Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

Wrong pail surfaces in few slices
by amirhossein manzouri 17 Feb '14

17 Feb '14

Hi all, There is incorrect pial surface lines (red and yellow) in the right hemisphere of some of my subjects. The white matter and grey matter are very close regarding intensity and this can be seen in just a few slices and then it gets correct. I tried control points but regarding the low intensity they can be effective. I wonder if there is a way to correct this, or if they may affect the qdec analysis between group afterwards a lot.(since they are present in one or few slices and create thick GM in those slices!) Best regards, Amirhossein Manzouri

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Interaction test
by Yang, Daniel 17 Feb '14

17 Feb '14

Dear FreeSurfer developers and experts, If I have a binary factor (Group1: patients, Group2: controls) and a continuous variable (age), I know I can follow Contrast2 in the following wiki to test the interaction effect. http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V Contrast2: [0 0 1 -1] tests if Age slope in patients (Group1) > controls (Group2), and if Age slope_Group1 - Age slope_Group2 > 0, I can see red/yellow. For example, cortical thickening is accelerated in patients (vs. controls). I am wondering how I can test for whether cortical thinning is accelerated in patients (vs. controls)? Here, the slope for Age would be negative. And if cortical thinning is accelerated in Group1 (vs. Group2), I should observe Age slope_Group1 < Age slope_Group2, that is, Age slope_Group1 - Age slope_Group2 < 0, thus, I should expect to see blue/cyan? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang(a)yale.edu

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Permission denied to write to freesurfer sub directory
by Dave Frank 17 Feb '14

17 Feb '14

Hello, I'm running OSX 10.8 and received an error when running recon-all (see screenshot). It appears i don't have permission to write to the freesurfer subject directory. How may i fix this? Thanks, Dave Frank [image: Inline image 1]

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one factor with three levels in qdec?
by Yang, Daniel 16 Feb '14

16 Feb '14

Dear FreeSurfer creators and experts, I am trying to run qdec with one discrete with three levels (i.e., https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) but there is some error message: ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y … I am wondering if three levels a discrete factor are currently supported in qdec in FS 5.3? Thanks! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang(a)yale.edu

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Join my network on LinkedIn
by Li Meng via LinkedIn 16 Feb '14

16 Feb '14

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recon-all pial reconstruction error
by charujing123 14 Feb '14

14 Feb '14

Hi FS experts, After running the recon-all -s CON_EIU12, I found some inappropriate error in pial reconstruction, which can be got in the attachment. I knew how to remove voxels from GM areas. But I did not know how to add some voxels into GM area in this case. Thanks. All the best. Rujing Zha 2014-02-15 charujing123

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FDR question
by pfotiad＠nmr.mgh.harvard.edu 14 Feb '14

14 Feb '14

Hi FS community, I am doing a cortical thickness comparison between a diseased and a healthy group. After running the mri_glmfit command for both hemispheres, I project the uncorrected significance map and there are a number of significant clusters showing (if you consider the p value to be at most 0.05). However, instead of using the clusterwise Correction for Multiple Comparisons, I wanted to use FDR to see what the results would look like, and I had a few questions regarding the whole process: 1) Is Tksurfer the only tool in FS that I can apply the FDR correction with, or are there any other ways? 2) In Tksurfer, I tried using the "Set Threshold Using FDR" tool, and when I set the rate from 0.88 to 0.87 it bumps down the minimum threshold from 1.37 to 3.24 hence resulting in no significant clusters for rates less than 0.88. Does that sound normal? Thanks in advance! Panos

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Fwd: Tracula Error: bvecs and bvals don't have the same number of entries
by Francesco Baldacchini 14 Feb '14

14 Feb '14

Hi, Sorry Anastasia, I'm seeing that my question was not so clear. The files I sent you in the first mail are the bvecs and bvals saved by trac-all -prep in the dmri directory. The original files are in attachment in this mail, Francesco Baldacchini 2014/1/13 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Hi Francesco - The bvecs file that you're attaching has only 3 vectors, > while the bvals file has 65 b-values. Are these your original files, or the > ones saved by trac-all in the dmri/ directory? > > a.y > > > On Mon, 13 Jan 2014, Francesco Baldacchini wrote: > > Hi everybody, >> I'm trying to run the trac all -prep command but after some times I get >> this >> error "bvecs and bvals don't have the same number of entries". I've >> checked >> my bvals and bvecs, which are in attach, but they seems to be formatted in >> the right way. What can I do? Thanks, >> >> Francesco Baldacchini >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

2 9

Other things to consider when setting -min_border_white -min_gray_at_white_border?
by Erik Lindberg 14 Feb '14

14 Feb '14

Dear Bruce and Freesufers, Adding to our previous discussion. You managed to fix a very bad segmentation by setting some expert options (mri_normalize -gentle and setting a fixed level for -min_border_white -min_gray_at_white_border). It was a very nice recovery of, what I thought to be, a hopeless image. As I in my project have around 800 images I was also testing these options on 10 more images that you used to "recover" the bad image. The test on the 10 other images (that also worked well without expert options) was quite good. The segmentation looked ok. What I am wondering now is if there is other aspects to consider when setting fixed levels in mris_make_sufaces? As I told you I looked into the recon-all log file and found that when FS is running normally in creates different levels of -min_border_white -min_gray_at_white_border for each image. As this is the Normal way for FS to run I suppose that this is the optimal way to run. So what is the disadvantages of setting fixed levels for -min_border_white -min_gray_at_white_border? Thanks! Erik

2 1

Number of pixel count
by Saurabh Thakur 14 Feb '14

14 Feb '14

Hello Free surfer Expert , I am kooking for the exact value of voxel / pixel which represent White ,Grey and CSF fluid matter in brain. I am trying to draw contour, and to measure the count...or How to count the pixel for particular region...? Thanks in advance for your timely advise. cheers Saurabh Thakur,

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