I used afni's 3dundump to create a 10mm sphere from MNI coordinates. I then ran the MNI template through freesurfer, and used the regheader from this to run mri_vol2surf to put the spherical ROI into fsaverage space. I am able to overlay the ROI created this way onto the fsaverage in freeview, and verify that it is in the correct location.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Friday, October 8, 2021 10:49 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] glmfit sig file all zeros
What do you mean it is based on a volumentric sphere? How did you create it?
On 10/8/2021 1:24 PM, Pedersen, Walker Scott wrote: If I run without the mask, the output sig file looks normal. If I overlay the surface ROI and the output sig file on the fsaverage, I can see that the maximum absolute pvalue in my ROI is around -2.2. Output below. Since the mask is based on a volumetric sphere, it is not contiguous after converting it to a surface ROI. Could that be causing mri_glmfit problems?
OUTPUT Reading source surface /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/subjects/fsaverage/surf/lh.white gdfRead(): reading /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt WARNING: gdfReadV1: no variables on 'Variables' line found INFO: gd2mtx_method is dods Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472
7.1.1 cwd /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast cmdline mri_glmfit --glmdir /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atCS+E/outputFiles/noMaskTest/ --y /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall//recall.sm5.lh/lCS+E_m_lCS-atCS+E/ces.nii.gz --surf fsaverage lh --fsgd /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt --C /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles//groupDiff.mtx --nii.gz --eres-save sysname Linux hostname uriline.nmr.mgh.harvard.edu machine x86_64 user wsp6 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_lCS-atCS+E/ces.nii.gz logyflag 0 usedti 0 FSGD /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt labelmask /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atCS+E/outputFiles/noMaskTest/ IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atCS+E/outputFiles/noMaskTest/ Loading y from /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_lCS-atCS+E/ces.nii.gz ... done reading. INFO: gd2mtx_method is dods Saving design matrix to /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atCS+E/outputFiles/noMaskTest//Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1.125 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 149955 voxels in mask Saving mask to /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atCS+E/outputFiles/noMaskTest//mask.nii.gz Reshaping mriglm->mask... search space = 74612.577841 DOF = 15 Starting fit and test Fit completed in 0.0100333 minutes Computing spatial AR1 on surface Residual: ar1mn=0.991551, ar1std=0.005518, gstd=4.393252, fwhm=10.345318 Writing results groupDiff MRImask(): AllowDiffGeom = 1 maxvox sig=-3.97251 F=27.102 at index 140685 0 0 seed=1634140058 mri_glmfit done ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Friday, October 8, 2021 9:25 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] glmfit sig file all zeros
what happens if you run it without the mask?
On 9/29/2021 2:33 PM, Pedersen, Walker Scott wrote: I just wanted to follow up on this - based on the output I sent previously, they seem to have the same resolution (unless I've missed something). They do have different orientations. Could this be an issue, or can gmlfit handle that? I'm also really stumped as to why I appear to be getting good F.nii.gz files, but bad sig.nii.gz files.
________________________________ From: Pedersen, Walker Scott WPEDERSEN@mgh.harvard.edumailto:WPEDERSEN@mgh.harvard.edu Sent: Thursday, September 23, 2021 1:40 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] glmfit sig file all zeros
Here is what I get for the mask: ______________________________________________________
Volume information for /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz type: nii dimensions: 163842 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 163842.000 dof: 1 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -68268.5000 : x_a = -0.0000, y_a = 1.0000, z_a = -0.0000, c_a = -17.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 16.5000 Orientation : LAS Primary Slice Direction: axial
voxel to ras transform: -1.0000 -0.0000 -0.0000 13652.5000 -0.0000 1.0000 -0.0000 -17.5000 0.0000 0.0000 1.0000 16.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 -0.0000 -0.0000 13652.5000 -0.0000 1.0000 -0.0000 17.5000 -0.0000 -0.0000 1.0000 -16.0000 -0.0000 -0.0000 -0.0000 1.0000
______________________________________________________
And here is what I get for the input ces file: ______________________________________________________
Volume information for /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_lCS-atCS+E/ces.nii.gz type: nii dimensions: 163842 x 1 x 1 x 17 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 163842.000 dof: 1 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 2560.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 17 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -68267.5000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -2.5000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 13653.5000 0.0000 0.0000 1.0000 -3.0000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 -0.0000 -0.0000 13653.5000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 3.0000 -0.0000 -0.0000 -0.0000 1.0000 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Thursday, September 23, 2021 10:19 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] glmfit sig file all zeros
It looks like the mask is the wrong size. What is the dimension of /autofs/cluster/neuromod/NIFTI/OCD_N M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz you can check with mri_info
On 9/17/2021 8:32 PM, Pedersen, Walker Scott wrote: Hi,
I am running glmfit on some functional data (using ces.nii.gz surface files as input) using ROIs and the --mask argument, that I plan to later submit to glmfit-sim for small volume correction. I have some rois that are subcortical and some that are surfaces. For the glmfit run within the surface ROIs the output sig.nii.gz files all voxels have a value of zero. However, this is not the case for the F.nii.gz and z.nii.gz files output by the same glmfit command - they have non-zero voxels. This issue only occurs for the surface ROIs, when I run glmfit in subcortical ROIs the sig.nii.gz files look normal.
The surface ROIs were created by using afnis 3dundump to create 10mm spheres from MNI coordinates. I then ran the MNI template through freesurfer, and used the regheader from this to run mri_vol2surf to put the spherical ROIs into fsaverage space. I am able to view the resulting surface ROIs projected onto the fsaverage surface in freeview, and have checked that my ces.nii.gz function files can also be overlayed onto the same fsaverage template in freeview.
The output of one of the glmfit commands in question is below.
thanks!
WARNING: gdfReadV1: no variables on 'Variables' line found Reading source surface /autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/subjects/fsaverage/surf/lh.white gdfRead(): reading /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles/ /fsgd.txt INFO: gd2mtx_method is dods Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472
7.1.1 cwd /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast cmdline mri_glmfit --glmdir /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lC S+E_m_lCS-atCS+E/outputFiles/lIFG/ --y /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recal l//recall.sm5.lh/lCS+E_m_lCS-atCS+E/ces.nii.gz --surf fsaverage lh --fsgd /autofs/space/uriline_003/users/projects/OC D_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt --C /autofs/space/uriline_003/users/projects/OCD_NM/ walker_pedersen/data/image/main/recall/inputFiles//groupDiff.mtx --nii.gz --mask /autofs/cluster/neuromod/NIFTI/OCD_N M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz --eres-save sysname Linux hostname r440-28.nmr.mgh.harvard.edu machine x86_64 user wsp6 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_lCS-atCS+E /ces.nii.gz logyflag 0 usedti 0 FSGD /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt mask /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz maskinv 0 glmdir /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atCS+E/outp utFiles/lIFG/ IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+ E_m_lCS-atCS+E/outputFiles/lIFG/ Loading y from /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_ lCS-atCS+E/ces.nii.gz ... done reading. INFO: gd2mtx_method is dods Saving design matrix to /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_ m_lCS-atCS+E/outputFiles/lIFG//Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1.125 Pruning voxels by thr: 1.175494e-38 Found 512 voxels in mask Saving mask to /autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atC S+E/outputFiles/lIFG//mask.nii.gz Reshaping mriglm->mask... search space = 222.026773 DOF = 15 Starting fit and test Fit completed in 0.0002 minutes Computing spatial AR1 on surface Residual: ar1mn=0.987586, ar1std=0.043927, gstd=3.620916, fwhm=8.526606 Writing results groupDiff MRImask(): AllowDiffGeom = 1 INFO: MRImask() using MRImaskDifferentGeometry() maxvox sig=-0 F=4.36504 at index 391 0 0 seed=1632900996 mri_glmfit done
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