Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30060 discussions

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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(no subject)
by Durastanti, Valentina (NIH/NINDS) [F] 09 Apr '06

09 Apr '06

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

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mri_convert in 4D
by Julia Hamstra 08 Apr '06

08 Apr '06

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

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Q: tkregister2 coronal/sagittal/horizontal discrepancy
by raij＠nmr.mgh.harvard.edu 07 Apr '06

07 Apr '06

Dear Fellow Surfers, After doing a reconstruction with the 3.0 Freesurfer stable version, I checked the Talairach auto-registration with tkregister2. The registration seemed fair enough. However I noticed a strange thing that has not caught my attention before - maybe this a property of the program and/or was there already earlier, maybe it is new, maybe it is a bug, or perhaps my volume is corrupt. The problem/property is observed within the original (target) volume. After launching tkregister2, if I click inside the target volume, the red cursor moves to that location and other orientations (coronal/sagittal/horizontal) slices also change accordingly (the sliders move). If I have understood correctly, the idea would be that the cursor shows the crossing in all 3 orientations. However if I look at the brain structure in the three different orientations where my cursor is, it is clearly different in all three images. For example, if I pick a mid-sagittal view and place the red cursor in the thalamus between AC and PC, and then click the "sagittal" button, the cursor is clearly higher (towards top of the head) in the interhemispheric fissure. If I click the "coronal" button, the cursor is in the frontal lobe between the hemispheres (ie much more anterior than the other views). Is this the way the program is supposed to work, or is this a bug, or is my volume plain corrupted? *** Here are the specifics: *** on machine ai source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT avml07 cd /space/cognito/5/users/raij/subjects_mri tkregister2 --mgz --s avml07 --fstal ... and there you go, click away... Thanks for your advice in advance, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. raij(a)nmr.mgh.harvard.edu

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Buckner Data
by rhaynes＠neuro.gatech.edu 07 Apr '06

07 Apr '06

Will the Buckner data set be reprocessed with version 3.0? If it already has been, where can we get it? I can't find it in the v3.0 release. Thanks. Ryan Haynes Children's Healthcare of Atlanta

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