ > _______________________________________________ > 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

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License problems
by Fornito, Alexander 19 Apr '05

19 Apr '05

Hi all, We've just installed Freesurfer and tried to use mri_convert and encountered some problems. In the csurf GUI, I tried to convert a subject's image, which we keep in analyze (.img, .hdr) format, and I got the message: "Convert (subj186) failed - working on: orig/001/subj186.img" I then loaded the flat files (I.001, I.002 ... etc.) into the directory and tried to convert these. The program hangs indefinitely once I press the convert button. Next I tried to run it thought the command line on the flat files and got a message saying "No valid license key!". To the best of our knowledge, all the license files are where they should be. Any ideas on what's happening? Thanks, Alex

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Freesurfer