Freesurfer January 2010

freesurfer@nmr.mgh.harvard.edu

78 participants
123 discussions

freesurfer/FSl
by Ricky Deepak Sachdeva 29 Jan '10

29 Jan '10

> Hi, > I am trying to work with the fMRI files (FSL) to create some label files to use them as reference in phase analysis. I have never really worked with fMRI data or any of the software for it. I am trying to use FSL viewer because it seems like all the processing is done (Feat folder) but I can't seem to get the desired results. I load the filtered file as described in a tutorial but I don't see any activation. I know I am screwing something up. Another thing, I tried using freesurfer (tksurfer) and I loaded an inflated surface from the mri directory (not fMRI) than I tried to load overlay data from the fMRI feat directory but I get nowhere with it. Can you point me to the right direction? And what software should I use tksurfer or FSLVIEW? Do I need to pick specific files from the feat directory (other than the filtered file)? > > Thanks, > -Ricky

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Problem with Autorecon all
by Janani Dhinakaran 29 Jan '10

29 Jan '10

Hello, I encountered a problem with the command recon-all -s jan -autorecon-all which is supposed to be for all the steps. A full reconstruction. INFO: set hdr.hist.orient to -1 ERROR: failure writing /usr/local/freesurfer/subjects/jan/mri/tmp-mri_motion_correct.fsl-5574/cor-2.img So I tried flipping the axis- X, Y, Z then, XY, XZ, and finally YZ...which is the format it converted into for it's .mgz file. It still says the same thing. Next I tried recon1 (from step 1 to 5). It doesn't recognise the command. Command not found, or unrecognised. Please tell me what I can try to make this work. Thank you. Jan

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(no subject)
by Guang Zeng 28 Jan '10

28 Jan '10

Hi, there, I want to know how the FS GCA atlas looks like, is there a way to load the FS GCA Atlas and view it using tkmedit or matlab? Is it possible to replace FS Atlas with our own Atlas and use it for analysis? Thanks a lot! Guang _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID2472…

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mri_extract_label scripting
by Pruce, Benjamin 28 Jan '10

28 Jan '10

I have managed to use the mri_extract_label to pull individual ROI's from the wmparc.mgz file and it works perfectly for my need. I'm wondering if it is possible to script this command to create individual ROI images for all non-zero regions in one step? Essentially I would like to be able to use the index value from the wmparc.stats file and then name each file according to the StructName column. If anyone has a working backbone to start off, or any helpful suggestions are greatly appreciated. Best, Ben -- Benjamin Pruce, R.A. Psychological and Brain Sciences Indiana University Bloomington, IN 47401

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fs4 selxavg question
by Sebastian Moeller 28 Jan '10

28 Jan '10

Hi Douglas, I am getting somewhat confused in switching from fs3 to fs4. I pre-prosessed the same (functional) session with freesurfer 3.0.5 (mc-sess, inorm-sess, spatialsmoothing-sess, mkanalysis-sess.new (3.0.5), selxavg-sess, mkcontrasts-sess, stx-grinfer-sess) and freesurfer 4.5.0 (mc-sess, inorm-sess, spatialsmoothing-sess, mkanalysis-sess (with the -fsv3 switch to be sure they do the same whitening)), unfortunately the results for the exact same contrast look strikingly different. If I extract a ROI from the fs3 analysis (averaged volume) and apply it to the fs4 averaged volume the extracted time-course (from all the face patches looks almost identical, with 4 nice dips for the face epochs), so the pre processing seems to be almost identical for fs3 and fs4, but the fs4 analysis does not show any face patch at all (see attached image). Note how even the hot-colored object activation is weaker in the upper row (fs4) compared to the lower row (fs3) (both with identical threshold and saturation values). So something is going on here and I have no clue. I used MION contrast agent so I expect signal extinction for activated epochs and it is non-human primates, but I assume that does not make a big difference (and I accounted for the different shape in the IRF in both analyses). Now the mkcontrast-sess I used invocation is identical between the two Fs-versions. mkanalysis-sess does differ somewhat: FS4: mkanalysis-sess -fsd bold -funcstem fmcs2 -analysis a1 -paradigm pardigm.para -dt blocked -sf sf -df df -force -inorm -timewindow 80 -polyfit 2 -motioncor -TR 3.000 -gammafit 0 8 -gammaexp 0.3 -nconditions 7 -runlistfile rlf1 -mask brain_fmc -taumax 40 -noautostimdur -acfbins 10 -fsv3 -mcextreg FS3: mkanalysis-sess.new -fsd bold -funcstem fmcs2 -analysis a1 -paradigm pardigm.para -dt blocked -sf sf -df df -force -inorm -polyfit 2 -motioncor -TR 3.000 -gammafit 0 8 -gammaexp 0.3 -nconditions 7 -runlistfile rlf1 -mask brain_fmc -taumax 40 -mcextreg the paradigm file is identical, I tried "-acfbins 10 -fix-acf" instead of "-fsv3" before with the identical unexpected low p result, I did not yet try no whitening as the fs3 analysis used whitening successfully. Do you have any idea what I must have done wrong to get there? Can it be the -timewindow 80 in the new analysis compared to the traditional 40 in the old analysis? Thanks for your insight Sebastian Moeller -- Sebastian Moeller telephone: 626-395-6713 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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Using a clipped image
by Pierson, Ronald K 28 Jan '10

28 Jan '10

We have a large number of scans with excellent, visually inspected and manually trimmed brain masks, so we would like to use these masks to assist the FreeSurfer processing. One way we have experimented with to achieve this is to clip the T1 to remove anything non-brain before importing it into the subject directory. In using brain-clipped T1 images as a starting point for FreeSurfer we notice that the Talairach transform checking is quite far off, scaled badly and rotated downward 10+ degrees in pitch. I assume that this is due to the lack of similarity to the moving image, which includes skull. However, even if we don't modify this transform, the final parcellation looks quite good, and very, very similar to that from using a standard, non-clipped T1 as input. Is there any reason not to use a clipped T1 as input into FreeSurfer? Is the Talairach-based information used for segmentation or parcellation, and are we potentially creating problems? Or would it be better to simply use our mask to trim up the images after autorecon1 (coregistering them into the same image space and clipping them with a custom routine)? Ron Pierson Department of Psychiatry Carver College of Medicine W-278 GH, 200 Hawkins Dr Iowa City, IA 52242

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resize (i.e., scale or stretch) a volume
by Reza Farivar 28 Jan '10

28 Jan '10

Dear all, Is there an easy way to resize a volume, as in stretch it? I've gone the tkregister2 route of making a dat file and applying it with mri_convert (after converting to xfm) but for some reason it crops my volume, even when there's no good reason why it should. I'm hoping for a function or flag of a function that allows me to enter an x,y,or z scaling factor. Thanks, Reza

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error message on "make_average_volume"
by lordowen 28 Jan '10

28 Jan '10

Dear freesurfer expertise: When I perform the make_average_subject to obtain the custom average template, I encountered following error message in make_average_volume step: ---- Loading mask /usr/local/freesurfer/subjects/avgsubject/mri/brainmask.mgz ninput = 64 Chcking inputs Checking 0 /usr/local/... ... Checking 63 /usr/local/... nframestot = 64 Allocing output MRIalloc(256, 256, 256): could not allocate 262144 bytes for 11578 slice Cannot allocate memory ERROR: make_average_volume ---- Does that mean insufficient memory? or something wrong within my data? All subjects finished recon-all step without error and the "make_average_surface" step also finished without any error. Thank you for any advise. -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Student Laboratory of Integrated Brain Research Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182

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problem with qdec
by Kevin Head 28 Jan '10

28 Jan '10

I am having a problem with qdec. My table.dat and levels files are correct. I have 2 discrete variables and 2 continuous variables. I can only seem to run a maximum of three of the above in any combination, otherwise I get the following error: Error in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/qdec/Untitledtest/y.mgh --fsgd /Applications/freesurfer/subjects/qdec/Untitledtest/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/qdec/Untitledtest --surf fsaverage lh --label /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label --C /Applications/freesurfer/subjects/qdec/Untitledtest/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitledtest/contrasts/lh-Avg-thickness-Age_At_MRI_days-Cor.mat --C /Applications/freesurfer/subjects/qdec/Untitledtest/contrasts/lh-Avg-thickness-gab-Cor.mat --C /Applications/freesurfer/subjects/qdec/Untitledtest/contrasts/lh-Diff-2-4-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitledtest/contrasts/lh-Diff-2-4-Cor-thickness-Age_At_MRI_days.mat --C /Applications/freesurfer/subjects/qdec/Untitledtest/contrasts/lh-Diff-2-4-Cor-thickness-gab.mat --C /Applications/freesurfer/subjects/qdec/Untitledtest/contrasts/lh-Diff-female-male-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitledtest/contrasts/lh-Diff-female-male-Cor-thickness-Age_At_MRI_days.mat --C /Applications/freesurfer/subjects/qdec/Untitledtest/contrasts/lh-Diff-female-male-Cor-thickness-gab.mat --C /Applications/freesurfer/subjects/qdec/Untitledtest/contrasts/lh-X-group-sex-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitledtest/contrasts/lh-X-group-sex-Cor-thickness-Age_At_MRI_days.mat --C /Applications/freesurfer/subjects/qdec/Untitledtest/contrasts/lh-X-group-sex-Cor-thickness-gab.mat I am running this on a Mac pro with snow leopard (patched up to date) Any help would be appreciated.

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mri_extract_label command and intensity of the image
by jun xu 28 Jan '10

28 Jan '10

> > Hi, Everyone, > > I was using mri_extract_label command to extract the region that I am > interested in, what I did was as follow: > > mri_extract_labe aparc+aseg.mgz 10 seg.nii > > It worked. However, when I tried to see it in the spm8, the intensity is > 128 (interested region) and 0(dark area). It is not like I saw it before for > the segmented image --- 1(interested region) and 0(dark region). Is there > any flag that I need to specified in order to get the the intensity number > to a normal number? > > Thanks, > > Jun >

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Freesurfer January 2010