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30099 discussions

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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reg.1mm.mni152.dat
by Yang, Daniel 16 Jun '14

16 Jun '14

Dear all, While there is the file ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat, there is no such file as: ${FREESURFER_HOME}/subjects/fsaverage/mri/reg.1mm.mni152.dat or ${FREESURFER_HOME}/subjects/fsaverage/mri/transforms/reg.1mm.mni152.dat ? I am wondering how we can create the reg.1mm.mni152.dat file? Thanks! Daniel

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Extract the mean cortical thickness of each significant clusters
by Santosh Yadav 16 Jun '14

16 Jun '14

Dear Freesurfer Experts, Please ignore the previous email. I would like the mean thickness measures of each clusters, survived after multiple comparison correction, in qdec. I used qdec for a group comparison in cortical thickness between a patient group and a healthy control group. I found 30 different significant clusters after FDR. I would like to extract the mean cortical thickness of each significant cluster in the patient group and in the healthy control group. I went though previous post and run the following command: mri_glmfit-sim --glmdir lh-Diff-Control-HF-Intercept-thickness --cache 1.3 abs --cwpvalthresh .99 and found following output: cmdline mri_glmfit --y /home/virtualuser/freesurfer/subjects/qdec/glmdir/y.mgh --fsgd /home/virtualuser/freesurfer/subjects/qdec/glmdir/qdec.fsgd doss --glmdir /home/virtualuser/freesurfer/subjects/qdec/glmdir --surf fsaverage lh --label /home/virtualuser/freesurfer/subjects/fsaverage/label/lh.aparc.label --C /home/virtualuser/freesurfer/subjects/qdec/glmdir/contrasts/lh-Avg-Intercept-thickness.mat --C /home/virtualuser/freesurfer/subjects/qdec/glmdir/contrasts/lh-Diff-Control-HF-Intercept-thickness.mat WARNING: unrecognized mri_glmfit cmd option doss SURFACE: fsaverage lh set: No match. FreeSurfer:~/freesurfer/subjects/qdec/glmdir> Please suggest where i can find out the file for thickness. Is above commond is correct? and program showed the warning: unrecognized mri_glmfit cmd option doss. Any help would be great. With regards, Santosh -- With Best Regards, Post Doctoral Fellow, Department of Anesthesiology University of California, Los Angeles, CA 90034 Phone No. 808-5896940

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Extract the mean cortical thickness of each significant clusters
by Santosh Yadav 16 Jun '14

16 Jun '14

Dear Freesurfer Experts, I would like the mean thickness measures of each clusters i found in qdec from both control and patient group. I used qdec for a group comparison in cortical thickness between a patient group and a healthy control group. I found 30 different significant clusters after FDR. I would like to extract the mean cortical thickness of each significant cluster in the patient group and in the healthy control group. I went though previous post and run the following command: mri_glmfit-sim --glmdir lh-Diff-Control-HF-Intercept-thickness --cache 1.3 abs --cwpvalthresh .99 and found following output: cmdline mri_glmfit --y /home/virtualuser/freesurfer/subjects/qdec/glmdir/y.mgh --fsgd /home/virtualuser/freesurfer/subjects/qdec/glmdir/qdec.fsgd doss --glmdir /home/virtualuser/freesurfer/subjects/qdec/glmdir --surf fsaverage lh --label /home/virtualuser/freesurfer/subjects/fsaverage/label/lh.aparc.label --C /home/virtualuser/freesurfer/subjects/qdec/glmdir/contrasts/lh-Avg-Intercept-thickness.mat --C /home/virtualuser/freesurfer/subjects/qdec/glmdir/contrasts/lh-Diff-Control-HF-Intercept-thickness.mat WARNING: unrecognized mri_glmfit cmd option doss SURFACE: fsaverage lh set: No match. FreeSurfer:~/freesurfer/subjects/qdec/glmdir> Any help would be great. With regards, Santosh -- With Best Regards, Post Doctoral Fellow, Department of Anesthesiology University of California, Los Angeles, CA 90034 Phone No. 808-5896940

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Problem of VolumeRoiCorticalThickness
by wangkangcheng_gmail 15 Jun '14

15 Jun '14

Hi all, I want to extract cortical thickness for a ROI (dlpfc) which was defined in volume space. I search it in Freesurfer Wiki and find the description in website (http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) But, in the second, it said it need an T1 volume (average of subjects) which was called TT_avg152T1.nii. How can I calculate it? What is the voxels of ROI and T1.nii, 1*1*1 mm2? Thank you Wang Kangcheng

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Re: [Freesurfer] Substantia Nigra Segmentation
by Katherine Fu 14 Jun '14

14 Jun '14

I was wondering if Freesurfer now segments the substantia nigra, since as of June 2013 it did not? Thank you for your help. Best, Katherine Fu On Sat, Jun 14, 2014 at 10:56 AM, Katherine Fu <kathfu(a)usc.edu> wrote: > I was wondering if Freesurfer now segments the substantia nigra, since as > of June 2013 it did not? > > Thank you for your help. > > Best, > Katherine Fu > > -- > Katherine Fu > Keck School of Medicine of USC > Class of 2017 > kathfu(a)usc.edu > -- Katherine Fu Keck School of Medicine of USC Class of 2017 kathfu(a)usc.edu

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Center vertex of label
by Martijn Steenwijk 14 Jun '14

14 Jun '14

Dear all, I was wondering, is there a way to to find the vertex in the middle of a label? Not in terms of center of gravity of voxels, but on the (spherical?) surface? Looking forward to suggestions, Best, Martijn

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protocol question
by Joshua Lee 13 Jun '14

13 Jun '14

Dear Freesurfer Experts, I am trying to better understand what regions of the hippocampal formation are meant to be included in the hippocampal label (e.g. inclusion of the alveus/fornix, lateral boundaries around the subiculum, superior boundaries in the tail, etc.). Has the protocol used to manually segment the hippocampus for the Freesurfer atlases been described in detail somewhere? I cannot seem to locate a specific reference. Thanks Joshua

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