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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Friday, October 8, 2021 9:25 AM
To: freesurfer@nmr.mgh.harvard.edu <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.edu>
Sent: Thursday, September 23, 2021 1:40 PM
To: freesurfer@nmr.mgh.harvard.edu <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.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Thursday, September 23, 2021 10:19 AM
To: freesurfer@nmr.mgh.harvard.edu <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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