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16 participants
30065 discussions

Hippocampus subfield
by Lin, Yizhi 10 Aug '17

10 Aug '17

Dear experts in Freesurfer, I am doing analysis on hippocampus subfield and I'm wondering if I could obtain cortical thickness data from each segmentation? Thanks so much! Best, Ariel

3 2

convert mgh to nii problems - cannot get output file to reshape properly
by Suzanne Witt 09 Aug '17

09 Aug '17

Hi. I am having a problem similar to that previously described on the freesurfer message boards from May 2011 (Subject: mgh conversion). Unfortunately, that thread ends with Doug asking the person to send him the files in question, so there does not appear to be any sort of publicly published solution. I was sent two .mgh files with the resulting activation maps from an fMRI analysis (both left and right hemispheres) and told that the maps were in fsaverage space. I was not sent any other accompanying files. I am trying to convert them to nii format. I have tried both: 1. mri_convert filename.mgh filename.nii.gz and mri_surf2surf (as was suggested in the previous thread) 2. mri_surf2surf —sval filename.mgh —tval filename.nii —reshape —reshape-factor 6 —s fsaverage —hemi lh (I realize that the command options should be preceded by double dashes, but my email program is quite insistent about automatically formatting these to long dashes.) In both cases the when checking the output file using mri_info, the dimensions are still: 163842 x 1 x 1. Are there any suggestions as to how best to proceed? Thanks in advance, Suzanne Witt

2 1

ROI labeling?
by Sadie Marvel 09 Aug '17

09 Aug '17

Hi again Freesurfers, I am doing a surface based ROI analysis where for each subject, isomorphic ROIs of 300 vertices (centered around peak functional activations) were found on the fsaverage surface space. I was wondering if I should register these masks that I have created back to each subject's individual surface before creating labels for these ROIs, and if so, what would the registration file be to register the fsaverage space back to each subject's space? The goal of this is to be able to run mri_glmfit on just the spaces within these labels. Is there a better method? Also, each subject will have a different number of labels considering that not every ROI was present on every subject. will this be a problem when running glmfit? ?Thanks

2 5

Optseq2 timing outputs
by Ruthie Shaffer 09 Aug '17

09 Aug '17

Hi all, I sent a message previously and just wanted to check in one more time about this question (apologies for the repeat message!). I’m using Optseq2 to generate stimulus / jitter schedules and, depending on the TR I use, in the output files I see onset times like 124.4001 (instead of 124.4) or 124.7999 (instead of 124.8). This is the command I’m using: optseq2 --ntp 75 --tr 3.2 --psdwin 0 22.4 3.2 --ev wordPair 3.2 45 --nkeep 6 --o CRtiming.2017 --nsearch 100000 --tnullmin 0 --tnullmax 6.4 Should I be concerned about the outputs (does it mean that I’ve specified something incorrectly in the above command), or is it correct to assume that something like 124.4001 just means 124.4? Anyway, thank you so much for your help on this! Best wishes, Ruth Shaffer

2 1

VBM
by Shane S 09 Aug '17

09 Aug '17

Hello Experts, Can we do VBM in MNI template using the outputs from recon all? Which file should I be using? And how do I smooth the volumes? Thank you for the tips! -- Shane S

2 1

ASL with rcbf-prep
by Tuominen, Lauri Johannes 09 Aug '17

09 Aug '17

Dear freesurfers, I have data collected here at the martinos using the Siemens ep2d_PASL sequence. I run the command "rcbf-prep —s subject —rcbf asl.nii —o tesfolder" or something like that. The resulting rcbf.nii looks good, but the values are negative? Is this just a matter of tag and ref images being in a wrong order and can I just fix it by removing the first image (after the M0)? Or is it more complicated? Thanks for your help Lauri

2 1

question about effects of changing server and freesurfer versions IF the entire study is consistent
by STACEY M SCHAEFER 09 Aug '17

09 Aug '17

Hello Freesurfer experts, We have processed, hand-edited, and QA'ed over 130 subjects' scans with version 5.3.0 on a linux sci6 box, and extracted the atlas-based ROI values for cortical thickness, volume, curvature, etc. The servers need upgrading but there are still whole brain analyses to run. Will there be any issues if we have processed all subjects identically, but then run analyses on the data with an upgraded linux and freesurfer's latest version? Thank you for your guidance! Stacey Stacey M. Schaefer, Ph.D. Center for Healthy Minds University of Wisconsin-Madison 625 W Washington Ave Madison WI 53703 608-263-9321

2 1

Sphere above a certain vetex
by Redwan Maatoug 09 Aug '17

09 Aug '17

Hi everybody, I have a .annot file and I would like to display a sphere above one certain vertex. (I know the coordinates of the vertex) Someone knows a way to do that ? Thank you very much, Redwan

2 1

Matrix ill-conditioned error for dods thickness mri_glmfit analysis
by Sullivan, Danielle Renee 09 Aug '17

09 Aug '17

Hi FreeSurfer Experts, I am trying to run a dods cortical thickness analysis examining the interaction of group on a continuous variable while controlling for other variables. Specifically, I have 6 classes (gender by three groups [zero, one, two]). I am interested in the group interaction with a continuous variable while controlling for gender (among 4 other continuous variables). I set up my fsgd file (see attached) and contrast file (36 dimensions- F test): 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [1 -1 0 1 -1 0]/2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [1 -0 -1 1 0 -1]/2 and ran this command: mri_glmfit --y lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.mgh --fsgd fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt dods --C /GLM_CONTRAST.MAT/Contrast.Male.Female.Age.PC1.PC2.PC3.GGT.RORAbySex.mtx --surf fsaverage lh --cortex --glmdir lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.glmdir But keep getting this error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- 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.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.mgh --fsgd fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt dods --C /Volumes/VA_Imaging/Projects/salat/2389_TRT/dmiller/GGT_CRP/GLM_CONTRAST.MAT/Contrast.Male.Female.Age.PC1.PC2.PC3.GGT.RORAbySex.mtx --surf fsaverage lh --cortex --glmdir lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Any idea on what I am doing wrong? Danielle R. Miller, Ph.D. National Center for PTSD VA Boston Healthcare System Jamaica Plain Boston University School of Medicine OFFICE: (857) 364-4022

2 1

Extracting pial surface from manually pareclated atlas
by Almarshad F. 09 Aug '17

09 Aug '17

Hi freesurfer team I'm just wondering if there is any way to extract left and right pial from manually parecllated file apar+aseg .mgh I need to view them with the new parecellation file Thanks in advance Fatima

2 1

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