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: [email protected]
<[email protected]> on behalf of Douglas N. Greve
<[email protected]>
Sent: Friday, October 8, 2021 9:25 AM
To: [email protected] <[email protected]>
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
<[email protected]><mailto:[email protected]>
Sent: Thursday, September 23, 2021 1:40 PM
To: [email protected]<mailto:[email protected]>
<[email protected]><mailto:[email protected]>
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:
[email protected]<mailto:[email protected]>
<[email protected]><mailto:[email protected]>
on behalf of Douglas N. Greve
<[email protected]><mailto:[email protected]>
Sent: Thursday, September 23, 2021 10:19 AM
To: [email protected]<mailto:[email protected]>
<[email protected]><mailto:[email protected]>
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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