Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

comparing multiple runs on the same scan
by Krieger, Donald N. 10 Feb '16

10 Feb '16

We would like to confirm that we are getting identical results from multiple freesurfer runs on the same data set. To do so we are comparing identically named files using md5sum and would very much appreciate your thoughts on our results. For multiple files, we concatenate them and pipe the output into md5sum. Below is a table showing what we've found so far. I take hope from the positive matches we get from all of the .annot files and from the fact that 001.mgz does not match. This latter suggests that there is a date or something embedded in some of the files from separate runs which defeats the match. Please let us know what you know about this and thanks. file(s) md5sum result label/*.annot match label/*.label match mri/wmparc.mgz mismatch surf/qsphere.nofix surf/rh.sphere mismatch mri/orig/001.mgz mismatch mri/transforms/talairach.m3z match mri/transforms/talairach.m3z.inv.x.mgz mri/transforms/talairach.m3z.inv.y.mgz mri/transforms/talairach.m3z.inv.z.mgz mismatch mismatch mismatch Best - Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh

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error in motion correction
by Ji Won Bang 10 Feb '16

10 Feb '16

Dear. Freesurfer team. Hi. I'm using freesurfer 4.5 version. While doing the motion correction, an error occurred. the command I used: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 the error I have: /home/jbang/Projects/replay/epi/replay01/bold_retino 3dvolreg -verbose -dfile 025/fmc.mcdat -base 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 degrees from plumb. ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees from plumb. ++ centers of base and input datasets are 9.09 mm apart ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't have same dimensions! Input: nx=74 ny=74 nz=32 Base: nx=74 ny=74 nz=33 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. I think it's because the volume size is different. The volume size for bold_retino is: number of slices 32 The volume size for bold_decode: number of slices 33 What should I do to correct this error? Thank you for taking your time. Best, Ji Won

4 7

Middle cerebellar peduncle segmentation
by Henri Pazro 10 Feb '16

10 Feb '16

Dear experts, I'm trying the brainstem segmentation from Juan Eugenio Iglesias and would like to know if the middle cerebellar peduncle will be added in a near future? Thanks! H.

2 1

FS 5.3 and OS X 10.11
by prasser 10 Feb '16

10 Feb '16

Hi, On the download page it mentions that Freesurfer v5.3 is not compatible with OS X 10.11 because of an implementation of SIP. As a test, I have run a few subjects with v5.3 under OS X 10.11.3 with SIP enabled but was unable to see any problems, with all test subjects completing without error. I was wondering what I should be looking for (i.e. in the .log etc?) that would indicate that v5.3 is not compatible with OS X 10.11.3. Thanks.

2 1

Free surfer- correcting for head size
by Christina van den Brink 10 Feb '16

10 Feb '16

Hello, I have a question regarding volume-correction for the morphometry stats obtained via recon-all. I’ve noted that eTIV is derived using the atlas scaling factor in order to account for head size. I’m wondering whether the other volumes given, e.g. TotalGray or lhCorticalWhiteMatter, have also been corrected for head size? If not, is there a recommended method in which to do so so that regional volumes can be compared between participants? Many thanks for your help! Best, Christina

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Re: [Freesurfer] Tracula_weighted dti metrics values
by Anastasia Yendiki 09 Feb '16

09 Feb '16

Hi John - The values are weighted (multiplied) by the probability distribution (path.pd.nii.gz) at the same voxel. So they are the expected values, from a probabilistic standpoint. The distribution is thresholded at 20% of its maximum by default (this is a parameter in dmri_pathstats). Best, a.y On Wed, 16 Sep 2015, John Anderson wrote: > Hi Anastasia, > How the script "dmri_pathstats" compute the weighted FA, MD, AD, and RD > values? > I checked the command "dmri_pathstats" inside the file "trac-all.log" but I > was unable to figure out how this weighting is working. Is it by multiplying > the mean DTI metrics by the number of voxel? > > If my FA maps is "dtifit_FA.nii.gz" and my probabilistic distribution map > for the cortico spinal tract is "path.pd.nii.gz" and I want to compute FA > value using the command "fslstats" like: > > fslstats dtifit_FA.nii.gz -k path.pd.nii.gz -m ==== >This command will > output the mean FA for the probabilistic distribution map. How can I weight > this FA value using the previous command line? > > Bests, > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > >

2 4

Combining lh. and rh. surfaces
by Maheen Siddiqui 09 Feb '16

09 Feb '16

Dear FreeSurfer Users, I have been using the recon-all FreeSurfer command to reconstruct surfaces from T1 weighted MRI scan. I need to import the surfaces I have into Homer2 Atlas Viewer and for this I need whole surface/volume files rather than the individual hemispheres. Does anybody have experience combining the hemispheres? Many thanks, Maheen Maheen Siddiqui BBSRC LIDo PhD Student Centre for Brain and Cognitive Development Birkbeck, University of London London

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segmentation errors in subject with severe atrophy
by Corinna Bauer 09 Feb '16

09 Feb '16

Dear all, We are working on editing the segmentation of a subject with severe atrophy due to a seizure event that occurred during infancy. In portions of the parietal and frontal lobe the atrophy is so severe that freesurfer can't find any WM or GM. Is there a way to manually fill in the GM so that it is captured within the surfs? Because we have other modalities that use the Desikan atlas, this is an important first step. I have attached a few figures for examples. Thanks!!

1 0

retinotopy analysis: wedge position, angle offset, tksurfer
by Kinga Littke 09 Feb '16

09 Feb '16

Hello everyone, I've analyzed my polar retinotopy data (2 runs with clockwise and counterclockwise wedge rotations) using FsFast. To better understand the analysis, I'd be very grateful if you could help me with the following questions: 1. I understand that freesurfer assumes that the rotating wedge starts at 12 o'clock, which means that the middle of the wedge has to be exactly aligned with the upper vertical meridian. Is that correct? In my task I used a 45 degree wedge that starts rotating with its left and right borders aligned to to 12 o'clock, respectively. Do I need to account for that somehow in the analysis or in the display of the results, for example by changing the angle offset while displaying the polar map (under: view -> configure -> Phase encoded data display)? 2. When searching through the archive, I came across this thread below about freesurfer assuming that a clockwise rotating wedge starts at 12:00 and a counterclockwise one at 15:00: *[Freesurfer] polar angle analysis with clockwise- and counterclockwise-rotating wedges* * Thomas Janssens thomasj at nmr.mgh.harvard.edu <freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20polar%20angle%20analysis%20with%20clockwise-%20and%0A%09counterclockwise-rotating%20wedges&In-Reply-To=%3CE0168CFF-41F9-4FE3-944B-29E5F6E2FAAC%40nmr.mgh.harvard.edu%3E> Mon Aug 13 08:24:37 EDT 2012* *Hi Doug, It seems that, our stimulus presentation is inconsistent with the way freesurfer processes the retinotopy clockwise and counter clockwise data. After going through the freesurfer code I found the following. The freesurfer code assumes that the wedge starts horizontally for both clockwise and counterclockwise runs. In the glm analysis, the difference between the two types of runs (specified in the paradigm file by "neg" or "pos") is programmed in the function $FREESURFER_HOME/fsfast/toolbox/flac_desmat.m as follows: for "pos" runs the real part equals cos(phz) and the imaginary part equals sin(phz) for "neg" runs the real part stays cos(phz) and the imaginary part equals -sin(phz). This is correct if the wedge starts in the horizontal positionm, but not if the wedge starts vertically. In that case the code above will lead to a phase shift of half a cycle for the "neg" runs compared to the "pos" runs. However, this problem is solved by changing the code for the "neg" runs to: the real part equals -cos(phz) and the imaginary part equals sin(phz). This small change fixed the problems for our data. Thomas* Should I also make the same adaptation, i.e. inverse the signs of sin and cos for negative runs in my analysis for my retinotopy analysis, given that in freesurfer v. 5.3, in flac_desmat.m file, the "pos" and "neg" runs are still specified as cos(phz), sin(phz) and cos(phz) and -sin(phz), respectively. 3. When displaying the results using rtview command, I see somewhat blurred retinotopic maps, whereas I do not use any smoothing in the analysis (mkanalysis-sess [...] - fwhm 0). I've noticed that one of the output message in terminal while running tksurfer is the following: tksurfer: polar-views.tcl: read and smooth real Fourier comp, surfer: smooth_val(2)? Is it possible that tksurfer smooths the maps before displaying them? If so, how to display unsmoothed results? rtview command I use to display polar maps on the left hemisphere: rtview --s subjNr --lh --polar \ --real subjNr/bold/rtopy.self.lh/polar/real.nii.gz --imag subjNr/bold/rtopy.self.lh/polar/imag.nii.gz --fsig subjNr/bold/rtopy.self.lh/polar/fsig.nii.gz Thank you very much for your help, Kinga Littke

1 0

Gray matter intensity
by Sabrina Yu 08 Feb '16

08 Feb '16

Hello, I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html> And have successfully gotten the wm-gm signal intensity contrast, but now have a few questions regarding signal intensity for white matter and gray matter intensity. 1) Does the wmparc.stats contain mean white matter intensity values for each ROI? 2) Is it possible to extract these same mean intensity values for gray matter? There is no gmparc.stats file. We know that it's possible to calculate these from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more direct way to get this data. Thank you, Sabrina Yu

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