Re: [Freesurfer] Fwd: qdec error

[Douglas N Greve]

Hi Seung-Gul, we are moving away from qdec, at least for now. Can you 
try re-doing your analysis using the "command line" stream? Ie, create 
an FSGD file, run mris_preproc, mri_surf2surf, then mri_glmfit.

doug


On 10/01/2017 08:25 PM, Seung-Gul Kang (강승걸) wrote:
> Dear Freesurfer Experts,
>
> Last week, I posted a question regarding the error during qdec.
> However, I did not receive any response yet.
>
> Could you give me a help to solve the problem?
>
> I am sincerely looking forward to receive your response soon.
>
> Best Regards,
> Seung-Gul Kang
>
>
> -- Forwarded message --
> From: *Seung-Gul Kang (강승걸)*  >
> Date: 2017-09-27 20:04 GMT+09:00
> Subject: qdec error
> To: Freesurfer support list  >
>
>
> Dear Freesurfer,
>
> I have a question during qdec.
>
> I tried to compare the surface area between two groups using qdec program.
> Strange to say, if I control some combination of confounding factors, 
> then the error develops and qdec is closed.
>
> When I control age, sex, HAMD (hamilton depression) score, and mean 
> surface area, there was no error.
> When I control age and sex, there was no error.
> When I control only surface area, there was no error.
> However, when I control age, sex, and mean surface area, then error 
> happens.
>
> Could you let me how to manage this problem?
>
> I am looking forward to receive your answer.
> Thank you.
>
> Best,
> Seung-Gul
>
> -below
>  
> is the messages containing error
>
> SUBJECTS_DIR is '/mnt/hgfs/share/suicide'
>
> lh-Avg-Intercept-area ---
>
> Does the average area differ from zero?
>
> Nuisance factors: age area
>
>  1.000 1.000   1.000   1.000 0.000   0.000   0.000 0.000   0.000   
> 0.000 0.000   0.000;
>
> lh-Diff-NS-S-Intercept-area ---
>
> Does the average area, accounting for sex, differ between NS and S?
>
> Nuisance factors: age area
>
>  1.000 -1.000   1.000  -1.000 0.000   0.000   0.000 0.000   0.000   
> 0.000 0.000   0.000;
>
> lh-Diff-M-F-Intercept-area ---
>
> Does the average area, accounting for diagnosis, differ between M and F?
>
> Nuisance factors: age area
>
>  1.000   1.000 -1.000  -1.000   0.000 0.000   0.000   0.000 0.000   
> 0.000   0.000 0.000;
>
> lh-X-diagnosis-sex-Intercept-area ---
>
> Is there a diagnosis--sex interaction in the mean area?
>
> Nuisance factors: age area
>
>  1.000 -1.000  -1.000   1.000 0.000   0.000   0.000 0.000   0.000   
> 0.000 0.000   0.000;
>
> ninputs = 38
>
> Checking inputs
>
> nframestot = 38
>
> Allocing output
>
> Done allocing
>
> nframes = 38
>
> Writing to /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.mgh
>
> gdfReadHeader: reading /mnt/hgfs/share/suicide/qdec/area_LH_AA/qdec.fsgd
>
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>
> Continuous Variable Means (all subjects)
>
> 0 age 41.5263 12.8201
>
> 1 area 163656 15524.4
>
> Class Means of each Continuous Variable
>
> 1 diagnosisNS-sexM  36.2000 176040.8391
>
> 2 diagnosisS-sexM  40.6250 170897.0234
>
> 3 diagnosisNS-sexF  46.5556 151977.3351
>
> 4 diagnosisS-sexF  42.9091 156686.6932
>
> INFO: gd2mtx_method is dods
>
> Reading source surface /mnt/hgfs/share/suicide/fsaverage/surf/lh.white
>
> Number of vertices 163842
>
> Number of faces327680
>
> 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/sgk
>
> cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.mgh 
> --fsgd /mnt/hgfs/share/suicide/qdec/area_LH_AA/qdec.fsgd dods --glmdir 
> /mnt/hgfs/share/suicide/qdec/area_LH_AA --surf fsaverage lh --label 
> /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C 
> /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts/lh-Avg-Intercept-area.mat 
> --C 
> /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts/lh-Diff-NS-S-Intercept-area.mat
>  
> --C 
> /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts/lh-Diff-M-F-Intercept-area.mat
>  
> --C 
> /mnt/hgfs/share/suicide/qdec/area_LH_AA/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
>  
>
>
> sysname Linux
>
> hostname localhost.localdomain
>
> machine x86_64
>
> user sgk
>
> FixVertexAreaFlag = 1
>
> UseMaskWithSmoothing 1
>
> OneSampleGroupMean 0
>
> y /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.mgh
>
> logyflag 0
>
> usedti 0
>
> FSGD /mnt/hgfs/share/suicide/qdec/area_LH_AA/qdec.fsgd
>
> labelmask /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label
>
> maskinv 0
>
> glmdir /mnt/hgfs/share/suicide/qdec/area_LH_AA
>
> IllCondOK 0
>
> ReScaleX 1
>
> DoFFx 0
>
> Creating output directory /mnt/hgfs/share/suicide/qdec/area_LH_AA
>
> Loading y from /mnt/hgfs/share/suicide/qdec/area_LH_AA/y.mgh
>
> INFO: gd2mtx_method is dods
>
> 

Re: [Freesurfer] Fwd: QDEC error

[Douglas N Greve]

Perhaps try saving it as a txt file directly from excel instead of doing 
the cut and paste

On 01/23/2014 08:14 PM, Wanda Truong wrote:
 Hi Doug,

 This was all done on a mac. What would be the best way to recreate it? 
 Was the above mentioned excel method adequate?

 Wanda


 On 23 January 2014 17:13, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:


 there is something wrong with the format. did you make your qdec table
 on a windows machine? If so, convert it to linux format or recreate it
 on a linux/mac machine

 doug

 On 01/23/2014 07:02 PM, Wanda Truong wrote:
 
 
  -- Forwarded message --
  From: *Wanda Truong* wanda.truong...@gmail.com
 mailto:wanda.truong...@gmail.com
  mailto:wanda.truong...@gmail.com
 mailto:wanda.truong...@gmail.com
  Date: 23 January 2014 16:57
  Subject: QDEC error
  To: freesurfer@nmr.mgh.harvard.edu
 mailto:freesurfer@nmr.mgh.harvard.edu
 mailto:freesurfer@nmr.mgh.harvard.edu
 mailto:freesurfer@nmr.mgh.harvard.edu
 
 
  Hello,
 
  I am having trouble with my group analysis using QDEC. I have 3
  groups, 72 subjects, and 4 covariates. This is the error I get:
 
  Loading data table
  /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/qdec.table.dat...
  Number of columns:  438
  fsid column:1
  Number of factors:  437
  Number of subjects: 0
  ERROR: QdecDataTable::Load: number of subjects = 0
  Error loading the data table.
 
  I've attached my qdec.table.dat file and fsgd file as well. I
  initially created the columns using excel and I copied and pasted it
  into a .txt. file. Could this be the problem? If so, what would be a
  better method?
 
  Thanks very much,
  Wanda
  --
  Wanda Truong, MSc
 
 
 
  --
  Wanda Truong, MSc
 
 
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 tel:617-724-2358
 Fax: 617-726-7422 tel:617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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 The information in this e-mail is intended only for the person to
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 addressed. If you believe this e-mail was sent to you in error and
 the e-mail
 contains patient information, please contact the Partners
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 -- 
 Wanda Truong, MSc

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Fwd: QDEC error

[Douglas N Greve]

there is something wrong with the format. did you make your qdec table 
on a windows machine? If so, convert it to linux format or recreate it 
on a linux/mac machine

doug

On 01/23/2014 07:02 PM, Wanda Truong wrote:


 -- Forwarded message --
 From: *Wanda Truong* wanda.truong...@gmail.com 
 mailto:wanda.truong...@gmail.com
 Date: 23 January 2014 16:57
 Subject: QDEC error
 To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu


 Hello,

 I am having trouble with my group analysis using QDEC. I have 3 
 groups, 72 subjects, and 4 covariates. This is the error I get:

 Loading data table 
 /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/qdec.table.dat...
 Number of columns:  438
 fsid column:1
 Number of factors:  437
 Number of subjects: 0
 ERROR: QdecDataTable::Load: number of subjects = 0
 Error loading the data table.

 I've attached my qdec.table.dat file and fsgd file as well. I 
 initially created the columns using excel and I copied and pasted it 
 into a .txt. file. Could this be the problem? If so, what would be a 
 better method?

 Thanks very much,
 Wanda
 -- 
 Wanda Truong, MSc



 -- 
 Wanda Truong, MSc


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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.