Freesurfer March 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
84 discussions

RE: autorecon1
by Durastanti, Valentina (NIH/NINDS) [F] 08 Mar '06

08 Mar '06

Of course I put the subject name that I prefer to keep hidden! thanks Valentina -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Wednesday, March 08, 2006 4:03 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: martinos-tech(a)yahoogroups.com; Freesurfer Mailing List Subject: Re: autorecon1 Hi Valentina, did you actually put "<subject name>" on your command-line? <subject name> is supposed to be the name of your subject, eg, "bert" (but without the quotes). What's a "Flug"? For your second question, there will not be a brain.mgz after the first step, but there will be a brainmask.mgz. Also, please see surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for how to pose questions so that we can answer them better. thanks doug Durastanti, Valentina (NIH/NINDS) [F] wrote: >Hi, >I have 2 questions: > >Number 1 > when I try to run the first step: > recon-all -subjid <su -autorecon1 >He said: > ERROR Flug <subject name> unrecognized > >Number 2 >After the first step of a subject I can't find the brain.mgz > >Thanks >Valentina > > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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FS-FAST registration across sessions
by Jane Aspell 08 Mar '06

08 Mar '06

Hi My question was asked last year by Tommi Raij (see email pasted below) but I couldn't find a reply to it in the archives. I am analysing retinotopy data that was collected over several sessions but I cannot see how to register scans from multiple sessions together, and to the subject's anatomical scan. Although Fs-Fast appears to combine the data from multiple sessions during the retinotopy analysis it only seems to be possible to use one registration file (register.dat) when overlaying the results onto the anatomical. I would have thought that registering scans from multiple sessions together would be a feature that many people would require. Is there anyway to do it? Tommi gives some possible methods in his email below. When I do try and overlay my data onto a surface I see 'gaps' in the blue/yellow colouring of the fieldsign map overlaid onto the cortical surface. I wonder if this could be due to the inaccuracy of the registration given that I only used the register.dat from the registration of the first session. hope that makes sense! i'd be grateful for any help with this! Jane -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ------------------------------------------- [Freesurfer] FS-FAST Registration Question: registration across sessions within subjects Tommi Raij Thu, 20 Oct 2005 15:43:46 -0700 Hi Doug/All, This is a question about registering several functional scans from the same subject in the same space. The functional scans are from different sessions, so even if the slice recording parameters are identical, the head will inavoidably be in different locations and with different rotation. The data have already been collected, so we cannot use any on-line corrections. Four different techniques come to mind that could be used to achieve this, but I would expect that the accuracy of the methods varies a lot. Optimally IMHO one should register the different functional runs with respect to each other directly, simply because the EPI images are very similar with respect to each other (or at least their T1 contrast is). The high-resolution structural image is very different compared to the EPI images so functional-to-structural registration is expected to be much more inaccurate. Here are the four different techniques (please tell me if you can think of more): 1. One possibility would be to use mc-sess for all runs from the same subject (place all the runs from the different sessions in a single "bold" directory and just run mc-sess). Possible problem: If I have understood correctly, mc- sess only corrects for motion within slices. Therefore the different head rotations would make this technique very inaccurate. Or does there exist an updated version of mc-sess that could handle even large displacements and rotations? 2. A second possibility would be to use one of the automatic functional-to- structural registration programs and register each functional run to the same hires structural image. However, based on the discussion above, there are expected to be inaccuracies in the functional-to- structural registration that could be large enough to make comparisons across the functional sessions meaningless (i.e., the differences would mainly be driven by inaccuracies in the registration). 3. A third possibility would be to use the same technique as for registration across subjects, i.e., resampling the different runs from the same subject into a spherical space calculated from this specific subject. Again this is just as variety of registration from functional to structural, and would be expected to provide suboptimal results. 4. A fourth possibility would be to find a method for registering all the functional images in a single space with respect to each other, e.g. by picking one of the functional sessions as the target space and resampling all other functional sessions from this subject into this space (without using the hires structurals at all). I guess this would be kind of motion correction but capable of handling rotations. If such a tool exists, it might be more accurate than any of the methods above, simply because the functional images are more similar compared to each other than compared to the subject's hires structural image. Any ideas/suggestions which method would give the most accurate result? And what kind of tools currently exist? Thanks, Tommi --- Tommi Raij MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Question re' surface simulations.
by zvalim＠gmail.com 06 Mar '06

06 Mar '06

Dear FreeSurfer mailing list, I have looked at the online documentation for the new version, and was wondering where one could find more details on the permutation algorithm implemented in the current version. Some issues I would like to understand better is how the smoothing in the dataset is captured in the algorithm, and what is being permutated at the group level. If there is any reference to a published paper implementing this exact algorithm it would be very useful as well. Specifically, what I found online was: The first parameter the nulltype, which is the method of generating the null data to be tested. Useable options are: (1) perm - perumation, randomly permute rows of X (cf FSL randomise) (2) mc-full - replace input with white gaussian noise (3) mc-z - do not actually do analysis, just assume the output is z-distributed (cf ANFI AlphaSim) I have two questions of this... In (1 perm), what does "X" stand for -- a conditionXsubject table for each voxel? In (2 mc-full), when WN gaussian is inputted, is it smoothed with the characteristics of the original dataset? Sincerely, Uri

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regarding fsfast in event related mode
by Sebastian Moeller 06 Mar '06

06 Mar '06

Hi All, after some time of doing block designs I am thinking about switvching to event-related paradigm desing. Now my question is does fsfast correct for the slice timing (usually we use interleaved acquisition of our epis to getz better signal to moise). While for my block designs (with block lengths integer multiples of the TR) this is almost irrelevant, it will be more interesting for my planned even related design, where I want to use sub TR time resolution (-TER should help with the analysis, no?). So is it feasible to analyze event related designs with sub TR event resolution with fsfast, and what swiotches should be used? Thanks 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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mkanalysis-sess.new bug
by Sebastian Moeller 06 Mar '06

06 Mar '06

Aloha fellow surfers, the last dev versions (centos4_x86_64-dev20060224-full) has a slight buglet in fsfasts mkanalysis-sess.new. If line 195 is changed from: set ln = `grep TR $sifile`; to: set ln = `grep "TR " $sifile`; (note the embedded space), mkanalysis-sess.new will accept sequence names with, e. g. TR4 inside the string. Yeah, most likely this is a case of "don't do that then", but I have way to many sessions with offending sequence names to go rebame them... 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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jittered event related design
by Bosky Ravindranath 03 Mar '06

03 Mar '06

Hello List, We are designing a rapid event related paradigm, wherein a stimulus is presented for a duration of 300ms. We have been using optseq for generating sequences in the past, however , optseq requires that the event duration be a multiple of of TR or dPSD( sampling interval). In that case is it ok to create a design with a stimulus duration of 2 s ( which is our TR) and then split it into 300ms + 1700 ms, where the 1700 ms adds to the null period immediately following the stimulus? ( There is a null condition between each stimulus). Also, is it not important to start a new volume at the beginning of each stimulus? Any input is appreciated. Regards, Bosky Ravindranath Laboratory for the Study of Emotion and Cognition, Stony Brook University, NY,11790

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Motion correct error
by Jenn Segawa 03 Mar '06

03 Mar '06

Hi, I'm having a problem motion correcting my data. My runs have been converted into .mgz files, and I run recon-all -motioncor -s <subjName>, which runs smoothly until it starts averaging, at which point I get the following: ------------------------------------------------------------------------------------------ Averaging Fri Mar 3 11:32:49 EST 2006 /autofs/space/oldcask_003/users/gow/LEX02/aMRI_new/LEX02011 inhibiting isotropic volume interpolation 1 of 6: reading /autofs/space/oldcask_003/users/gow/LEX02/aMRI_new/LEX02011/mri/tmp-mri_mot ion_correct.fsl-9069/cor-1.img... 2 of 6: reading /autofs/space/oldcask_003/users/gow/LEX02/aMRI_new/LEX02011/mri/tmp-mri_mot ion_correct.fsl-9069/cor-2.img... 3 of 6: reading /autofs/space/oldcask_003/users/gow/LEX02/aMRI_new/LEX02011/mri/tmp-mri_mot ion_correct.fsl-9069/cor-3.img... INFO: analyzeRead(): min = 0, max = 940 INFO: analyzeRead(): min = 0, max = 820.699 frame = 1, slice = 0, k=128, row = 0 nread = 0, nexpected = 256 analyzeRead2(): error reading from file /autofs/space/oldcask_003/users/gow/LEX02/aMRI_new/ LEX02011/mri/tmp-mri_motion_correct.fsl-9069/cor-3.img mri_average: MRIread(/autofs/space/oldcask_003/users/gow/LEX02/aMRI_new/LEX02011/mri/tmp-mr i_motion_correct.fsl-9069/cor-3.img) failed Linux oldcask 2.6.9-22.ELsmp #1 SMP Sat Oct 8 19:11:43 CDT 2005 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Fri Mar 3 11:33:10 EST 2006 -------------------------------------------------- This happens with all my subjects. Any suggestions as to what I'm doing wrong? Thanks, Jenn

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autorecon3 parcellations and corresponding lists of labels
by Eli Diamond 02 Mar '06

02 Mar '06

Hello, I'm hoping someone can help me clear something up about the different parcellations now performed as part of autorecon3. In tksurfer, when I select file-->Label-->Import Annotation, I can choose from (for the lh, for example) lh.aparc.annot or lh.aparc.a2005s.annot. I understand that one of these is the "old" parcellation and one is the newer one done in (for the moment) the dev version of Freesurfer. My question is which of the aseg.mgz's correspond to which parcellation, and also which list in FREESUFER_HOME contains the list of labels created by which parcellation. When I look in $FREESURFER_HOME, there are several texts with numbered lists of cortical and subcortical areas. Having the correct "match" between aseg and $FREESURFER_HOME/<list> seems to be necessary in the sense that, to load a segmentation in tkmedit, the aseg volume that is loaded must correspond to the appropriate color list in order to get the segmentation labeled properly. My experience has been that aparc+aseg.mgz and FreeSurferColorLUT.txt match one another and that these correspond to the annotation lh.aparc.annot when loaded upon a surface. It has also been my experience that the labels/regions in lh.aparc.a2005s.annot correspond to the list contained in $FREESURFER_HOME/Simple_surface_labels2005.txt. I am hoping someone can help me figure out which aseg volume, if any, contains this particular parcellation. As it happens, my area of interest is the superior temporal gyrus, which is subdivided in this aparc.a2005s.annot but not in the aparc.annot, and because I will be extracting functional and volumetric data about these ROI, I would like to work with as small anatomical areas as possible. The way that this ROI extraction works (as the scripts I am using are set up) involves inputing a particular aseg volume and the number of a given label as it appears on the appropriate corresponding list, and I have been unable to find a way to use the cortical areas identified in the aparc.a2005s.annot annotation. Sorry this email is long, and likely not using the most accurate terminology, but I hope I got my question across. Thanks so much! Best, Eli Diamond

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problem in curv surface
by Reza Rajimehr 02 Mar '06

02 Mar '06

Hi, I have recently reconstructed a brain using "recon-all -autorecon" in dev environment. First I converted anatomicals to mgz format and then I ran the following commands sequentially: recon-all -subjid subject -autorecon1 -legacy recon-all -subjid subject -autorecon2 The reconstruction has been done successfully without error. The inflated surface is almost fine (without topological defects) but the "curv" surfaces (curv.lh and curv.rh) do not look normal. They have only red boundaries (sulci); the green boundaries (gyri) are absent. The sulc surfaces look fine though. on machine monkeylove source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/ship/3/users/reza/mvp022106/3danat which recon-all /usr/local/freesurfer/dev/bin//recon-all cd /space/ship/3/users/reza/mvp022106/MYSTUDY Thanks for any comments, Reza ******************************** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: reza(a)nmr.mgh.harvard.edu ********************************

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mri_convert documentation error
by Johannes Klein 02 Mar '06

02 Mar '06

Hi folks, There's a small bug in the online help for mri_convert I found when trying to get my input Nifti's left/right to match with freesurfer conventions. When run without any parameters, the last paragraph describes the use of the --in-orientation switch. That must read --in_orientation (probably same for out-/out_). Took me a while to figure that one out ;) Cheers, Johannes

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Freesurfer March 2006