Hi all,
Is there a place where I could find an atlas with all of the Brodmann areas? Or is the one available with a portion of the areas the only existing atlas?
Thanks, Mike
Nvm just read an old thread. Sorry about that. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019825.ht...
On Fri, Aug 16, 2013 at 11:24 AM, Michael Kranz mbkranz@gmail.com wrote:
Hi all,
Is there a place where I could find an atlas with all of the Brodmann areas? Or is the one available with a portion of the areas the only existing atlas?
Thanks, Mike
the ones that are automatically generated by recon-all and stored in the subject's label dir are all we have at the moment. We have a bunch more that we've been trying to get out for a while, but have been having technical issues with
cheers Bruce On Fri, 16 Aug 2013, Michael Kranz wrote:
Hi all, Is there a place where I could find an atlas with all of the Brodmann areas? Or is the one available with a portion of the areas the only existing atlas?
Thanks, Mike
Dear FS,
I just started reanalyzing my data using FS5.3 (based on your feedback) after experiencing problems in the 5.0 version.
Here however, I'm having a new problem: the pial surface of a number of subjects is missing only for the right hemisphere, while the white matter surface looks perfect. Similar to http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29628.html
See the pictures below.
https://www.dropbox.com/s/fr4ve5mb0ioy1o2/no_pial_coronal.tiff https://www.dropbox.com/s/s36o8y0hkfw0gix/no_pial_surface.tiff
I checked the brainmasks, and these were all ok. To be sure I reran the recon-all process for these subjects, but unfortunately this didn't solve my problems. However, I do get an error after autorecon2, yet the commandline responsible for the error is part of autorecon3:
#@# ASeg Stats Mon Sep 9 17:31:53 CEST 2013 /home/cedric/data/Anatomy_BD/freesurfer/FS5.3/CREA/CREA_915_12_1
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz -- in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject CREA_915_12_1
ERROR: Option --euler unknown ----------- Full log for 2 subjects, though similar errors: https://www.dropbox.com/s/jzbp2vpzfb12wsu/recon-all.o128590 https://www.dropbox.com/s/so5jfd7wuo19ax6/recon-all.o128591
Do you have any idea what might be causing this? And of course, how to fix this?
Many thanks!
Cheers, Cédric
------------------------------------------------------------ P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain and Cognition Weesperplein 4; Room 3.07 1018 XA Amsterdam The Netherlands E P.C.M.P.Koolschijn@uva.nlmailto:P.C.M.P.Koolschijn@uva.nl T +31-20-525-2427 W http://www.dutcharc.nl
Dear FS,
I' ve run into some strange things in QDEC which I haven't encountered before. I'm running FS 5.3.
First, loading data file in QDEC works, yet terminal output displays the message below:
Data table /home/FreesurferSubjects/qdec/Base_File_FreeSurfer.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '123' in SUBJECTS_DIR etc.
Until: Too many subjects not found! Input table: /home/FreesurferSubjects/qdec/Base_File_FreeSurfer.dat Subj#, SubjID, Data... 1 123 423.000000 2.000000 3.000000 23.534247 Male 1.000000 2.000000 1461390.000000 490566.000000 755239.000000 706151.000000 -0.096959 0.641372 -0.09 etc.
So it does load the data. Subjectsdir = correct, all files are in place, no missings or whatsoever. If I check the dataview option, all looks wel. Also, qdec.fsgd looks good, no missing values or subjects.
This is similar to an old post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08288.html
Should I just ignore this? Or is something going wrong? If so, how should I fix this?
Second, and this is by far the strangest thing, I have in my qdec.table.dat file 2 independent groups for a exploration – validation study. So, I load my .dat file, including the errors above, then import stats data => aseg volume =>ICV, and then for a sanity check, in a simple design I have sex as discrete variable, clinical score as continuous covariate, and age and ICV as nuisance variables. This all works perfect. If I select only group 1 (by excluding group 2), also no problem. Yet, when I only select group 2, with the same design as stated above, QDEC crashes during loading of the regression coefficients:
(..) (No errors before) (..) Continuous Variable Means (all subjects) 0 clinvar1 57.0299 8.72632 1 AgeYears 22.825 1.72886 2 IntraCranialVol 1.10829e+06 129670 Class Means of each Continuous Variable 1 sexMale 57.8301 22.7324 1189880.5686 2 sexFemale 56.2027 22.9207 1023944.1351 MatrixMultiply: m1 is null!
No such file or directory For full output, see below
If I exclude ICV from the analyses, again the analyses work out fine for group2. Just out of curiosity I tested the same design adding total gray volume next to ICV, and this works fine. In addition, sex as discrete variable, clinical score as continuous covariate, and age and TGV as nuisance variables works also fine. Separating group2 in a single .dat file didn't resolve this issue. Somehow ICV is causing this problem, but I can't get my head around why it does work for group1 or the whole group, but not for group2.
In previous posts it was suggested to demean ICV as a solution for this issue, though this doesn't explain why it works for the other group? E.g.: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21744.html (though in contrast to that post, I don't have missing values (NaN).
The only difference between group 1 and 2 is sample size, 204 and 301 respectively (and of course different subjects, scores, ages etc).
Any thoughts on both problems?
Many thanks, Cédric
Full output after QDEC crash with ICV as nuisance variable for group 2:
lh-Avg-Intercept-thickness ----------------------- Does the average thickness differ from zero? Nuisance factors: AgeYears IntraCranialVol 1.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000;
lh-Avg-thickness-clinvar1-Cor ----------------------- Does the correlation between thickness and clinvar1, accounting for sex, differ from zero? Nuisance factors: AgeYears IntraCranialVol 0.000 0.000 1.000 1.000 0.000 0.000 0.000 0.000;
lh-Diff-Male-Female-Intercept-thickness ----------------------- Does the average thickness differ between Male and Female? Nuisance factors: AgeYears IntraCranialVol 1.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000;
lh-Diff-Male-Female-Cor-thickness-clinvar1 ----------------------- Does the thickness--clinvar1 correlation differ between Male and Female? Nuisance factors: AgeYears IntraCranialVol 0.000 0.000 1.000 -1.000 0.000 0.000 0.000 0.000;
ninputs = 301 Checking inputs nframestot = 301 Allocing output Done allocing nframes = 301 Writing to /home/FreesurferSubjects/qdec/Untitled/y.mgh gdfReadHeader: reading /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 clinvar1 57.0299 8.72632 1 AgeYears 22.825 1.72886 2 IntraCranialVol 1.10829e+06 129670 Class Means of each Continuous Variable 1 sexMale 57.8301 22.7324 1189880.6867 2 sexFemale 56.2027 22.9207 1023944.2196 INFO: gd2mtx_method is dods Reading source surface /home/FreesurferSubjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/FreesurferSubjects/qdec cmdline mri_glmfit --y /home/FreesurferSubjects/qdec/Untitled/y.mgh --fsgd /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd dods --glmdir /home/FreesurferSubjects/qdec/Untitled --surf fsaverage lh --label /home/FreesurferSubjects/fsaverage/label/lh.aparc.label --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-thickness-clinvar1-Cor.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor-thickness-clinvar1.mat sysname Linux hostname tux08 machine x86_64 user cedric FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/FreesurferSubjects/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd labelmask /home/FreesurferSubjects/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/FreesurferSubjects/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/FreesurferSubjects/qdec/Untitled Loading y from /home/FreesurferSubjects/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /home/FreesurferSubjects/qdec/Untitled/Xg.dat Normalized matrix condition is 2142.57 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /home/FreesurferSubjects/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 DOF = 293 Starting fit and test Fit completed in 0.24555 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995767, ar1std=0.000990, gstd=6.213820, fwhm=14.632428 Writing results lh-Avg-Intercept-thickness maxvox sig=1e+10 F=293.283 at index 274 0 0 seed=1379991059 lh-Avg-thickness-clinvar1-Cor maxvox sig=3.50473 F=13.3076 at index 30493 0 0 seed=1379991059 lh-Diff-Male-Female-Intercept-thickness maxvox sig=3.35828 F=12.6481 at index 14613 0 0 seed=1379991059 lh-Diff-Male-Female-Cor-thickness-clinvar1 maxvox sig=-2.55573 F=9.09923 at index 128858 0 0 seed=1379991059 mri_glmfit done ninputs = 4 Checking inputs nframestot = 4 Allocing output Done allocing nframes = 4 Writing to /home/FreesurferSubjects/qdec/Untitled/contrasts.sig.mgh reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) gdfReadHeader: reading /home/FreesurferSubjects/qdec/Untitled/y.fsgd INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 clinvar1 57.0299 8.72632 1 AgeYears 22.825 1.72886 2 IntraCranialVol 1.10829e+06 129670 Class Means of each Continuous Variable 1 sexMale 57.8301 22.7324 1189880.5686 2 sexFemale 56.2027 22.9207 1023944.1351 MatrixMultiply: m1 is null!
No such file or directory
Cédric,
Does the first column of your Base_File_FreeSurfer.dat contain the freesurfer subject id? the first column must contain that. from the email below, where you show one line of the file, it looks like Subj# is the first column and SubjID is the second.
Nick
On Thu, 2013-09-19 at 14:07 +0000, Koolschijn, Cédric wrote:
Dear FS,
I' ve run into some strange things in QDEC which I haven't encountered before. I'm running FS 5.3.
First, loading data file in QDEC works, yet terminal output displays the message below:
Data table /home/FreesurferSubjects/qdec/Base_File_FreeSurfer.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '123' in SUBJECTS_DIR etc.
Until: Too many subjects not found! Input table: /home/FreesurferSubjects/qdec/Base_File_FreeSurfer.dat Subj#, SubjID, Data... 1 123 423.000000 2.000000 3.000000 23.534247 Male 1.000000 2.000000 1461390.000000 490566.000000 755239.000000 706151.000000 -0.096959 0.641372 -0.09 etc.
So it does load the data. Subjectsdir = correct, all files are in place, no missings or whatsoever. If I check the dataview option, all looks wel. Also, qdec.fsgd looks good, no missing values or subjects.
This is similar to an old post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08288.html
Should I just ignore this? Or is something going wrong? If so, how should I fix this?
Second, and this is by far the strangest thing, I have in my qdec.table.dat file 2 independent groups for a exploration – validation study. So, I load my .dat file, including the errors above, then import stats data => aseg volume =>ICV, and then for a sanity check, in a simple design I have sex as discrete variable, clinical score as continuous covariate, and age and ICV as nuisance variables. This all works perfect. If I select only group 1 (by excluding group 2), also no problem. Yet, when I only select group 2, with the same design as stated above, QDEC crashes during loading of the regression coefficients:
(..) (No errors before) (..) Continuous Variable Means (all subjects) 0 clinvar1 57.0299 8.72632 1 AgeYears 22.825 1.72886 2 IntraCranialVol 1.10829e+06 129670 Class Means of each Continuous Variable 1 sexMale 57.8301 22.7324 1189880.5686 2 sexFemale 56.2027 22.9207 1023944.1351 MatrixMultiply: m1 is null!
No such file or directory For full output, see below
If I exclude ICV from the analyses, again the analyses work out fine for group2. Just out of curiosity I tested the same design adding total gray volume next to ICV, and this works fine. In addition, sex as discrete variable, clinical score as continuous covariate, and age and TGV as nuisance variables works also fine. Separating group2 in a single .dat file didn't resolve this issue. Somehow ICV is causing this problem, but I can't get my head around why it does work for group1 or the whole group, but not for group2.
In previous posts it was suggested to demean ICV as a solution for this issue, though this doesn't explain why it works for the other group? E.g.: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21744.html (though in contrast to that post, I don't have missing values (NaN).
The only difference between group 1 and 2 is sample size, 204 and 301 respectively (and of course different subjects, scores, ages etc).
Any thoughts on both problems?
Many thanks, Cédric
Full output after QDEC crash with ICV as nuisance variable for group 2:
lh-Avg-Intercept-thickness -----------------------
Does the average thickness differ from zero?
Nuisance factors: AgeYears IntraCranialVol
1.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000;
lh-Avg-thickness-clinvar1-Cor -----------------------
Does the correlation between thickness and clinvar1, accounting for sex, differ from zero?
Nuisance factors: AgeYears IntraCranialVol
0.000 0.000 1.000 1.000 0.000 0.000 0.000 0.000;
lh-Diff-Male-Female-Intercept-thickness -----------------------
Does the average thickness differ between Male and Female?
Nuisance factors: AgeYears IntraCranialVol
1.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000;
lh-Diff-Male-Female-Cor-thickness-clinvar1 -----------------------
Does the thickness--clinvar1 correlation differ between Male and Female?
Nuisance factors: AgeYears IntraCranialVol
0.000 0.000 1.000 -1.000 0.000 0.000 0.000 0.000;
ninputs = 301
Checking inputs
nframestot = 301
Allocing output
Done allocing
nframes = 301
Writing to /home/FreesurferSubjects/qdec/Untitled/y.mgh
gdfReadHeader: reading /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 clinvar1 57.0299 8.72632
1 AgeYears 22.825 1.72886
2 IntraCranialVol 1.10829e+06 129670
Class Means of each Continuous Variable
1 sexMale 57.8301 22.7324 1189880.6867
2 sexFemale 56.2027 22.9207 1023944.2196
INFO: gd2mtx_method is dods
Reading source surface /home/FreesurferSubjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.648438
AvgVtxArea 0.399267
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/FreesurferSubjects/qdec
cmdline mri_glmfit --y /home/FreesurferSubjects/qdec/Untitled/y.mgh --fsgd /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd dods --glmdir /home/FreesurferSubjects/qdec/Untitled --surf fsaverage lh --label /home/FreesurferSubjects/fsaverage/label/lh.aparc.label --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-thickness-clinvar1-Cor.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor-thickness-clinvar1.mat
sysname Linux
hostname tux08
machine x86_64
user cedric
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /home/FreesurferSubjects/qdec/Untitled/y.mgh
logyflag 0
usedti 0
FSGD /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd
labelmask /home/FreesurferSubjects/fsaverage/label/lh.aparc.label
maskinv 0
glmdir /home/FreesurferSubjects/qdec/Untitled
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /home/FreesurferSubjects/qdec/Untitled
Loading y from /home/FreesurferSubjects/qdec/Untitled/y.mgh
INFO: gd2mtx_method is dods
Saving design matrix to /home/FreesurferSubjects/qdec/Untitled/Xg.dat
Normalized matrix condition is 2142.57
Matrix condition is 1e+08
Found 148151 points in label.
Pruning voxels by thr: 0.000000
Found 148025 voxels in mask
Saving mask to /home/FreesurferSubjects/qdec/Untitled/mask.mgh
Reshaping mriglm->mask...
search space = 73649.347769
DOF = 293
Starting fit and test
Fit completed in 0.24555 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995767, ar1std=0.000990, gstd=6.213820, fwhm=14.632428
Writing results
lh-Avg-Intercept-thickness
maxvox sig=1e+10 F=293.283 at index 274 0 0 seed=1379991059
lh-Avg-thickness-clinvar1-Cor
maxvox sig=3.50473 F=13.3076 at index 30493 0 0 seed=1379991059
lh-Diff-Male-Female-Intercept-thickness
maxvox sig=3.35828 F=12.6481 at index 14613 0 0 seed=1379991059
lh-Diff-Male-Female-Cor-thickness-clinvar1
maxvox sig=-2.55573 F=9.09923 at index 128858 0 0 seed=1379991059
mri_glmfit done
ninputs = 4
Checking inputs
nframestot = 4
Allocing output
Done allocing
nframes = 4
Writing to /home/FreesurferSubjects/qdec/Untitled/contrasts.sig.mgh
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
gdfReadHeader: reading /home/FreesurferSubjects/qdec/Untitled/y.fsgd
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
INFO: NOT demeaning continuous variables
Continuous Variable Means (all subjects)
0 clinvar1 57.0299 8.72632
1 AgeYears 22.825 1.72886
2 IntraCranialVol 1.10829e+06 129670
Class Means of each Continuous Variable
1 sexMale 57.8301 22.7324 1189880.5686
2 sexFemale 56.2027 22.9207 1023944.1351
MatrixMultiply: m1 is null!
No such file or directory
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
The first column is fsid, the reason why you see a number before fsid, is because it's a line-number copied from g/n-edit.
Cheers Cédric
-----Original Message----- From: Nick Schmansky nicks@nmr.mgh.harvard.edu Date: Wednesday, September 25, 2013 6:44 PM To: Cédric Koolschijn P.C.M.P.Koolschijn@uva.nl Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC double trouble: 1. VerifySubjects 2. MatrixMultiply: m1 is null!
Cédric,
Does the first column of your Base_File_FreeSurfer.dat contain the freesurfer subject id? the first column must contain that. from the email below, where you show one line of the file, it looks like Subj# is the first column and SubjID is the second.
Nick
On Thu, 2013-09-19 at 14:07 +0000, Koolschijn, Cédric wrote:
Dear FS,
I' ve run into some strange things in QDEC which I haven't encountered before. I'm running FS 5.3.
First, loading data file in QDEC works, yet terminal output displays the message below:
Data table /home/FreesurferSubjects/qdec/Base_File_FreeSurfer.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '123' in SUBJECTS_DIR etc.
Until: Too many subjects not found! Input table: /home/FreesurferSubjects/qdec/Base_File_FreeSurfer.dat Subj#, SubjID, Data... 1 123 423.000000 2.000000 3.000000 23.534247 Male 1.000000 2.000000 1461390.000000 490566.000000 755239.000000 706151.000000 -0.096959 0.641372 -0.09 etc.
So it does load the data. Subjectsdir = correct, all files are in place, no missings or whatsoever. If I check the dataview option, all looks wel. Also, qdec.fsgd looks good, no missing values or subjects.
This is similar to an old post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08288.html
Should I just ignore this? Or is something going wrong? If so, how should I fix this?
Second, and this is by far the strangest thing, I have in my qdec.table.dat file 2 independent groups for a exploration validation study. So, I load my .dat file, including the errors above, then import stats data => aseg volume =>ICV, and then for a sanity check, in a simple design I have sex as discrete variable, clinical score as continuous covariate, and age and ICV as nuisance variables. This all works perfect. If I select only group 1 (by excluding group 2), also no problem. Yet, when I only select group 2, with the same design as stated above, QDEC crashes during loading of the regression coefficients:
(..) (No errors before) (..) Continuous Variable Means (all subjects) 0 clinvar1 57.0299 8.72632 1 AgeYears 22.825 1.72886 2 IntraCranialVol 1.10829e+06 129670 Class Means of each Continuous Variable 1 sexMale 57.8301 22.7324 1189880.5686 2 sexFemale 56.2027 22.9207 1023944.1351 MatrixMultiply: m1 is null!
No such file or directory For full output, see below
If I exclude ICV from the analyses, again the analyses work out fine for group2. Just out of curiosity I tested the same design adding total gray volume next to ICV, and this works fine. In addition, sex as discrete variable, clinical score as continuous covariate, and age and TGV as nuisance variables works also fine. Separating group2 in a single .dat file didn't resolve this issue. Somehow ICV is causing this problem, but I can't get my head around why it does work for group1 or the whole group, but not for group2.
In previous posts it was suggested to demean ICV as a solution for this issue, though this doesn't explain why it works for the other group? E.g.: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21744.html (though in contrast to that post, I don't have missing values (NaN).
The only difference between group 1 and 2 is sample size, 204 and 301 respectively (and of course different subjects, scores, ages etc).
Any thoughts on both problems?
Many thanks, Cédric
Full output after QDEC crash with ICV as nuisance variable for group 2:
lh-Avg-Intercept-thickness -----------------------
Does the average thickness differ from zero?
Nuisance factors: AgeYears IntraCranialVol
1.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000;
lh-Avg-thickness-clinvar1-Cor -----------------------
Does the correlation between thickness and clinvar1, accounting for sex, differ from zero?
Nuisance factors: AgeYears IntraCranialVol
0.000 0.000 1.000 1.000 0.000 0.000 0.000 0.000;
lh-Diff-Male-Female-Intercept-thickness -----------------------
Does the average thickness differ between Male and Female?
Nuisance factors: AgeYears IntraCranialVol
1.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000;
lh-Diff-Male-Female-Cor-thickness-clinvar1 -----------------------
Does the thickness--clinvar1 correlation differ between Male and Female?
Nuisance factors: AgeYears IntraCranialVol
0.000 0.000 1.000 -1.000 0.000 0.000 0.000 0.000;
ninputs = 301
Checking inputs
nframestot = 301
Allocing output
Done allocing
nframes = 301
Writing to /home/FreesurferSubjects/qdec/Untitled/y.mgh
gdfReadHeader: reading /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 clinvar1 57.0299 8.72632
1 AgeYears 22.825 1.72886
2 IntraCranialVol 1.10829e+06 129670
Class Means of each Continuous Variable
1 sexMale 57.8301 22.7324 1189880.6867
2 sexFemale 56.2027 22.9207 1023944.2196
INFO: gd2mtx_method is dods
Reading source surface /home/FreesurferSubjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.648438
AvgVtxArea 0.399267
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/FreesurferSubjects/qdec
cmdline mri_glmfit --y /home/FreesurferSubjects/qdec/Untitled/y.mgh --fsgd /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd dods --glmdir /home/FreesurferSubjects/qdec/Untitled --surf fsaverage lh --label /home/FreesurferSubjects/fsaverage/label/lh.aparc.label --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickne ss.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-thickness-clinvar 1-Cor.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Inte rcept-thickness.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor- thickness-clinvar1.mat
sysname Linux
hostname tux08
machine x86_64
user cedric
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /home/FreesurferSubjects/qdec/Untitled/y.mgh
logyflag 0
usedti 0
FSGD /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd
labelmask /home/FreesurferSubjects/fsaverage/label/lh.aparc.label
maskinv 0
glmdir /home/FreesurferSubjects/qdec/Untitled
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /home/FreesurferSubjects/qdec/Untitled
Loading y from /home/FreesurferSubjects/qdec/Untitled/y.mgh
INFO: gd2mtx_method is dods
Saving design matrix to /home/FreesurferSubjects/qdec/Untitled/Xg.dat
Normalized matrix condition is 2142.57
Matrix condition is 1e+08
Found 148151 points in label.
Pruning voxels by thr: 0.000000
Found 148025 voxels in mask
Saving mask to /home/FreesurferSubjects/qdec/Untitled/mask.mgh
Reshaping mriglm->mask...
search space = 73649.347769
DOF = 293
Starting fit and test
Fit completed in 0.24555 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995767, ar1std=0.000990, gstd=6.213820, fwhm=14.632428
Writing results
lh-Avg-Intercept-thickness
maxvox sig=1e+10 F=293.283 at index 274 0 0 seed=1379991059
lh-Avg-thickness-clinvar1-Cor
maxvox sig=3.50473 F=13.3076 at index 30493 0 0 seed=1379991059
lh-Diff-Male-Female-Intercept-thickness
maxvox sig=3.35828 F=12.6481 at index 14613 0 0 seed=1379991059
lh-Diff-Male-Female-Cor-thickness-clinvar1
maxvox sig=-2.55573 F=9.09923 at index 128858 0 0 seed=1379991059
mri_glmfit done
ninputs = 4
Checking inputs
nframestot = 4
Allocing output
Done allocing
nframes = 4
Writing to /home/FreesurferSubjects/qdec/Untitled/contrasts.sig.mgh
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desik an_killiany.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desik an_killiany.txt)
gdfReadHeader: reading /home/FreesurferSubjects/qdec/Untitled/y.fsgd
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
INFO: NOT demeaning continuous variables
Continuous Variable Means (all subjects)
0 clinvar1 57.0299 8.72632
1 AgeYears 22.825 1.72886
2 IntraCranialVol 1.10829e+06 129670
Class Means of each Continuous Variable
1 sexMale 57.8301 22.7324 1189880.5686
2 sexFemale 56.2027 22.9207 1023944.1351
MatrixMultiply: m1 is null!
No such file or directory
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Cédric,
can you send me the .dat file?
N.
On Wed, 2013-09-25 at 16:58 +0000, Koolschijn, Cédric wrote:
Hi Nick,
The first column is fsid, the reason why you see a number before fsid, is because it's a line-number copied from g/n-edit.
Cheers Cédric
-----Original Message----- From: Nick Schmansky nicks@nmr.mgh.harvard.edu Date: Wednesday, September 25, 2013 6:44 PM To: Cédric Koolschijn P.C.M.P.Koolschijn@uva.nl Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QDEC double trouble: 1. VerifySubjects 2. MatrixMultiply: m1 is null!
Cédric,
Does the first column of your Base_File_FreeSurfer.dat contain the freesurfer subject id? the first column must contain that. from the email below, where you show one line of the file, it looks like Subj# is the first column and SubjID is the second.
Nick
On Thu, 2013-09-19 at 14:07 +0000, Koolschijn, Cédric wrote:
Dear FS,
I' ve run into some strange things in QDEC which I haven't encountered before. I'm running FS 5.3.
First, loading data file in QDEC works, yet terminal output displays the message below:
Data table /home/FreesurferSubjects/qdec/Base_File_FreeSurfer.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '123' in SUBJECTS_DIR etc.
Until: Too many subjects not found! Input table: /home/FreesurferSubjects/qdec/Base_File_FreeSurfer.dat Subj#, SubjID, Data... 1 123 423.000000 2.000000 3.000000 23.534247 Male 1.000000 2.000000 1461390.000000 490566.000000 755239.000000 706151.000000 -0.096959 0.641372 -0.09 etc.
So it does load the data. Subjectsdir = correct, all files are in place, no missings or whatsoever. If I check the dataview option, all looks wel. Also, qdec.fsgd looks good, no missing values or subjects.
This is similar to an old post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08288.html
Should I just ignore this? Or is something going wrong? If so, how should I fix this?
Second, and this is by far the strangest thing, I have in my qdec.table.dat file 2 independent groups for a exploration validation study. So, I load my .dat file, including the errors above, then import stats data => aseg volume =>ICV, and then for a sanity check, in a simple design I have sex as discrete variable, clinical score as continuous covariate, and age and ICV as nuisance variables. This all works perfect. If I select only group 1 (by excluding group 2), also no problem. Yet, when I only select group 2, with the same design as stated above, QDEC crashes during loading of the regression coefficients:
(..) (No errors before) (..) Continuous Variable Means (all subjects) 0 clinvar1 57.0299 8.72632 1 AgeYears 22.825 1.72886 2 IntraCranialVol 1.10829e+06 129670 Class Means of each Continuous Variable 1 sexMale 57.8301 22.7324 1189880.5686 2 sexFemale 56.2027 22.9207 1023944.1351 MatrixMultiply: m1 is null!
No such file or directory For full output, see below
If I exclude ICV from the analyses, again the analyses work out fine for group2. Just out of curiosity I tested the same design adding total gray volume next to ICV, and this works fine. In addition, sex as discrete variable, clinical score as continuous covariate, and age and TGV as nuisance variables works also fine. Separating group2 in a single .dat file didn't resolve this issue. Somehow ICV is causing this problem, but I can't get my head around why it does work for group1 or the whole group, but not for group2.
In previous posts it was suggested to demean ICV as a solution for this issue, though this doesn't explain why it works for the other group? E.g.: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21744.html (though in contrast to that post, I don't have missing values (NaN).
The only difference between group 1 and 2 is sample size, 204 and 301 respectively (and of course different subjects, scores, ages etc).
Any thoughts on both problems?
Many thanks, Cédric
Full output after QDEC crash with ICV as nuisance variable for group 2:
lh-Avg-Intercept-thickness -----------------------
Does the average thickness differ from zero?
Nuisance factors: AgeYears IntraCranialVol
1.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000;
lh-Avg-thickness-clinvar1-Cor -----------------------
Does the correlation between thickness and clinvar1, accounting for sex, differ from zero?
Nuisance factors: AgeYears IntraCranialVol
0.000 0.000 1.000 1.000 0.000 0.000 0.000 0.000;
lh-Diff-Male-Female-Intercept-thickness -----------------------
Does the average thickness differ between Male and Female?
Nuisance factors: AgeYears IntraCranialVol
1.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000;
lh-Diff-Male-Female-Cor-thickness-clinvar1 -----------------------
Does the thickness--clinvar1 correlation differ between Male and Female?
Nuisance factors: AgeYears IntraCranialVol
0.000 0.000 1.000 -1.000 0.000 0.000 0.000 0.000;
ninputs = 301
Checking inputs
nframestot = 301
Allocing output
Done allocing
nframes = 301
Writing to /home/FreesurferSubjects/qdec/Untitled/y.mgh
gdfReadHeader: reading /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 clinvar1 57.0299 8.72632
1 AgeYears 22.825 1.72886
2 IntraCranialVol 1.10829e+06 129670
Class Means of each Continuous Variable
1 sexMale 57.8301 22.7324 1189880.6867
2 sexFemale 56.2027 22.9207 1023944.2196
INFO: gd2mtx_method is dods
Reading source surface /home/FreesurferSubjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.648438
AvgVtxArea 0.399267
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/FreesurferSubjects/qdec
cmdline mri_glmfit --y /home/FreesurferSubjects/qdec/Untitled/y.mgh --fsgd /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd dods --glmdir /home/FreesurferSubjects/qdec/Untitled --surf fsaverage lh --label /home/FreesurferSubjects/fsaverage/label/lh.aparc.label --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickne ss.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-thickness-clinvar 1-Cor.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Inte rcept-thickness.mat --C /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor- thickness-clinvar1.mat
sysname Linux
hostname tux08
machine x86_64
user cedric
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /home/FreesurferSubjects/qdec/Untitled/y.mgh
logyflag 0
usedti 0
FSGD /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd
labelmask /home/FreesurferSubjects/fsaverage/label/lh.aparc.label
maskinv 0
glmdir /home/FreesurferSubjects/qdec/Untitled
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /home/FreesurferSubjects/qdec/Untitled
Loading y from /home/FreesurferSubjects/qdec/Untitled/y.mgh
INFO: gd2mtx_method is dods
Saving design matrix to /home/FreesurferSubjects/qdec/Untitled/Xg.dat
Normalized matrix condition is 2142.57
Matrix condition is 1e+08
Found 148151 points in label.
Pruning voxels by thr: 0.000000
Found 148025 voxels in mask
Saving mask to /home/FreesurferSubjects/qdec/Untitled/mask.mgh
Reshaping mriglm->mask...
search space = 73649.347769
DOF = 293
Starting fit and test
Fit completed in 0.24555 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995767, ar1std=0.000990, gstd=6.213820, fwhm=14.632428
Writing results
lh-Avg-Intercept-thickness
maxvox sig=1e+10 F=293.283 at index 274 0 0 seed=1379991059
lh-Avg-thickness-clinvar1-Cor
maxvox sig=3.50473 F=13.3076 at index 30493 0 0 seed=1379991059
lh-Diff-Male-Female-Intercept-thickness
maxvox sig=3.35828 F=12.6481 at index 14613 0 0 seed=1379991059
lh-Diff-Male-Female-Cor-thickness-clinvar1
maxvox sig=-2.55573 F=9.09923 at index 128858 0 0 seed=1379991059
mri_glmfit done
ninputs = 4
Checking inputs
nframestot = 4
Allocing output
Done allocing
nframes = 4
Writing to /home/FreesurferSubjects/qdec/Untitled/contrasts.sig.mgh
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desik an_killiany.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desik an_killiany.txt)
gdfReadHeader: reading /home/FreesurferSubjects/qdec/Untitled/y.fsgd
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
INFO: NOT demeaning continuous variables
Continuous Variable Means (all subjects)
0 clinvar1 57.0299 8.72632
1 AgeYears 22.825 1.72886
2 IntraCranialVol 1.10829e+06 129670
Class Means of each Continuous Variable
1 sexMale 57.8301 22.7324 1189880.5686
2 sexFemale 56.2027 22.9207 1023944.1351
MatrixMultiply: m1 is null!
No such file or directory
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Koolschijn, Cédric -
Michael Kranz -
Nick Schmansky