Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Poor labeling
by Jason S. Minamora 06 Jan '09

06 Jan '09

Hello, I'm using a home-grown GCA constructed from five acallosal subjects to try to improve the automatic labeling and segmentation of volumes from this population. However, the labeling was quite bad when performed on a representative subject, and the ventricles were only partially filled and crossed the IHF in areas: Left_Lateral_Ventricle (4): linear fit = 1.00x + 0.0 (713 voxels, overlap=0.480) Left_Lateral_Ventricle (4): linear fit = 1.00x + 0.0 (713 voxels, peak = 38), gca=37.8 Right_Lateral_Ventricle (43): linear fit = 1.00x + 0.0 (370 voxels, overlap=0.292) Right_Lateral_Ventricle (43): linear fit = 1.00x + 0.0 (370 voxels, peak=38) I also noticed that the 152-subject MNI atlas that came with FS had ventricles that were much "darker" (when converted to NIFTI and displayed in fslview) than my own atlas: the mean ventricle intensities were about 15 and 30, respectively. We suffer from a lack of data, too. Is it possible to improve the GCA and labeling with such limited data? Jason

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Problem with post-spm registered data
by Dave Brohawn 06 Jan '09

06 Jan '09

Hello, Josh Roffman and I recently ran an fMRI scan. Our subject's data viewed in tkmedit seemed to be shifted inferiorly in the coronal view by a wide margin (an inch or so), leaving no functional activation in the top of the cortex, even when set at an extremely low threshold. When running the fMRI scan, we checked our slice prescription and ensured the area of view covered the entire cortex. We also checked the raw data output during the scan in the viewing window, and functional activity was present. After running the unpacking and recon-all processes, I ran the pre-proc command and spm-register, and viewed the output using tkregister2. The registered functional data matched up beautifully with the underlying anatomy, and went right to the top of the cortex in the coronal view. We ran our analysis using the appropriate paradigm files (has worked without fail for our previous subjects) and there is no functional activity in the top inch or so of the cortex whatsoever. Please let me know if you have an answer to how this could have happened. Dave Brohawn

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reg-feat2anat failed
by Wang, Xin 06 Jan '09

06 Jan '09

Hello, Freesurfer group, I am registering the fMRI results to surface using reg-feat2anat (v 1.26.2.1 2007/08/15) and tkregister2. The automatic registration catastrophically failed in the subject space, but worked fine in the standard space. The orientations of example_func.nii.gz in the subject space are flipped in any view. I use the tkmedit to view the example_func, and found the orientation is wrong. It seems Freesurfer can not read nifti header correctly. I attach the reg-feat2anat log file and an example_func.nii.gz. I found the following message from Freesurfer email list. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html Does Freesurfer have a solution for this type of problems by now? Thank you in advance, Xin

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open *.mgh
by Feng-Xian 06 Jan '09

06 Jan '09

Hi, Thank you for your help before. And, I have a problem today. How do I open the file called *.mgh as F.mgh and sig.mgh in the dictionary “qedc”? This problem has been nagging me for some time. Thank you in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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questions about region-wise analysis data
by Siddharth Srivastava 06 Jan '09

06 Jan '09

Hi everyone, while the machine is busy crunching through our data set, i would like to prepare myself from the next step of the analysis, which is a region-wise analysis of the computed metrics by the freesurfer pipeline. Being a complete novice in the use of this software, i would like to know how do i go about doing the following: 1) With the parcellations already available in freesurfer, i would like to extract metrics (curvature, lgi, thickness) etc. for each label, and process them outside freesurfer (matlab, since i am more used to it). Is it possible to do this within freesurfer or without, i.e read these values on the pial/white matter/inflated surfaces, ans also extract ones corresponding to a particular label? 2) How do i go about generating a group average of the various maps that freesurfer generates (curvature/thickness/lgi) ? As i understand, the analysis is done entirely in the subject space. Can i apply a transformation to the generated surfaces for averaging? Or does it require a re-processing after registering/reslicing all the data to a common space? 3) I am still struggling with a proper colormap, which can bring out the structure in out data. I see very nice renderings in various publications, of data generated with freesurfer. Is it possible to tweak the colormap to get such a rendering? Thanking you all in anticipation, sid.

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Re: [Freesurfer] How to overlap FSL statistical map onto surface in Matlab? (fwd)
by Yunjie Tong 05 Jan '09

05 Jan '09

Hi Thanks for the reply. I think all I need are the vertices and faces of a image to show it in Matlab. I can get the vertices and faces of lh.inflated and lh.aparc.annot of the subject. I do not know how to get the vertices and faces of zstat1.nii.gz generated by FSL of the same subject? What kind of transformation I should apply? Best, YJ On Jan 5, 2009, at 4:54 PM, Thomas Yeo wrote: > Hi, can you explain more what you mean by "overlap" the statistical > map onto the surface? If you can overlay the cortical parcellation > onto the surface, why can't you overlay the statistical map onto the > surface? > > Cheers, > Thomas > > >> >> >> >> ---------- Forwarded message ---------- >> Date: Mon, 5 Jan 2009 15:11:59 -0500 >> From: Yunjie Tong <tongyj(a)gmail.com> >> To: freesurfer(a)nmr.mgh.harvard.edu >> Subject: [Freesurfer] How to overlap FSL statistical map onto >> surface in >> >> Hi >> >> I was able to view the statistical maps (from FSL) on the subject's >> surface following the tutorial (FsTutotial/FSLFeatFreeSurfer). I >> would >> like to see the same image in Matlab. I could show the subject's >> surface as well as the the cortical parcellation in Matlab by >> modifying the functions freesurfer_read_surf.m and read_annotation.m. >> I do not know how to overlap the statistical map onto the surface >> then. Is there any Matlab function I can use? Thanks. >> >> Best, >> >> Yunjie >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

QDEC on multiple datasets
by nels5614＠umn.edu 05 Jan '09

05 Jan '09

Hello, I have run qcache on two separate datasets, and now would like to combine them and look at the data using QDEC. What is the proper way to go about doing this? Will I need to run an entirely separate instance of qcache on all of the datasets at once? Thanks for any information!

2 1

vertex/talairach coordinates
by Keller, Corey J. 05 Jan '09

05 Jan '09

Hi Freesurfers, I have a list of 50 vertices picked from an average subject's inflated brain in mne_analyze and would like to find the talairach coordinates for each of these vertices. Is there a more efficient way to do this than to load tksurfer and find these vertices by hand? Thanks again. -Corey

4 3

unpacking err runs
by Adrienne McCallister 05 Jan '09

05 Jan '09

Hello, I am unpacking recent functional data and during a function run we needed to stop it early and so now when I view it in unpacksdcmdir, it has a err next to the run. Since those runs are typically skipped when unpacking, is it possible to override that and download the file anyway? Any help would be appreciated. Sincerely, Adrienne

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[recon-all] [MacOS Leopard] Global Region of the brain empty
by Pedro Paulo de Magalhães Oliveira Junior 05 Jan '09

05 Jan '09

Hi, I'm running 100 cases in a MacPro with 8 core and in all cases I'm receiving this message in skull strip step: GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073732725 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=218 , nb = -1073752790 LEFT_CER CSF_MIN=0, CSF_intensity=3, CSF_MAX=8 , nb = -1073753244 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = -1608887106 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = -1073749725 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1859277276 mri_watershed Error: GLOBAL region of the brain empty ! Darwin lim44-macpro.local 9.4.0 Darwin Kernel Version 9.4.0: Mon Jun 9 19:30:53 PDT 2008; root:xnu-1228.5.20~1/RELEASE_I386 i386 Any Ideas are welcome. ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom

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