Freesurfer June 2014

freesurfer@nmr.mgh.harvard.edu

155 participants
234 discussions

question on summary file from monte carlo simulation
by Govindarajan, Koushik Athreya 16 Jun '14

16 Jun '14

Dear Freesurfers, When I do the Monte-Carlo simulation after mri_glmfit between my groups, I get an output summary file for each of my contrast. In that summary file, there are multiple columns for coordinates, threshold values, number of vertices and size (mm2). My question is, how is this area in mm2 calculated? Is it from the number of vertices? If so, is there a standard algorithm for arriving at the area? Thanks in advance Koushik

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Re: [Freesurfer] Problem of VolumeRoiCorticalThickness
by kangchengwang0808＠gmail.com 16 Jun '14

16 Jun '14

Dear Douglas Greve, Thank you very much. I change it and change the option of reshape into noreshape. Then, it could be sucessful.

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Re: [Freesurfer] Problem of VolumeRoiCorticalThickness
by kangchengwang0808＠gmail.com 16 Jun '14

16 Jun '14

Dear Bruce, Now, I change the standard atlas to avg152T1.nii.gz which was included in the FSL and make a mask of superior frontal gyrus (Harvard-Oxford Cortical Structural Atlas). I can map the ROI-mask to the fsaverage surface to create an fsaverage-ROI surface overlay. But when I map one subject thickness data to the fsaverage subject using the following command: mri_surf2surf --s s12129 --trgsubject fsaverage --hemi lh --sval s12129/surf/rh.thickness --tval ~/Desktop/mask/rh.thickness.fsaverage.mgh --reshape it said: Reading source surface reg /Users/wangkangcheng/Desktop/dataplus_60/s12129/surf/lh.sphere.reg Loading source data ERROR: dimension inconsistency in source data Number of surface vertices = 146027 Number of value vertices = 145656 How could solve this problem? Thank you Wang Kangcheng

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volume-based controls
by kristen yoo 16 Jun '14

16 Jun '14

I am attempting to do volume-based analysis using a data from normals as my control. Does fsaverage provide volume-based data for this purpose? Where can I find these values? Are they found anywhere outside of the freesurfer suite? Thanks in advance!

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Messages not appearing on Mail Archive
by Sherryse Corrow 16 Jun '14

16 Jun '14

Hi, The messages I am sending to free surfer(a)nmr.mgh.harvard.edu are not showing up on the site here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/maillist.html. But they are showing up on the digest emails that I am receiving. Is that normal? For example, the message pasted below is this morning’s digest. And my message is listed there, however, my previous two messages are not listed on the new mail archive from the website linked above. Am I doing something wrong? Appreciated, Sherryse Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu<mailto:freesurfer-owner@nmr.mgh.harvard.edu> When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: aparc manual correction (Bruce Fischl) 2. Fwd: Extracting mean diffusivity values from diffusion data in freesurfer 5.3 (Rotem Saar) 3. ?Sequence for Hippo_subfields (Kev) 4. Displaying subset of labels on template (nmw) 5. Re: Displaying subset of labels on template (dgw) 6. Re: From NIfTI T1 to its volume cortical thickness map in MNI152 space. (Fred Sampedro) 7. Re: Displaying subset of labels on template (Bruce Fischl) 8. Re: From NIfTI T1 to its volume cortical thickness map in MNI152 space. (Bruce Fischl) 9. FW: Registration of Functional Data to the Inflated Brain (Sherryse Corrow) -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 360A-2550 Willow Street Vancouver, BC, V5Z 3N9 Tel: 604-875-4111 ext 67672 Cell: 604-315-6717 sherryse.corrow(a)eyecarecentre.org<mailto:sherryse.corrow@eyecarecentre.org>

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Displaying subset of labels on template
by nmw 16 Jun '14

16 Jun '14

Greetings, Is there any way to display just a subset of cortical labels onto one of the Freesurfer template brains (e.g., cvs_avg35) rather than all that are listed in lh.aparc.annot? I'm interested in loading frontal pole, superior frontal, superior parietal, etc onto a standard Freesurfer brain. My first thought was to create a new lh.aparc.annot file; however, I am having trouble editing it. Any thoughts? Thanks, Nate

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Error Covarying for Gender
by Thomas DeRamus 16 Jun '14

16 Jun '14

Sorry to be a bother, but I seem to be having an issue with my analysis. I have a control and a patient group, and I'm trying to covary gender the majority is skewed towards one gender. I'm looking across 4 metrics (thickness, surface area, volume, and lgi) of the cortex. My continuous variables include Age for all metrics, Total incracranial volume for the volume analysis, total intracranial surface area for the area measure (cubed root squared transform of eTICV), and Mean thickness for the left and right hemisphere (each separate for their respective hemispheres) for thickness. My goal is to look at changes in these as a function of age, relative to total ICV/SA metrics (because my patient population has arrested brain development in theory), and diagnosis. So I'm examining the following interactions: DiagnosisXAge, AgeXICV, DiagnosisXICV, DiagnosisXAgeXICV Which originally gave me 6 columns for the "total vol/area/thick" analyses: Control, Patient, ControlAge, PaitentAge, ConICV, PatICV if I'm not mistaken and 4 for the non-tICV lgi analysis. On the recommendation of the tutorial, I coded my change my 2 class variables to 4 to account for gender (so now its MaleControl, MalePatient, FemaleControl, Female Patient) Which should give me 12 columns right? ConMale, ConFemale, PatMale, PatFemale, ConMaleAge, ConFemAge, PatMaleAge, PatFemaleAge, ConMaleICV, ConFemICV, PatMaleICV, PatFemaleICV This analysis will run for volume, area, and lgi (no icv so 8 columns), but I keep getting the following Message from the terminal for thickness: -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 16115.7 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.diagnosisxagexleftThickslopetest.thickness.10.mgh --fsgd GenderGroupingSBM_glmLeftthick.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage lh --cortex --glmdir GenderGrouplh.Controlled_diagnosis_agethickness.glmdir 2. The FSGD file (if using one) 3. And the design matrix above I see this has been a problem for others, but I'm not sure if its a scaling issue, a problem with my FSGD file, or that mean thicknesses correlate too much with age. I've attache the FSGD file in question along with the contrast matrixes and the X file (cue theme) from the analysis. Any input would be greatly appreciated, thanks. -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 *Phone*: 205-934-0971 *Email:* tpderamus(a)gmail.com, faustus(a)uab.edu

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mri_glmfit for longitudinal 3 group analyses
by Elijah Mak 16 Jun '14

16 Jun '14

Hello FS experts, I have 3 groups, e.g : normal, MCI, and AD. Am I correct in my understanding that QDEC would not be applicable here? In my subjectdir, I created a folder for mri_glmfit analyes called FSGD. In that folder, I have the FSDG file and the relevant contrasts. GroupDescriptorFile 1 Class HC Class MCI Class AD input sub1-base MCI input sub2-base AD input sub3-base HC My contrast is a simple [1 0 -1] for HC > AD. I called it HC-AD.mtx and saved it in the FSGD folder. Then, in the SUBJECTdir/FSGD folder, I run the mri_glmfit command as follows: mri_glmfit --glmdir fsgd/ --y y.mgh --fsgd g3v0.fsgd --C normal-ad.mtx My question is, what is y.mgh as shown in the examples on the Wiki? It is supposed to be an input file, but what file is this? Thank you very much! Best Regards, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge *| *Department of Psychiatry Trinity College, Cambridge, CB2 1TQ

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Get thickness of one peak vertex for a group subject
by Xiangzhen Kong 16 Jun '14

16 Jun '14

Hi, all. Is there any FS tool for extracting the thickness value of a peak vertex ? From glmfit, I have got the vertex index of the peak. Thanks. Best, Xiang-zhen 【小孔成像】http://www.conxz.net

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Questions about cluster-wise correction
by wangzhiwei3233 16 Jun '14

16 Jun '14

Hi, all, I have two quesiotns about clusterwise correction for multiple comparsion. I run 2 corrections for one same result,and commands are as follows: a. mri_glmfit-sim --glmdir g2v0.weight --cache 2.0 abs --cwpvalthresh .05 --2spaces b. mri_glmfit-sim --glmdir g2v0.weight --cache 2.0 pos --cwpvalthresh .05 --2spaces The only difference is the sign of voxel-wise results. Question 1 : Should the postive clusters from "abs" be same as the cluster from "pos"? If yes, why cluster size from "pos" are different from postive cluster from "abs" in my case?(see results) Resluts form a (only positive clusters are listed): # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 3 6.483 140982 222.17 -14.8 58.9 -6.1 0.01510 0.01350 0.01670 281 rostralmiddlefrontal 8 5.208 45661 266.48 -6.7 42.3 -22.2 0.00450 0.00370 0.00540 454 medialorbitofrontal 9 5.103 84832 241.36 -32.0 30.7 -2.3 0.00830 0.00710 0.00950 655 lateralorbitofrontal Resluts form b: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 6.483 140982 253.31 -14.8 58.9 -6.1 0.02000 0.01820 0.02180 326 rostralmiddlefrontal 2 5.208 45661 402.16 -6.7 42.3 -22.2 0.00080 0.00050 0.00120 727 medialorbitofrontal 3 5.103 84832 287.61 -32.0 30.7 -2.3 0.01010 0.00880 0.01140 772 lateralorbitofrontal Question 2 : Is the simulation from pre-cached independent from my results waiting for being corrected? Thanks a lot! Wilder 2014/06/15

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Freesurfer June 2014