Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

(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

1 0

retinotopy analysis viewing in Freesurfer 5
by Katie Bettencourt 16 Feb '12

16 Feb '12

I have a question about the retinotopy analysis in freesurfer 5. I was following these instructions : http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis with some minor edits because we don't have eccen data. And now I'm ready to view the data, but I'm confused by what I am seeing. I have a lot of previous retinotopy experience with older versions of freesurfer, and have this data all analyzed using Freesurfer4.5 and it works fine. However, with Freesurfer 5 when I use this command (with the correct sessid and hemisphere added in): tksurfer-sess -a rtopy.self.?h -s sessid it gives me a heat map, instead of the standard colors that match to the upper, lower, and horizontal meridians (i.e. red, green, and blue). I also tried using the "raw angle" code: tksurfer-sess -a rtopy.self.?h -s sessid -map angle but it doesn't give me the three colors either, but a sort of heat like map with 2 colors, but the colors don't map to the different visual areas, even in occipital cortex. Field sign doesn't work because I don't have the eccen data (and because I'm care about parietal retinotopy, not occipital). Is there a way to get the standard view of retinotopy out of freesurfer 5? For reference in freesurfer4.5, I would load retinotopy data by using this command: tksurfer subjname ?h inflated and then load the map-imag-lh.w in one overlay layer, and map-real-lh.w in the second overlay layer, then configuring the overlay to display the color wheel color scale and complex display options, and then configuring the phase encoding display to 2 angle cycles and an appropriate angle offset. Can you help me figure out how to get my data to display correctly? Thanks, Katie

3 5

Freeview Surface Editing
by Tina Jeon 16 Feb '12

16 Feb '12

Dear freesurfer experts, I am new to the freeview interface. How do I go about drawing a ROI on the surfaces to create my own label? Both the voxel edit and ROI edit buttons are not useful in this case. Thank you in advance, Tina Jeon PhD Candidate Advanced Imaging Research Center UT Southwestern Medical Center 2201 Inwood Rd Dallas, TX 75204 ________________________________ UT Southwestern Medical Center The future of medicine, today.

2 1

transforming aseg.mgz, brain.mgz to native scanner space and dimensions
by Mario Ortega 16 Feb '12

16 Feb '12

Hello Freesurfer Mailing list, I would like to know how to do the item mentioned in the subject> Ideally not just write out the brain and aseg regions into isotropic voxels in standard space, but also accomplish converting back to the *original*resolution, would I have to specify an inverse transform file? If I follow the directions in the mri_label2vol, I get volumes in a scanner like orientation, but not the correct x,y,z, dimensions. Ie, I get 256x 256 x 256 as x,y,z. When in fact we scan at 256x256x176 Thanks Mario

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