Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

Re: [Freesurfer] Optseq download
by Douglas Greve 17 Feb '14

17 Feb '14

Hi Goi, please remember to post to the freesurfer list. Thanks! The max psd depends upon how long it takes for the HRF to return to baseline (and do not related to the TR). This is usually something like 20 sec + the duration of your stimulus. doug On 2/17/14 1:31 PM, Goi Khia Eng wrote: > Dear Prof, Previously I was having problems running optseq, and so > have left it off for a while. I have went back to try again, and > managed to get it to churn sequences. Thank you very much for your > advice and patience. > I have one more query: How much do you think we should set the psdmax > if we have TR of 1, and 2? > > Thanks for your advice! > Regards > Goi khia > > > On Tue, Nov 12, 2013 at 11:50 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > are you running "optseq" or "optseq2"? It should be optseq2. You > may need to make it executable (looks like you have the right > chmod command line, but don't put the "./" before it). I can't see > what you are trying to accomplish with the find command. Once you > have it exectuable, you should be able to run it with ./optseq2 > (if it is in the current directory). > doug > > > > On 11/10/13 12:06 PM, Goi Khia Eng wrote: >> Dear Doug, >> >> Thanks so much for your reply. I've downloaded VirtualBox, and >> have also loaded Ubuntu linux OS into the VirtualBox. I managed >> to put in the linux version of optseq2, but was unable to get it >> to run or locate the file. I've ran commands via the terminal >> using terms such as ./optseq2 , ./chmod a+x optseq2, find~/ -type >> f -name "optseq2". However, the messages that I get are either >> "optseq: command not found" or "No such file or directory.". I >> suspect this could be due to my limited knowledge on using linux OS. >> Do you happen to have a manual that you could share on how to >> load Optseq? >> >> Any advice would be very helpful. >> Thanks much! >> Regards >> Goi khia >> >> >> On Sun, Nov 10, 2013 at 1:41 AM, Douglas Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> >> Hi Goi khia, it does not really run under windows. The >> version there is if you have a program called CygWin which is >> a linux emulator. We have not used that in a long time. You >> can do the same thing with VirtualBox (another linux emulator >> that runs under windows). >> doug >> >> >> >> >> >> On 11/9/13 12:17 PM, Goi Khia Eng wrote: >>> Dear Prof Greve, >>> >>> I am trying to download Optseq from >>> http://surfer.nmr.mgh.harvard.edu/optseq/ on my Windows >>> machine (Windows 7), but an error message keeps coming up, >>> that cygwin1.dll is missing. >>> I've downloaded the cygwin file from cygwin.com >>> <http://cygwin.com>, but am still unable to download Optseq, >>> and the same error message appears. >>> >>> Do you have any advice on how I can try to resolve this? >>> Thanks much! >>> >>> Regards >>> Goi khia >> >> 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. >> >> > >

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Fwd: Edit hyperintense regions in aseg.mgz file in long or base?
by Linn Christin Bonaventure Norbom 17 Feb '14

17 Feb '14

---------- Forwarded message ---------- From: Linn Christin Bonaventure Norbom <linnnorbom(a)gmail.com> Date: Mon, Feb 10, 2014 at 4:06 PM Subject: Edit hyperintense regions in aseg.mgz file in long or base? To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi everyone, I am registering hyperintense lesions as "lh-lesion" or "rh-lesion" and I was wondering if it is better to do this as the base or the long stage. I see that the freesurfer wiki page says I can do it at both stages depending on the problem, but I was not sure if lesion registration counted as "incorrect labeling" or "correcting the volume of importaint structures". Thank you in advance! Regards Linn Norbom

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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. > >

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Freesurfer February 2014