Freesurfer February 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
199 discussions

optimal parcellation example
by Keefe, Helen L 20 Feb '12

20 Feb '12

Does anyone have a template/atlas/graphic showing what the optimal parcellation should look like, with the areas labeled? I'm particularly interested in medial "Show Main Surface" view after running tksurfer - but would also like inflated and other orientations as well if anyone has them On medial I am especially interested in the boundary between rostralanteriorcingulate - medialorbitofrontal and lingual - pericalcarine - cuneus Thanks, Helen ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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overlay question
by LAOUCHEDI MAKHLOUF 20 Feb '12

20 Feb '12

hi all excuse me for this "simple question" but i am quiet new to freesurfer (i use it just for the parcellations). i've some functionnal maps (i've used spm for that) that i want to use as an overlay on the pial surface of the subject. is there an easy way to do it thanks

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freesurfer license file
by Christopher Bell 19 Feb '12

19 Feb '12

How do I obtain a freesurfer license file?

2 1

(no subject)
by Antonella Kis 17 Feb '12

17 Feb '12

Hi, I have few questions and I will appreciate if anyone can help: 1) Can I get more clusters after I correct for multiple comparison than the number of clusters I have in the uncorrected results? Is this possible? 2)When I change the smoothing from fwhm 10 to fwhm 20 for example why I am loosing from my clusters (uncorrected results)? Also in this case my clusters show became larger no? 3) I found my significant clusters after multiple comparisons for the FA group analysis study and I would like to dilate all regions for a better visualization, using the dilM function of the FSL tool fslmaths.Can you please advise me how to do it if I have the significant clusters file permcsd.sig.cluster.mgh? 4) As I mentioned before,I completed my DTI group analysis at subcortical level on the CVS space and found clusters that survived by multiple comparisons. The results shows that FA is decreasing in patients vs. controls. I used then the same subjects to do a structural group analysis to compare the cortical thickness between the two classes. I found some clusters on the fsaverage but this time they different located then the clusters found in my DTI data. Is this right? I suppose it should be since I compare two different data sets for the same subjects: FA clusters on subcortical CVS space vs. structural data on the fsaverage. I still found that my cortical thickness is decreasing in patients vs. controls but is there any relation that I can established between the two studies? Can I merge my structural results with my subcortical results? I was reading about this on your webpage:http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastG… but I am not sure if in this case the structural analysis is using the same functional data set while in my case I have same subjects but structural data for the structural group analysis and DTI data for the subcortical analysis. Can you please make this a little clear for me? How can I run a structural analysis on my DTI data? Many thanks! Antonella

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white matter volumes
by Lugar, Heather 17 Feb '12

17 Feb '12

I'm sorry if I've overlooked this in the mail archives, but is there a way to use aparcstats2table to extract the cortical white matter volume values from wmparc.stats for multiple subjects, as you do for thickness, volume, meancurv, etc? Thanks, Heather

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Question regarding axial diffusivity
by Antonella Kis 17 Feb '12

17 Feb '12

Dear All, I was running dt_recon on my DTI data and one output file is the eigvals.nii -- maps of the eigenvalues. I know that the diffusivity along the principal axis, λ1 represents the longitudinal diffusivity or the axial diffusivity (or even the parallel diffusivity λ∥).Can you please advise me how I can get my first eigenvalueλ1 from my maps of the eigenvalues? Thank you for your time and help. AK

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Origin of MNI coordinates
by Korhonen Onerva 17 Feb '12

17 Feb '12

Dear all, I am trying to find vertices corresponding to (or as near as possible) a given set of MNI coordinates. I use freesurfer_read_surf and freesurfer_surf2tal to get the MNI coordinates of the vertices - however, place of the origin (0,0,0) in the brain seems to vary between subjects - especially the origin of our subjects is different from that of the given set, which of course makes it terribly difficult to find corresponding vertices. So, I would like to know if there is a anatomically fixed origin for the MNI coordinates given by freesurfer_surf2tal and where it is. Of course I would also be happy for any other pieces of advice to get through this problem. The Freesurfer analysis for our subjects is done during a relatively long period of time (between 2007 and 2010) so one possible reason for the subject-to-subject differences might also be a change of e.g. MNI template used by the Freesurfer - has there been any changes of that kind? Many thanks already in advance! Best regards, Onerva Korhonen

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Number of entries error in trac-all
by Fidel 17 Feb '12

17 Feb '12

Dear all, I have tried to execute trac-all and I have found this error in the process (From the log): > > > > > > > > > > > dtifit -k /X/subjects//S1/dmri/dwi.nii.gz -m /X/subjects//S1/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r /X/subjects//S1/dmri/bvecs -b /X//S1/dmri/bvals -o /X/subjects//S1/dmri/dtifit Error: data and bvals/bvecs do not contain the same number of entries > > > > > > > > > > > I have seen in the mailing list that it has happened before, but I have not found the solution. You can find the bvals and bvecs files attached. As far as I can see, they have the same number of rows, so... What is the problem? Thanks and best regards, Fidel.

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Question regarding conversion to mgz
by Hemant Bokil 16 Feb '12

16 Feb '12

Hello, I had posted this question earlier but no one picked it up so I am trying again. Briefly, I have been having difficulties with the very first step of the recon-all pipeline, namely, in conversion of my dicom datasets to freesurfer's mgz format. The error message (attached below) suggests that freesurfer is able to find the files correctly, but is unable to find the slice direction because it gets 'nan' for the variable Vs. This seems to result is problems with reslicing and program exits with errors. Has anyone encountered this issue ? The MR files themselves look fine when viewed in other viewers (note that this problem has now occurred with several different datasets). Would appreciate any input. Thanks, Hemant *recon-all -s 101 -i DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/hemant/FreeSurferSubjects Actual FREESURFER_HOME /usr/local/freesurfer Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux /home/hemant/FreeSurferSubjects/101 mri_convert /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM /home/hemant/FreeSurferSubjects/101/mri/orig/001.mgz mri_convert /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM /home/hemant/FreeSurferSubjects/101/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM... Starting DICOMRead2() dcmfile = /home/hemant/DICOM_MR_DATA/101/1000430544_ST3445_SR10_V10000.DICOM dcmdir = /home/hemant/DICOM_MR_DATA/101 Ref Series No = 10 Found 139 files, checking for dicoms Found 136 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 136 nslices = 1 ndcmfiles = 136 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data MRIresample(): error inverting matrix; determinant is -nan, matrix is: TR=5.25, TE=2.00, TI=450.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation -0.938 0.000 nan nan; 0.000 -0.938 nan nan; 0.000 0.000 -nan -nan; 0.000 0.000 0.000 1.000; Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 101 exited with ERRORS at Fri Feb 10 16:00:03 EST 2012 *

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whole brain volume
by Dana W. Moore 16 Feb '12

16 Feb '12

I have a follow-up question to my inquiry about whole brain volume. I have some subjects completed with the older version, where I have BrainSegNotVent, and some subjects completed with the new version. If I combine Supratentorial with cerebellum to calculate whole brain, is this comparable to the BrainSegNotVent measure? Thanks, Dana -- Dana W. Moore, Ph.D. Instructor of Neuropsychology Department of Neurology & Neuroscience Weill Cornell Medical College 428 East 72nd Street, Suite 500 New York, NY 10021

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Freesurfer February 2012