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30088 discussions

clusterwise correction ocn.annot missing and ICV in aseg.stats
by Pieter van de Vijver 02 Mar '11

02 Mar '11

Dear Freesurfer experts, I’m doing a longitudinal study on cortical thickness and subcortical volumes and got some questions. I used the longitudinal stream for the preprocessing 1. On cortical thickness, I’m doing a paired analysis as described in https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis, and then a cluster-wise correction as described in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis, with 5000 simulations instead of 5, and a vertex-wise threshold of 3 . But I don’t get the ocn.annot map, instead I get a ocn.mgh and ocn.lut. The CSD file also looks weird (constantly about 150 clusters with max size one or 2) and the resulting cluster.summary also gives a huge list of very small but significant clusters. Am I doing something wrong? How should I go about this? I’m using FS 4.5. Files are included (jpg for sig.mgh and cluster.mgh for negative simulation, and csd (zipped), summary and simulation log) 2. For the subcortical volumetric analysis I use the aseg.stats. Is the ICV a reliable measure to correct for overall brain size? I heard ICV measurements are not very reliable on T1’s (I get a mean of 2,4% decrease over 16 months...). Are other methods preferable to this one. 3. Is there a logic or rule of thumb for choosing the vertex-wise threshold? Thanks for your help! Pieter

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label to volume
by Adil Javed 02 Mar '11

02 Mar '11

Hi, I am a bit new to freesurfer. I want to convert rh.V1.label to volume. I have read the wiki for it but still having some problems. All I want is just a volume in the native space. Can someone just detail the script for me. Thanks. AJ

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question on contrast matrix
by j janssen 02 Mar '11

02 Mar '11

FreeSurfer version: 4.5 Background: we have 6 subjects, each subject has 1 scan per site, there are 6 sites (so each subject has 6 scans). Aim: to assess whether thickness is different per site: a F-test. what we did so far: we used mri_glmfit with the following .fsdg file (here we only show the Input of the first 2 subjects) GroupDescriptorFile 1 Title scanner MeasurementName thickness Class Site1 Class Site2 Class Site3 Class Site4 Class Site5 Class Site6 Input Subject1 Site1 Input Subject1 Site2 Input Subject1 Site3 Input Subject1 Site4 Input Subject1 Site5 Input Subject1 Site6 Input Subject2 Site1 Input Subject2 Site2 Input Subject2 Site3 Input Subject2 Site4 Input Subject2 Site5 Input Subject2 Site6 . . Input Subject6 Site6 we used the following .mtx file for mri_glmfit: 1 -1 0 0 0 0 0 1 -1 0 0 0 0 0 1 -1 0 0 0 0 0 1 -1 0 0 0 0 0 1 -1 we doubt that this is correct since our contrasts do handle the subjects at each site as an independent group, i.e. it does not take into account that each subject had 6 different scans (one at each site). any advice on how we should set up our contrast matrix? i repeat: our aim is to do a F-test to assess whether thickness is affected by site. thanks, -joost

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mri_surfcluster -ocn
by Mandy Nagy 01 Mar '11

01 Mar '11

Hi all, We ran mri_surfcluster on our group data (we didn't do montecarlo simulations), so we used our .mgh file. We used the -ocn flag to make an output file so we could look at the specific clusters. When we looked at the data of the ocn file using tksurfer, the most significant cluster wasn't visible at the .05 level (which is the min threshold we specified in the mri_surfcluster). We tried playing with the threshold, but it was the opposite of what we expected. The most significant clusters disappeared at the lowest threshold but the less significant ones appeared even when we raised the threshold. This happened when we ran the other hemisphere as well. Do you have any idea how to fix this? we are using freesurfer v5 subjects_dir: cluster/manoach/milton/subjects Our commands: mri_surfcluster --in ./group_analysis/mct_lh/osgm/sig.mgh --hemi lh --thmin 1.3 --thmax infinity --subject fsaverage --sum ./group_analysis/mct_lh/osgm/mst_v_mct.txt --ocn /cluster/manoach/milton/subjects/group_analysis/mct_lh/osgm/sig.cluster.p05.ocn.mgh tksurfer fsaverage lh inflated -overlay sig.cluster.p05.ocn.mgh Thanks in advance! Best, Mandy Nagy

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Func2ROI in Stable 4 --> FuncROI in Stable 5
by Adam Nitenson 01 Mar '11

01 Mar '11

Hi Freesurfers, I'm trying to analyze functional data in Stable 5, but have noticed that the func2roi command is no longer used. My analysis involves 9 conditions (not including Fixation) and 1 timepoint for each. The steps I used in Stable 4 to generate this data are as follows: func2roi-sess -roidef LH_16MTH_7v1_DLPFC -analysis fmcsm5_functionals -anatlabel LH_16MTH_7v1_DLPFC -sf /cluster/roffman/users/MTH_Study/Subject_Lists_MTH/16_PreScan_Genotyped -d /cluster/roffman/users/MTH_Study roisummary-sess -roidef LH_16MTH_7v1_DLPFC -analysis fmcsm5_functionals -sf /cluster/roffman/users/MTH_Study/Subject_Lists_MTH/16_PreScan_Genotyped -d /cluster/roffman/users/MTH_Study -sumfile /cluster/roffman/users/MTH_Study/ROI_Analysis/LH_16MTH_7v1Label_DLPFC In Stable 5, I see that there are several commands, funcroi-config, funcroi-sess, and funcroi-table-sess. Looking at other threads, it seems like I need to make a roicfg file for each contrast. So far I have tried: funcroi-config -analysis SIRP_Stable5 -label LH_16MTH_7v1_DLPFC -roi MTH_7vFix_DLPFC.roicfg -contrast Cond7vFix -sign abs and then funcroi-sess -roi MTH_7vFix_DLPFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH ...but for the latter, I get the following error: PVF (null) Thesholding hit volume. done mri_binarize --i /autofs/cluster/roffman/users/Stable5_PerRun/MTH20002AA/bold/SIRP_Stable5/Cond7vFix/sig.nii --frame 0 --mask /autofs/cluster/roffman/users/Stable5_PerRun/MTH20002AA/bold/SIRP_Stable5/MTH_7vFix_DLPFC.nii --o /autofs/cluster/roffman/users/Stable5_PerRun/MTH20002AA/bold/SIRP_Stable5/MTH_7vFix_DLPFC.nii --abs --min ERROR: --min flag needs 1 argument I don't see the --min argument described for either funcroi-config or funcroi-sess, so I was wondering what I needed to add/change to generate data similar to what I did for Stable 4. Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

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Constrasts in imbalanced design
by daniel geisler 01 Mar '11

01 Mar '11

Hi Freesurfers, I am currently dealing with some examples of group analysis from freesurfer-wikipages (see http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G0V) Could you please give some clarifications in the following scenario: Assume we have four groups MaleRight, MaleLeft, FemaleRight, and FemaleLeft (from factors gender and handedness). Now we want to set a contrast that is equivalent to the question: "Is there a difference between Males and Females regressing out the effects of handedness?" An appropriate contrast would be [0.5 0.5 -0.5 -0.5]. (see http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G0V#Contrast5male-female.mtx) Is that also true for an imbalanced design, where MaleRight and MaleLeft consist of 15 and 5 subjects, respectively? I suspect that in this case the above contrast would weigh MaleLeft more heavily, i.e. each subject in this rather small subgroup would have a greater effect on the final result. If that is true - I am wondering whether the contrast [0.75 0.25 ...] would fix this issue, i.e. adjust for the unbalanced design. Do you have any ideas? Best, Daniel

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folding index to table
by Chris Hyatt 01 Mar '11

01 Mar '11

Hi all, I'm trying to extract the folding index for each subject/hemisphere/roi from ?h.aparc.stats into a single table with all subjects. It appears though that aparcstats2table will only extract area, volume, thickness, thicknessstd and meancurv, not folding index, even though these values are in the ?h.aparc.stats file. Is there a way of extracting folding index for each subject and importing into a file? Thanks, Chris

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Re: [Freesurfer] -normalization2 does not run mri_mask
by Y. Mohammed 01 Mar '11

01 Mar '11

Dear Freesurfer team, is mri_mask actually a part of normalization2 as stated here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02175.html? while trying to run freesurfer stepwise, the normalization2 step "recon-all -subjid subject -normalization2" is not executing "mri_mask" when it is called separately (while running "recon-all -subjid subject -all" executes indeed mri_mask). This is preventing "recon-all -subjid subject -finalsurfs" later from running successfully. Do you have any suggestion/idea/workaround how to solve/fix this? is there something like "recon-all -s subject -mri_mask" or shall I run mri_mask directly from the command line? Thanking you in advance for your reply Yassene

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laterality analysis
by Ritobrato Datta 01 Mar '11

01 Mar '11

Hello All, I am trying to do a laterality analysis for a cortical reorganization project in blind patients. Since each hemisphere has slightly different gyral and sulcal patterns, in theory, one hemisphere could be mirrored and compared; in the surface space this amounts to turning one of the spheres inside-out (so to speak). Are there are any extant tools available to do this for freesurfer ? I remember seeing something in the discussion boards in the past. Please let me know. Thank you very much Ri

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load individuel a2009s labels
by LAOUCHEDI MAKHLOUF 28 Feb '11

28 Feb '11

hi i am new to freesurfer, i want to load somme specific (individuel) labels on a brain.mgz thanks

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