There is some rogue character after the "0" in "Class 0". If you run od -c fsgd_file.fsgd It comes out as 312. I have no idea what it is
On 4/29/2020 6:21 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote:
External Email - Use Caution
Dear Freesurfer experts,
I'm having a persistent error with mri_glimfit. The fsgd file isn't being read correctly, despite following the exact requirements of the wiki. Also, the output mentions this "carriage returns warning", and despite running this conversion: cat fsgd_file.fsgd | sed 's/\r/\n/g'
new.fsgd_file.fsgd, the *_new fsgd still doesn't work_* (this code
somehow alters the Group Descriptor at the top of the file, giving another error). I've attached my fsgd file (that I used while running the code below) Also, please see the full error of the glim_fit below:
WARNING: carriage returns have been detected in file fsgd_file.fsgd
Was it created on a Windows computer?
This may cause an error in reading the FSGD file.
If so, try running:
cat fsgd_file.fsgd | sed 's/\r/\n/g' > new.fsgd_file.fsgd
Then use new.fsgd_file.fsgd
INFO: ignoring tag Tile
INFO: ignoring tag nput
INFO: ignoring tag nput
INFO: gd2mtx_method is dods
Reading source surface /Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces327680
Total area 65020.839844
AvgVtxArea 0.396851
AvgVtxDist 0.717994
StdVtxDist 0.193566
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Applications/freesurfer/BAP/group_analysis_data/qdec
cmdline mri_glmfit.bin --y fsgd_RH_thickness.mgh --fsgd fsgd_file.fsgd dods --C contrasts.mtx --surf fsaverage rh --glmdir rhBAP_thickness.glmdir
sysnameDarwin
hostname CCASPH-A1900447.cloud.ccas.gwu.edu http://CCASPH-A1900447.cloud.ccas.gwu.edu
machinex86_64
user ajobsaid
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/Applications/freesurfer/BAP/group_analysis_data/qdec/fsgd_RH_thickness.mgh
logyflag 0
usedti0
FSGD fsgd_file.fsgd
labelmask/Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/label/rh.cortex.label
maskinv 0
glmdir rhBAP_thickness.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory rhBAP_thickness.glmdir
Loading y from /Applications/freesurfer/BAP/group_analysis_data/qdec/fsgd_RH_thickness.mgh
... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to rhBAP_thickness.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1e+10
Design matrix ------------------
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+10
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:
- Your command line:
mri_glmfit.bin --y fsgd_RH_thickness.mgh --fsgd fsgd_file.fsgd dods --C contrasts.mtx --surf fsaverage rh --glmdir rhBAP_thickness.glmdir
The FSGD file (if using one)
And the design matrix above
Attempting to diagnose further
SumSq: Min=99999997952.000000 (col 0), Max=0.000000 (col 0)
... could not determine the cause of the problem
Thanks!
Alex Job
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer