Freesurfer April 2005

freesurfer@nmr.mgh.harvard.edu

25 participants
35 discussions

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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Problem converting IMA files
by Kristine Beate Walhovd 19 Apr '05

19 Apr '05

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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Requirements for thickness analysis
by Fornito, Alexander 18 Apr '05

18 Apr '05

Hi, I am looking at running some thickness analyses on some MRI data we have already collected. I noticed that the manual states that "a minimum of two anatomical acquisitions is required for morphometric studies". Is it possible to run a valid thickness analysis in Freesurfer if I only have 1 T1 scan per person? Alternatively, a subset of our cohort have a T1 and T2, T1 and PD, or all three. Would it be possible to use a T1 and T2 instead of two T1s? Thanks for your help, Alex

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mri_convert orientation
by Wan Park 15 Apr '05

15 Apr '05

Unfortunately I only have img/hdr files. when I put mri_info I have this message: [ash:14725/mri/orig] wpark% ls 14725.hdr 14725.img [ash:14725/mri/orig] wpark% mri_info 14725.img INFO: analyzeRead(): found 1 files for /usr/local/freesurfer_package/freesurfer subjects/14725/mri/orig/14725.img ----------------------------------------------------------------- INFO: could not find /usr/local/freesurfer_package/freesurfer/subjects/14725/mr /orig/14725.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default) INFO: if not valid, please provide the information in /usr/local/freesurfer_pac age/freesurfer/subjects/14725/mri/orig/14725.mat file ----------------------------------------------------------------- Volume information for 14725.img type: analyze3d dimensions: 256 x 256 x 124 voxel sizes: 0.7812, 0.7812, 1.5000 type: SHORT (4) fov: 0.000 xstart: 0.0, xend: 0.0 ystart: 0.0, yend: 0.0 zstart: 0.0, zend: 0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degre s nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 0.000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.000 voxel to ras transform: -0.7812 0.0000 0.0000 100.0000 0.0000 0.7812 0.0000 -100.0000 0.0000 0.0000 1.5000 -93.0000 0.0000 0.0000 0.0000 1.0000 [ash:14725/mri/orig] wpark% I know that doing mri_convert -iid x_r x_a x_s -ijd y_r y_a y_s -ikd z_r z_a z_s I can change the orientation. In this case it would be mri_convert -iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1 14725.img . My questions: 1) Are these the "default" values that the mri_convert use if I do not specify anything? (mri_convert 14725.img .) 2) If I want to change, the possible values are -1 0 and 1? Thank you very much. Wan

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threshold graph value
by Nguyen, Thang Q 14 Apr '05

14 Apr '05

Hello all, After running a mris_glm analysis, I load the sigt.w file as a overlay. When configuring the threshold value for this overlay, one can adjust the min/mid/max values on the x-axis based on the y-axis values. What do the min/mid/max values and count values on the graph indicate? Thank you, Thang Nguyen

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Freesurfer April 2005