Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Dipole localization
by Leonardo Barbosa 05 Jan '11

05 Jan '11

Hi, I'm trying to save the white matter surface as a gifti file so I can use it outside the freesurfer to implement an EEG dipole fitting, but I'm not sure if this is the best way to do it. I searched old posts in the list, but didn't find an answer. The problem is how to export the whole cortex, and not only one hemisphere. I'm using mris_convert subjects/subj1/surf/lh.white ~/subj1.lh.white.gii mris_convert subjects/subj1/surf/rh.white ~/subj1.rh.white.gii and trying to mix the two surfaces inside my program, but I guess it's not right, because the middle of the brain is opened. I have two closed surfaces, and I would like to have one close mesh, without creating new faces and ignoring vertices in the middle. Sorry i this is confusing, but the question is: Can I export one closed surface of the whole brain with freesurfer? Thanks in advance for any help... and Happy New Year! Leonardo Barbosa www.if.usp.br

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X error help
by Zhang, Aifeng 04 Jan '11

04 Jan '11

Dear FreeSurfer, I followed the tksurfer example in QaImageScript (http://surfer.nmr.mgh.harvard.edu/fswiki/QaImageScripts) and I can see the output images swipe through but the tiff images I saved using save_tiff is entirely black. And also I received the following error: Received X error! Error code : 8 Request code : 73 Minor code : 0 Error text : 'BadMatch (invalid parameter attributes)' Can you please help me figure this out? I am using VMWare&Ubuntu9.10 on my Windows 7 machine. Your help will be greatly appreciated ! thanks, Aifeng

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ROI Analysis Discrepency
by Garth Coombs 04 Jan '11

04 Jan '11

Hi Doug, I am running into a similar problem that Yuko describes in Martinos Tech message 5099 (wouldn't let me reply directly). Using Stable 4, I made an old analysis last spring and extracted ROI values, yielding significant differences between two conditions as expected. I believe I originally used mkanalysis-sess.new. I later redid some func2roi analyses after redoing mkanalysis-sess (rather than .new) and the significant difference was gone even though the data set and label were the same, so I tried to recreate the same old analysis with the .new added back in. However, I noticed that my roisummary-sess outputs are still different: *Original --> ID100 104 104 395.4163 31.5163 258.00 3.000 -0.00 7 1 -0.1397 0.6388 3.3232 3.9929 -18.0485 -6.8824 -7.0568 mkanalysis-sess -inorm (autosets -TER to 0.15) = mkanalysis-sess (no -inorm) (autosets -TER to 0.15) --> ID100 104 104 431.8531 31.1137 258.00 0.150 -0.00 7 1 -1.6920 -1.7342 -1.6874 -2.2781 -1.9065 -1.6461 -2.1075 *mkanalysis-sess.new -TER 3.000 -inorm = mkanalysis-sess -TER 3.000 -inorm = mkanalysis-sess -TER 3.000 (no -inorm) --> ID100 104 104 431.296 31.1078 258.00 3.000 -0.00 7 1 -33.3915 -34.3076 -33.5928 -44.2051 -37.5009 -31.9037 -41.6321 mkanalysis-sess.new -TER 3.000 (no -inorm) --> ID100 104 104 233.0353 16.8080 258.00 3.000 -0.00 7 1 -18.0419 -18.5369 -23.8846 -20.2622 -17.2380 -22.4944 The two * analyses should be identical (all the same settings during mkanalysis-sess.new), but for some reason aren't. Besides there being a large range among the values (-0.1397, -1.6920, -18.0419, -33.3915), in the previous extraction there were some positive values, whereas now there are mostly negative values. I noticed that the TER column was different between the original and the new one (both were originally nonspecified and used the autoset -TER of 3 for the original and 0.15 for the new), so I tried making a new analysis specifying TER as 3.000 in both mkanalysis-sess and mkanalysis-sess.new, as well as turning -inorm and -autostimdur on and off. When using mkanalysis-sess I primarily get large negative values (-33.3915 -34.3076) and -inorm, -autostimdur, & -noautostimdur don't make much of a difference if any. If I change the -TER (3.000 0.0300 0.150) my values change, with larger negative values with 3.000 and smaller values with 0.0300. However, even with setting the TER to 3.000 as in the original analysis, my values do not come out the same as we originally found. I was wondering, what is the difference between the mkanalysis-sess and mkanalysis-sess.new commands and why do they result in such different func2roi values? The volumetric maps look identical for all of the analyses, so the problem seems specific to the ROI signal extraction. Also, how do you decide what TER to use? Our TR = 3.000 s, TE = 0.0300 s, and the paradigm files were set up in intervals of 3.000 s. I'm not sure if the scan parameters' TE value is the same as the mkanalysis-sess TER setting. We would like to compare ROI % signal change extracted from the same ROI from two different phases (day 1, day 2). However, if we use the original ROI extraction values, we get % Sig Ch values in the -0.3 to 0.3 range, whereas with the new ROI extraction values, we get % Sig Ch in the -0.008 to 0.01 range, and the scale of the values seem incomparable. Any idea what might be going on or how to get something more like the original values? Thanks, Garth

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Transferring surfaces to the original image space
by Navid Shiee 04 Jan '11

04 Jan '11

Hi, I want to transfer the inner and outer surfaces generated by freesurfer to the original image space, ie the input image space before being transformed in a coronal 256^3. Would you please let me know how should I do this? Thanks, -- Navid Laboratory of MEDical Image Computing (MEDIC) Johns Hopkins University

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surface area vs. areal expansion
by Ecker, Christine 04 Jan '11

04 Jan '11

Dear FreeSurfer experts, I would like to compare surface area in a vertex-by-vertex fashion across two subject groups. There has been some discussion already on the mailing list and it seems that areal expansion is a better measure than simply area.pial for doing so. I also remember reading that when the data is converted from native space to a template (e.g. fsaverage), the values are automatically transformed to areal expansion measures. Please could you let me know if the output of –qcache (e.g. lh.area.pial.fsaverage.mgh) contains the area values (i.e. average area across triangles touching vertex) or areal expansion values. I believe these values are also compared in qdec. Many thanks, Christine ----------------------------------------------------------------------------------------- Dr. Christine Ecker Department of Forensic and Neurodevelopmental Science, PO50 Institute of Psychiatry De Crespigny Park, Denmark Hill London SE5 8AF Phone: +44(0)207 848 0947 Email: christine.ecker(a)kcl.ac.uk -----------------------------------------------------------------------------------------

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Talairach normalization fails for 7T structural datasets
by Sebastian Jentschke 04 Jan '11

04 Jan '11

Hi, I have some 7T-T1 datasets that I would like to process with FreeSurfer. However, regardless of whether I use the complete or the skull-stripped volumes as input, the Talairach normalization fails (in both cases the standard brain appears smaller than the individual brain when opened with tkregister2). The reason seems to be that the skull is dark in these volumes while its bright in the template. FSL flirt seems to work properly, so I would like to know whether there is any chance of replacing the talairach.xfm files with the output from this normalization? Any ideas are very much appreciated! Thanks a lot! Sebastian

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Freesurfer Color LUT & Saving ROIs
by Vy Dinh 03 Jan '11

03 Jan '11

Dear Freesurfer experts, Is there a way to save out ROIs for all the regions listed in the Freesurfer LUT? I've found posts and tutorials for saving multiple labels from an annotation file, saving an annotation file from multiple labels, and saving rois via the GUI. However, I don't quite understand how Freesurfer comes up with the labels from the LUT. To come up with the annotation file from the LUT, I tried: (while in Freesurfer/subjects/) >>mris_label2annot --subject SUBID/ --hemi lh --ctab ../../FreeSurferColorLUT.txt --a test --ldir annot_test but get the error message: subject 00303226_1/ hemi lh SUBJECTS_DIR /Applications/fmri_progs/freesurfer/subjects ColorTable annot_test/lh.ctx-lh-unknown.label AnnotName annot_test/lh.ctx-lh-bankssts.label nlables 5003 Loading /Applications/fmri_progs/freesurfer/subjects/00303226_1//surf/lh.orig No such file or directory mris_label2annot: could not open label file annot_test/lh.Unknown.label No such file or directory ERROR: reading annot_test/lh.Unknown.label Any suggestions would be much appreciated. Thanks, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu>

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Small bug in mri_probedicom
by Inge Amlien 03 Jan '11

03 Jan '11

Hi, trying to chuck together a script to do consistency checking for when our scans get off the scanner using mri_probedicom with the --compare flag. There is a small bug with the tag for software version, the program reports the tag for model twice. The tag for software version I believe should be (18,1020). eg. 0 Manufacturer (8,70) SIEMENS SIEMENS 1 Model (8,1090) Avanto Avanto 2 Software Version (8,1090) Avanto Avanto Merry xmas! Inge Amlien University of Oslo --------------------------------------------------------------------- Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 RedHat release: Red Hat Enterprise Linux Client release 5.5 (Tikanga) Kernel info: Linux 2.6.18-194.26.1.el5 x86_64 cmdline: mri_probedicom --compare 1.IMA 2.IMA

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mri_vol2surf --cortex and --mask flags appear ineffective
by Michael Waskom 03 Jan '11

03 Jan '11

Hey developers, It seems as if the --cortex and --mask flags for mri_vol2surf are not doing anything. E.g., if I use the exact same command line: mri_vol2surf --hemi rh --o rh.w-cortex.nii.gz --out_type niigz --reg register.dat --reshape --projfrac-avg 0 1 .1 --mov cope2.nii.gz --cortex With and without "--cortex" and then diff the output, they are identical. When you load the overlay in tksurfer, the medial wall has values that are not 0. Here's my bugr data: FREESURFER_HOME: /software/Freesurfer/5.0.0 Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 Debian version: squeeze/sid Kernel info: Linux 2.6.31-22-generic x86_64 Best, Mike

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Whole Surface SNR Calculation for Individual Functional Runs
by Adam Nitenson 03 Jan '11

03 Jan '11

Hello Freesurfers, We are beginning to perform QC on our subjects and want to look at signal to noise ratio. I've taken a look at the fsnr.nii overlay files, but we would like to be able to calculate a whole surface value for SNR for each functional run of each subject, so that we can exclude runs if that SNR values falls below our designated threshold. Is there a way to accomplish this? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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