Freesurfer April 2006

freesurfer@nmr.mgh.harvard.edu

50 participants
83 discussions

mri_convert in 4D
by Julia Hamstra 11 Apr '06

11 Apr '06

I am viewing it with tkmedit. For the timeseries, it only displayed some of it. I also tried viewing it with fslview. There it was a single dashed line in the coronal view. Here is the output: mri_convert -it dicom -ot nii i6757552.MRDC.1 run.nii.gz reading from i6757552.MRDC.1... 1260 DICOM 3.0 files in list Found 1260 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 1260. reading DICOM image... ------------------------------------------------- DICOM meta-header file name /data/Cued_Recall/CR_ds7/s6757551/i6757552.MRDC.1 Date and time study date 20050601 study time 183408 series time 190627 acquisition time 190627 Identification patient name ds060105 manufacturer GE MEDICAL SYSTEMS Dimensions number of rows 64 number of columns 64 number of frames 1260 pixel width 3.43752 pixel height 3.4375 slice thickness 7 field of view 220.001 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 30 repetition time 720 inversion time 0 echo number 1 flip angle 1.5708 bits allocated 16 Spatial information first image position -108.281 -113.295 54.3301 last image position -108.281 -60.2276 88.2841 image orientation 1 -0 0 -0 0.538953 -0.842336 ------------------------------------------------- TR=720.00, TE=30.00, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -0.538953, - 0.842336) k_ras = (0, -0.842337, 0.538951) writing to run.nii.gz... thanks ~julia On 4/8/06, Bruce Fischl < fischl(a)nmr.mgh.harvard.edu> wrote: > > how are you displaying it? And can you send the entire output? > > On Fri, 7 Apr > 2006, Julia Hamstra wrote: > > > Hi, > > I am getting two errors when creating NIFTI files from dicoms using > > mri_convert. > > The first is that the 4D images are being spatially contactonated. It > does > > not seem to be treating it as a timeseries. This is the command: > > > > mri_convert -it dicom -ot nii s6761334/i6761335.MRDC.1 run.nii.gz > > > > Additionally it is an oblique acquizition so the coronal view is not > > displaying the plane of acquizition (as intended), but an orthogonal cut > > through multiple slices. Am I missing an option or additional > information? I > > searched the options and couldn't figure out anything that helped. The > > problem applies to the co-planar oblique structural scan too. > > > > I'm guessing there is something simple that I am overlooking. What may > that > > be? > > thanks > > ~julia > > > -- Human Memory Lab 8950 Villa La Jolla Drive Suite C212 La Jolla, CA 92093 phone: (858)534-1227 fax: (858)534-1240 jhamstra(a)gmail.com

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segmentation error.
by Martin Ystad 11 Apr '06

11 Apr '06

Hi, I'm running the stable release v 3.0.1 for centos4 and I've had some problems with the segmentation. The main surface doesn't follow the wm-surface in some of the sulci, it rather 'jumps' across to the next gyri. (see picture) I've tried to edit the wm-surface and running autorecon2 again, but it doesn't work. Any ideas? Thanks, Martin Ystad University of Bergen, Norway.

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Freesurfer - autorecon1 will not write to established directory
by adam walczak 11 Apr '06

11 Apr '06

Hi, I have been having some basic problems with regard to paths. Freesurfer doesn't seem to want to write to directories that already exist. I was wondering if there is something different I need to do (I am running the reconstruction tutorial) to make this work. -------- freesurfer-Linux-rh9-stable-pub-v3.0.1 -------- SUBJECTS_DIR is /cajal/public/programs/freesurfer/subjects which: recon-all / autorecon1 pwd - /cajal/public/programs/freesurfer/subjects/13667/mri command line - recon-all -i orig.mgz -autorecon1 -s 13667 --------error--------- INFO: SUBJECTS_DIR is /cajal/public/programs/freesurfer/subjects ERROR: /cajal/public/programs/freesurfer/subjects/13667 exists I am at a loss as to why this happens. Any help would be appreciated. Adam Walczak --------------------------------- Love cheap thrills? Enjoy PC-to-Phone calls to 30+ countries for just 2¢/min with Yahoo! Messenger with Voice.

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Curvature
by anthony gallo 11 Apr '06

11 Apr '06

How should one interpret the curvature function.......what is the essence of it's being.......what does it mean?

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regarding mkanalysis-sess.new and brainmasks
by Sebastian Moeller 10 Apr '06

10 Apr '06

Hi All, as the subject line reveals, I have a question regarding mkanalysis-sess.new (running centos4_x86_64 3.0.1 pub stable, on SuSE 9.3, not that it matters...). My question is, is there any heuristic how to chose the -taumax parameter, that can be used in combination with a brainmask? I am wondering as the example usage from the fsfast workflow specifies a brainmask, but does not set -taumax, is that a useful approach? One more question about the brainmask I have is, (at least without a specified taumax) I still see non-uniform values in the sig volume, while actually expecting close to nothing, but I guess I have not groked how the masking is supposed to work... I would be happy for any pointers about this issue. And while on the matter, is there a way to allow empty conditions, i.e. use a sparse condition numbering in the .para files (trading the check for missing conditions versus the possibility to use stable identifiers for loads of conditions used over different days). Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Recommendation for Linux machine
by Chunchun Ni 10 Apr '06

10 Apr '06

Hi, We plan to buy Linux machine for freesurfer and other brain image processing. Any recommendation and related links? Thanks Chunchun

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Short Course in fMRI
by Doug Greve 10 Apr '06

10 Apr '06

Mark Vangel and I are offering a short course in the statistical signal processing of fMRI. October 31 (Mon) & November 1 (Tue), 2005 7th Floor Auditorium Building 149 Charlestown Navy Yard Free, but limited to 40 attendees. Register at: http://www.nmr.mgh.harvard.edu/martinos/training/shortCoursefMRIStats.php doug

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tksurfer - view - information - distance
by anthony gallo 10 Apr '06

10 Apr '06

tksurfer -> view -> information - > distance what is the reference point for this command, ie when the cursor is on point x with a value of, say 0.02 what is that the distance of? Thanks.

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fsfast "selxavg-sess" error
by Paymon Hosseini 10 Apr '06

10 Apr '06

hi i am going over the fsfast tutorial. i have completed all steps up to "FsFastTutorial/905 Average session-level data by condition" https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20… when i run "selxavg-sess -sf sessid -df sesspar -analysis sem_assoc", i get the following error: " ??? Undefined function or variable 'MRIread'. Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m On line 160 ==> rstd = MRIread(instem,1); >> ??? Undefined function or variable 'r'. >> quiting matlab ------------------------------------------ ERROR: fast_selxavg() failed\n ERROR (/autofs/space/engram_012/users/pman/bert-functional): selxavg failed " can you please tell me why i am getting this error? thanks paymon hosseini

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RE: [Freesurfer] (no subject)
by Durastanti, Valentina (NIH/NINDS) [F] 10 Apr '06

10 Apr '06

Dear Nick, I tried to run recon-all -s <subjname> -skullstrip but always came out an error: read error I tried to run recon-all -subjid <subjname> -autorecon1 on the same subjects and it looks good have you any suggestion? Thanks Valentina -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Saturday, April 08, 2006 7:23 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: Bruce Fischl; Julia Hamstra; Freesurfer Mailing List Subject: Re: [Freesurfer] (no subject) Use: recon-all -s <subj> -skullstrip Also, recon-all -help will list-out most of the steps which can be run individually (see section titled STEP-WISE DIRECTIVES). On Sat, 2006-04-08 at 19:47 -0400, Durastanti, Valentina (NIH/NINDS) [F] wrote: > > Hi, > I'm using Freesurfer and I'd like to run the autorecon1 just for the > skull stripping (without intensity and spatial normalization). Is there > a command just to do that? > > Thanks > valentina > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Freesurfer April 2006