Freesurfer

freesurfer@nmr.mgh.harvard.edu

9 participants
30092 discussions

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/

1 0

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

2 2

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

2 1

"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 ----------------------------><>

2 1

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

1 0

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

1 0

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

2 1

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

3 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer