Re: [Freesurfer] Longitudinal QDEC

[Martin Reuter]

also note the file name starts with a “.”

.Qdecrc


> On 18. Mar 2019, at 21:16, Martin Reuter  wrote:
> 
> Hi Theo,
> 
> the file should be :
> $SUBJECTS_DIR/qdec/.Qdecrc
> 
> it is important that it is at that location and should not have an extension 
> (not .txt !)
> 
> Best, Martin
> 
>> On 18. Mar 2019, at 16:16, AKUDJEDU, THEOPHILUS > > wrote:
>> 
>> External Email - Use Caution
>> Dear All,
>> 
>> I am running a longitudinal (2-time points) group cortical analysis in 
>> Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
>> cross-sectional form, I added a text file containing the lines
>> MEASURE1 = long.thickness-avg
>> MEASURE2 = long.thickness-rate
>> MEASURE3 = long.thickness-pc1
>> MEASURE4 = long.thickness-spc
>> in the qdec directory to guide qdec to know about the newly created files 
>> (e.g. lh.long.thickness-spc...). However, it doesn't seem to be 
>> recognizing/picking up the new files or not reading the text file named 
>> Qdecrc.txt (which has the lines above. 
>> 
>> Will be glad if you could offer any help. 
>> 
>> Thanks 
>> 
>> Theo
>> 
>> 
>> 
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>> 

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Re: [Freesurfer] Longitudinal QDEC

[Martin Reuter]

Hi Theo,

the file should be :
$SUBJECTS_DIR/qdec/.Qdecrc

it is important that it is at that location and should not have an extension 
(not .txt !)

Best, Martin

> On 18. Mar 2019, at 16:16, AKUDJEDU, THEOPHILUS  
> wrote:
> 
> External Email - Use Caution
> Dear All,
> 
> I am running a longitudinal (2-time points) group cortical analysis in 
> Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
> cross-sectional form, I added a text file containing the lines
> MEASURE1 = long.thickness-avg
> MEASURE2 = long.thickness-rate
> MEASURE3 = long.thickness-pc1
> MEASURE4 = long.thickness-spc
> in the qdec directory to guide qdec to know about the newly created files 
> (e.g. lh.long.thickness-spc...). However, it doesn't seem to be 
> recognizing/picking up the new files or not reading the text file named 
> Qdecrc.txt (which has the lines above. 
> 
> Will be glad if you could offer any help. 
> 
> Thanks 
> 
> Theo
> 
> 
> 
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
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Re: [Freesurfer] Longitudinal QDEC

[Greve, Douglas N.,Ph.D.]

Hi Theo, sorry, QDEC is not really being supported anymore. Try using the 
command line stream.

On 3/18/19 11:16 AM, AKUDJEDU, THEOPHILUS wrote:

External Email - Use Caution

Dear All,

I am running a longitudinal (2-time points) group cortical analysis in 
Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
cross-sectional form, I added a text file containing the lines

MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc

in the qdec directory to guide qdec to know about the newly created files (e.g. 
lh.long.thickness-spc...). However, it doesn't seem to be recognizing/picking 
up the new files or not reading the text file named Qdecrc.txt (which has the 
lines above.

Will be glad if you could offer any help.

Thanks

Theo






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[Freesurfer] Longitudinal QDEC

[AKUDJEDU, THEOPHILUS]

External Email - Use Caution

Dear All,

I am running a longitudinal (2-time points) group cortical analysis in 
Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
cross-sectional form, I added a text file containing the lines

MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc

in the qdec directory to guide qdec to know about the newly created files (e.g. 
lh.long.thickness-spc...). However, it doesn't seem to be recognizing/picking 
up the new files or not reading the text file named Qdecrc.txt (which has the 
lines above.

Will be glad if you could offer any help.

Thanks

Theo



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[Freesurfer] Longitudinal QDEC

[AKUDJEDU, THEOPHILUS]

External Email - Use Caution

Dear All,

I am running a longitudinal (2-time points) group cortical analysis in 
Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
cross-sectional form, I added a text file containing the lines

MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc

in the qdec directory to guide qdec to know about the newly created files (e.g. 
lh.long.thickness-spc...). However, it doesn't seem to be recognizing/picking 
up the new files or not reading the text file named Qdecrc.txt (which has the 
lines above.

Will be glad if you could offer any help.

Thanks

Theo

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Re: [Freesurfer] longitudinal qdec contrasts

[Diers, Kersten /DZNE]

External Email - Use Caution

Hi Courtney,

I have two general remarks:

1.)
For comparing n groups, the general rule is to have (n-1) binary
indicator variables (and possibly n-1 interaction variables). One group
(a reference group) will be implictly modeled by the intercept (1) and
time (2) regressors. As a consequence, you should drop one group
regressor and one interaction regressor from your design matrix
(assuming that you have exactly 3 groups).
As an analogy to your analysis, consider the example given on the
Freesurfer LME tutorial page where there are 4 groups (HC, sMCI, cMCI,
AD), but only 3 group indicators (sMCI, cMCI, AD) and 3 interaction
terms. HC is chosen as the reference group in this example and not
explicitly modeled.

2.)
Any single (possibly multi-row) contrast matrix is expected to give
only one single result, i.e. one F- and p-value. For example, a
classical F-contrast that tests whether or not there is a difference
between *any* pair of (more than 2) groups would be specified as a
multi-row contrast matrix. To test for a difference between a specific
pairs of groups, use a single-row contrast matrix (more precisely,
vector).

Best regards,

Kersten


On Mi, 2018-07-25 at 16:19 +0200, Courtney Haswell wrote:
> External Email - Use Caution
> 
> We are working in Matlab to analyze longitudinal data using the mass-
> univariate approach to Linear Mixed Effects (LME) Modeling.
> 
> 
> Step 1: Below is the design matrix (first few rows) we created in an
> effort to compare subjects with low, moderate, and high drinking
> behavior with respect to time (3 groups).
> 
> 
> 1 0 1 0 0 0 0 0
> 1 3.0 1 3.0 0 0 0 0
> 1 0 1 0 0 0 0 0
> 1 1.2 0 0 1 1.2 0 0
> 1 2.3 0 0 0 0 1 2.3
> 1 3.5 0 0 0 0 1 3.5
> 1 0 1 0 0 0 0 0
> 
> Column 1 - intercept ones; 2 - time (years since baseline scan); 3 -
> low drinking group; 4 - low drinking x time; 5 - mod drinking group;
> 6 - mod drinking x time; 7 - high drinking group; 8 - high drinking x
> time
> 
> 
> Step 2: To compare low/moderate drinking, mod/high drinking, and
> low/high drinking, we created the contrast matrix below:
> 
> 
> CM=[0 0 0 1 0 -1 0 0; 0 0 0 0 0 1 0 -1; 0 0 0 1 0 0 0 -1]
> 
> 
> Row 1 - low/mod drinking; Row 2 - mod/high drinking; Row 3 - low/high
> drinking
> 
> 
> Please let us know if the contrast matrix is appropriate for our
> design matrix and the comparisons we would like to make. This seems
> incorrect since there is only one output from
> "lme_mass_F(lhstats,CM);"
> 
> 
> Thank you for your help.

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[Freesurfer] longitudinal qdec contrasts

[Courtney Haswell]

External Email - Use Caution

We are working in Matlab to analyze longitudinal data using the
mass-univariate approach to Linear Mixed Effects (LME) Modeling.


Step 1: Below is the design matrix (first few rows) we created in an effort
to compare subjects with low, moderate, and high drinking behavior with
respect to time (3 groups).


1 0 1 0 0 0 0 0
1 3.0 1 3.0 0 0 0 0
1 0 1 0 0 0 0 0
1 1.2 0 0 1 1.2 0 0
1 2.3 0 0 0 0 1 2.3
1 3.5 0 0 0 0 1 3.5
1 0 1 0 0 0 0 0

Column 1 - intercept ones; 2 - time (years since baseline scan); 3 - low
drinking group; 4 - low drinking x time; 5 - mod drinking group; 6 - mod
drinking x time; 7 - high drinking group; 8 - high drinking x time


Step 2: To compare low/moderate drinking, mod/high drinking, and low/high
drinking, we created the contrast matrix below:


CM=[0 0 0 1 0 -1 0 0; 0 0 0 0 0 1 0 -1; 0 0 0 1 0 0 0 -1]


Row 1 - low/mod drinking; Row 2 - mod/high drinking; Row 3 - low/high
drinking


Please let us know if the contrast matrix is appropriate for our design
matrix and the comparisons we would like to make. This seems incorrect
since there is only one output from "lme_mass_F(lhstats,CM);"


Thank you for your help.
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Re: [Freesurfer] longitudinal qdec tables

[Martin Reuter]

So you exported CSV from excel on Mac with space separation and it does not work?
Try to export only a few lines to make sure it is not a weird character somewhere else. 
Best Martin
On Jul 11, 2016 5:44 PM, "Andrews, Derek" <derek.andr...@kcl.ac.uk> wrote:





Hi Martin,


Thank you for the tip. Indeed there is some issue with the character spacing in my qdec file. 


I usually generate subject text files like this in excel and save them as csv .txt files. Do you have any suggestions for easily writing the qdec file without going line by line, space by space?


Best, Derek 








Derek
 Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental
 Sciences 

Institute of Psychiatry, Psychology
 & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: Derek.Andrews@kcl.ac.uk 








From: Martin Reuter <mreuter@nmr.mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Mon, 11 Jul 2016 13:59:53 +0200
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] longitudinal qdec tables



Hi Derek,
For debugging try a simple file with two lines (header and first row). Separate columns only with a space. Once that works add more rows.
Best Martin
On Jul 11, 2016 12:58 PM, "Andrews, Derek" <derek.andrews@kcl.ac.uk> wrote:




Dear FreeSurfer Developers and Community,


I have been trying to run some commands using the —qdec-long flag (I.e. asegstats2table & mris_preproc) but am encountering errors. In the past I have used .rtf files to read in my data using the —fsgd flag but am unsure of how to go about this with longitudinal
 data, therefore I am using the qdec.dat file structure.


I believe something must be wrong with the format of my qdec file. I’m working on MacOSx 10.9.3. I created the qdec in text editor and changed the suffix to .dat under get info (1). I also created one in gedit and saved it using a .dat suffix (2). See
 these qdec files attached. 


I receive the following errors:




asegstats2table --qdec-long long.qdec.table.dat -t ./outdir/aseg.long.table

SUBJECTS_DIR : /Users/dandrews/Data/MIAMRC/MIAMRC_SPGR_FS

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 514, in 

    subj_listoftuples = assemble_inputs(options)

  File "/Applications/freesurfer/bin/asegstats2table", line 320, in assemble_inputs

    for row in reader:

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 103, in next

    self.fieldnames

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 90, in fieldnames

    self._fieldnames = self.reader.next()



_csv.Error: new-line character seen in unquoted field - do you need to open the file in universal-newline mode?




And




mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi -lh --meas thickness --out lh.thickness.mgh

ERROR: no subjects specified



I imagine something silly with the qdec file must be going on. Any advice would be very appreciated.


Best, Derek 





Derek
 Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental
 Sciences 

Institute of Psychiatry, Psychology
 & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: Derek.Andrews@kcl.ac.uk 








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Re: [Freesurfer] longitudinal qdec tables

[Andrews, Derek]

Hi Martin,

Thank you for the tip. Indeed there is some issue with the character spacing in 
my qdec file.

I usually generate subject text files like this in excel and save them as csv 
.txt files. Do you have any suggestions for easily writing the qdec file 
without going line by line, space by space?

Best, Derek




Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental Sciences

Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk


From: Martin Reuter 
<mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Mon, 11 Jul 2016 13:59:53 +0200
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] longitudinal qdec tables


Hi Derek,
For debugging try a simple file with two lines (header and first row). Separate 
columns only with a space. Once that works add more rows.

Best Martin

On Jul 11, 2016 12:58 PM, "Andrews, Derek" 
<derek.andr...@kcl.ac.uk<mailto:derek.andr...@kcl.ac.uk>> wrote:
Dear FreeSurfer Developers and Community,

I have been trying to run some commands using the -qdec-long flag (I.e. 
asegstats2table & mris_preproc) but am encountering errors. In the past I have 
used .rtf files to read in my data using the -fsgd flag but am unsure of how to 
go about this with longitudinal data, therefore I am using the qdec.dat file 
structure.

I believe something must be wrong with the format of my qdec file. I'm working 
on MacOSx 10.9.3. I created the qdec in text editor and changed the suffix to 
.dat under get info (1). I also created one in gedit and saved it using a .dat 
suffix (2). See these qdec files attached.

I receive the following errors:


asegstats2table --qdec-long long.qdec.table.dat -t ./outdir/aseg.long.table

SUBJECTS_DIR : /Users/dandrews/Data/MIAMRC/MIAMRC_SPGR_FS

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 514, in 

subj_listoftuples = assemble_inputs(options)

  File "/Applications/freesurfer/bin/asegstats2table", line 320, in 
assemble_inputs

for row in reader:

  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py",
 line 103, in next

self.fieldnames

  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py",
 line 90, in fieldnames

self._fieldnames = self.reader.next()

_csv.Error: new-line character seen in unquoted field - do you need to open the 
file in universal-newline mode?

And


mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi -lh 
--meas thickness --out lh.thickness.mgh

ERROR: no subjects specified

I imagine something silly with the qdec file must be going on. Any advice would 
be very appreciated.

Best, Derek



Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental Sciences

Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk<mailto:derek.andr...@kcl.ac.uk>

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Re: [Freesurfer] longitudinal qdec tables

[Martin Reuter]

Hi Derek,
For debugging try a simple file with two lines (header and first row). Separate columns only with a space. Once that works add more rows.
Best Martin
On Jul 11, 2016 12:58 PM, "Andrews, Derek"  wrote:






Dear FreeSurfer Developers and Community,


I have been trying to run some commands using the —qdec-long flag (I.e. asegstats2table & mris_preproc) but am encountering errors. In the past I have used .rtf files to read in my data using the —fsgd flag but am unsure of how to go about this with longitudinal
 data, therefore I am using the qdec.dat file structure.


I believe something must be wrong with the format of my qdec file. I’m working on MacOSx 10.9.3. I created the qdec in text editor and changed the suffix to .dat under get info (1). I also created one in gedit and saved it using a .dat suffix (2). See
 these qdec files attached. 


I receive the following errors:




asegstats2table --qdec-long long.qdec.table.dat -t ./outdir/aseg.long.table

SUBJECTS_DIR : /Users/dandrews/Data/MIAMRC/MIAMRC_SPGR_FS

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 514, in 

    subj_listoftuples = assemble_inputs(options)

  File "/Applications/freesurfer/bin/asegstats2table", line 320, in assemble_inputs

    for row in reader:

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 103, in next

    self.fieldnames

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py", line 90, in fieldnames

    self._fieldnames = self.reader.next()



_csv.Error: new-line character seen in unquoted field - do you need to open the file in universal-newline mode?




And




mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi -lh --meas thickness --out lh.thickness.mgh

ERROR: no subjects specified



I imagine something silly with the qdec file must be going on. Any advice would be very appreciated.


Best, Derek 





Derek
 Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental
 Sciences 

Institute of Psychiatry, Psychology
 & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: Derek.Andrews@kcl.ac.uk 







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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] longitudinal qdec tables

[Andrews, Derek]

Dear FreeSurfer Developers and Community,

I have been trying to run some commands using the -qdec-long flag (I.e. 
asegstats2table & mris_preproc) but am encountering errors. In the past I have 
used .rtf files to read in my data using the -fsgd flag but am unsure of how to 
go about this with longitudinal data, therefore I am using the qdec.dat file 
structure.

I believe something must be wrong with the format of my qdec file. I'm working 
on MacOSx 10.9.3. I created the qdec in text editor and changed the suffix to 
.dat under get info (1). I also created one in gedit and saved it using a .dat 
suffix (2). See these qdec files attached.

I receive the following errors:


asegstats2table --qdec-long long.qdec.table.dat -t ./outdir/aseg.long.table

SUBJECTS_DIR : /Users/dandrews/Data/MIAMRC/MIAMRC_SPGR_FS

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 514, in 

subj_listoftuples = assemble_inputs(options)

  File "/Applications/freesurfer/bin/asegstats2table", line 320, in 
assemble_inputs

for row in reader:

  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py",
 line 103, in next

self.fieldnames

  File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/csv.py",
 line 90, in fieldnames

self._fieldnames = self.reader.next()

_csv.Error: new-line character seen in unquoted field - do you need to open the 
file in universal-newline mode?

And


mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi -lh 
--meas thickness --out lh.thickness.mgh

ERROR: no subjects specified

I imagine something silly with the qdec file must be going on. Any advice would 
be very appreciated.

Best, Derek



Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment

Department of Forensic and Neurodevelopmental Sciences

Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk



1.long.qdec.table.dat
Description: 1.long.qdec.table.dat


2.long.qdec.table.dat
Description: 2.long.qdec.table.dat
fsidfsid-base   years
0008Y1  00080
0011Y1  00110
0011Y2  00110.490410959
0012Y1  00120
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0033Y1  00330
0033Y2  00330
0093Y1  00930
0095Y1  00950
0095Y2  00950.95890411
0097Y2  00970
0098Y1  00980
0101Y1  01010
0101Y2  01010.989041096
0101Y3  01011.980821918
0104Y1  01040
0105Y3  01050
0106Y1  01060
0106Y2  01061.208219178
0107Y3  01070
0108Y2  01080
0110Y1  01100
0110Y3  01102.169863014
0112Y1  01120
0112Y2  01121.054794521
0114Y1  01140
0114Y2  01141.315068493
0116Y1  01160
0116Y2  01160.989041096
0117Y1  01170
0120Y1  01200
0127Y1  01270
0128Y1  01280
0134Y1  01340
0135Y1  01350
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0136Y1  01360
0136Y2  01361.002739726
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0137Y3  01370
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0139Y1  01390
0139Y3  01390.978082192
0146Y3  01460
0153Y1  01530
0153Y2  01530.95890411
0153Y3  01531.994520548
0158Y1  01580
0158Y2  01581.169863014
0160Y2  01600
0160Y3  01601.035616438
0175Y1  01750
0175Y2  01750
0180Y1  01800
1004Y2  10040
1005Y1  10050
1005Y2  10051.178082192
1005Y3  10052.301369863
1006Y2  10060
1006Y3  10060.997260274
1007Y1  10070
1009Y1  10090
1016Y2  10160
1017Y1  10170
1017Y2  10171.054794521
1017Y3  10172.123287671
1022Y1  10220
1023Y1  10230
1023Y2  10231.476712329
1027Y1  10270
1027Y2  10270.961643836
1032Y2  10320
1032Y3  10321.054794521
1034Y1  10340
1034Y2  10341.112328767
1034Y3  10342.109589041
1041Y1  10410
1041Y3  10412.293150685
1042Y2  10420
1042Y3  10420.997260274
1044Y1  10440
1045Y2  10450
1046Y1  10460
1046Y2  10461.109589041
1046Y3  10462.068493151
1052Y1  10520
1052Y2  10521.156164384
1052Y3  10522.271232877
1054Y2  10540
1054Y3  10541.073972603
1057Y2  10570
1057Y3  10570.912328767
1071Y2  10710
1071Y3  10710
1073Y3  10730
1075Y2  10750
1075Y3  10750.978082192
1077Y1  10770
1091Y1  10910
1091Y2  10910
1091Y3  10911.994520548
1096Y2  10960
Y1  0
Y3  2.473972603
1121Y1  11210
1121Y2  11211.22739726
1141Y1  11410
1144Y3  11440
1151Y1  11510
1159Y1  11590
1159Y2  11590.989041096
1159Y3  11592.024657534
1161Y1  11610
1161Y2  1161-0.115068493
1164Y1  11640
1164Y2  11641.035616438___
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addressed. If you 

Re: [Freesurfer] Longitudinal Qdec Statistics

[Martin Reuter]

HI Kari,

whenever you change a statistical model, you get different results, as 
you are 'asking' different questions. For example testing for factor A, 
when regressing out Factor B is very different from testing A when 
regressing out C.
Let's say A is weight and B is IQ, so you look for an weight effect, 
adjusting for IQ. You find something. Now instead of IQ, you adjust for 
height, the effect disappears. That is because height and weight are 
probably highly correlated and shadow each other. You only look for any 
effect of weight on top of what is explained already by height. Since IQ 
was not correlated with weight, you had an effect there as there is a 
strong weight (or height) effect.


There is also a good paper about 'residualizing predictors in 
regression': 
http://www.sciencedirect.com/science/article/pii/S0749596X13001368 (you 
did not propose residualizing, but I thought, since we talk about 
co-linearity, this may be interesting).


Best, Martin

On 06/22/2015 07:34 PM, Kari Haws wrote:

Hello Freesurfers,

I am using Qdec for longitudinal statistics with symmetrized percent 
change (spc) on 3 different discrete/fixed factors across 2 
time-points. Given that Qdec limits the discrete factors to 2, I ran 
the effects with different combinations of the discrete factors and I 
get very different main effect results for each of the factors in the 
different models.


For example, Factor A main effect's are significant when entered with 
Factor B, but are non-significant when I have Factor A and Factor C in 
the model.


I know Qdec accounts for the other factor in their main effects 
analyses, but it's still unclear why my results would be so distinctly 
different.


Some insight on this would be greatly appreciated.

Many thanks,
Kari

--
Kari Haws, M.A.
Doctoral Candidate
Clinical Neuropsychology Program
Brain Imaging, Behavior  Aging Lab
Department of Psychology
University of Arizona
kh...@email.arizona.edu mailto:kh...@email.arizona.edu



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--
Dr. Martin Reuter

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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[Freesurfer] Longitudinal Qdec Statistics

[Kari Haws]

Hello Freesurfers,

I am using Qdec for longitudinal statistics with symmetrized percent change
(spc) on 3 different discrete/fixed factors across 2 time-points. Given
that Qdec limits the discrete factors to 2, I ran the effects with
different combinations of the discrete factors and I get very different
main effect results for each of the factors in the different models.

For example, Factor A main effect's are significant when entered with
Factor B, but are non-significant when I have Factor A and Factor C in the
model.

I know Qdec accounts for the other factor in their main effects analyses,
but it's still unclear why my results would be so distinctly different.

Some insight on this would be greatly appreciated.

Many thanks,
Kari

-- 
Kari Haws, M.A.
Doctoral Candidate
Clinical Neuropsychology Program
Brain Imaging, Behavior  Aging Lab
Department of Psychology
University of Arizona
kh...@email.arizona.edu
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[Freesurfer] longitudinal QDEC help

[Taylor North]

Hello, 
 
I am having some troubles using QDEC to analyze the cortical thickness changes 
in my 
group study and I was hoping someone may be able to give me a hand. The steps I 
have done are as follows: 
 
I am working on a study looking at 40 subjects scanned at two time points (base 
and 6 months after). I have followed all the steps for longitudinal processing 
for each subject (cross,base, and longitudinals) and made edits where they were 
necessary to the base. I then entered all 40 subjects into a QDEC table as 
follows 
 
fsid fsid-base time gender age
crosstpN1 base1 0 female 20
crosstpN2 base1 6 female 20 
.. continues for rest of the subjects
 
 
then I ran the QCHACHE on the data, made a Qdecrc. file in the subject DIR, and 
then transformed the longitudinal QDEC table into a QDEC table which looks like:
 
fsid time gender age 
Base1 3 female 20 
.. continues for the rest of the subjects. 
 
I then followed the QDEC steps outlined In the group tutorial. (import cross 
sectional table, generate stats data table, import aseg volume, set 
longitudinal dependent variables and pick continuous variable.
 
1) the first problem I am having is that when I go to process the longitudinal 
group results through QDEC it makes me pick a continuous variable when I just 
want to analyze the dependent variable The symmetrized percent change. So I 
have tried picking different continuous variables ( such as age or importing 
rhcortex volume etc...) with choosing symmetrized percent change as the 
dependent variable. No matter what continuous variable I pick the question: 
``does the average symmetrized percent change differ from zero? always comes 
up, the problem is depending on what continuous variable I pick the results 
change. Is there a way to just look at the longitudinal thickness changes 
across a group alone, because I first want to look at the atrophy across the 
whole group over 6 months and then compare the differences in atrophy against 
the diagnosed and non diagnosed group. 
 
2) another thing I don't quite understand is it seems like the longitudinal 
qdec tables are made with the cross of the subjects under fsid, but why 
wouldn't you use the longitudinals under the fsid for the longitudinal table 
instead? Also it seems like in the cross sectional qdec table the base is the 
subject being analyzed under fsid, which also doesn't make sense to me because 
in the tutorial it says base should not be used directly for analysis. 
 
thanks for the help!
 
Taylor 
 
 
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dispose of the e-mail.

Re: [Freesurfer] longitudinal QDEC help

[Martin Reuter]

Hi Taylor,

first, in your description you mention 'base and 6 month'. Better call it 
'baseline' or 'first and second time points at 0 and 6 months' in order to not 
confuse the first time point with the 'base' = within-subject template created 
as the second step. I think you did not confuse it, but just want to make sure.

From your description it is not clear how you computed the symmetrized percent 
change. You say you ran QCACHE, but how? Did you use long_mris_slopes as 
described here:
http://freesurfer.net/fswiki/LongitudinalTwoStageModel 
http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial 

That step computes slopes for each subject and (instead of having 2 thickness 
maps) reduces the information to a single map (here the symmetrized percent 
change is simply: 100 * tp2-tp1/(0.5*(tp1+tp2)) ) . These maps are stored in 
the base directories (one for each subject and of corse each hemisphere that 
you run).

Now to your questions:
1) I think a 'one sample group mean' analysis is not possible in QDEC. For that 
you have to use mri_glmfit -osgm …. 
I wish we had this functionality and I'll see how hard it would be to implement 
it in future versions of QDEC (this came up frequently and it should not be too 
hard).

2) a) the longitudinal qdec table use the cross id's in the fsid column for 
simplicity. When it is used in many programs (e.g. long_mris_slopes, 
long_stats_slopes and other scripts with the long-qdec option) the scripts 
knows that it is a longitudinal qdec table (because of the existing fsid-base 
column) and internally use the longitudinal directories for processing. The 
cross sectional directories are never used.
b) as mentioned above, the results from the first stage analysis (creation of 
the within subject slopes and percent changes) are stored in the base 
directories. They are used in this step and found there. (and you are right, 
the recon-all results from the base should not be analyzed directly, but here 
the data that is used is derived from the longitudinal directories and just 
placed in the base so that it can be found for each subject).

Hope that explains it.
Best, Martin

On Sep 4, 2014, at 9:33 PM, Taylor North taylornorth...@hotmail.ca wrote:

 Hello, 
 
 I am having some troubles using QDEC to analyze the cortical thickness 
 changes in my 
 group study and I was hoping someone may be able to give me a hand. The steps 
 I 
 have done are as follows: 
 
 I am working on a study looking at 40 subjects scanned at two time points 
 (base 
 and 6 months after). I have followed all the steps for longitudinal 
 processing 
 for each subject (cross,base, and longitudinals) and made edits where they 
 were 
 necessary to the base. I then entered all 40 subjects into a QDEC table as 
 follows 
 
 fsid fsid-base time gender age
 crosstpN1 base1 0 female 20
 crosstpN2 base1 6 female 20 
 .. continues for rest of the subjects
 
 
 then I ran the QCHACHE on the data, made a Qdecrc. file in the subject DIR, 
 and 
 then transformed the longitudinal QDEC table into a QDEC table which looks 
 like:
 
 fsid time gender age 
 Base1 3 female 20 
 .. continues for the rest of the subjects. 
 
 I then followed the QDEC steps outlined In the group tutorial. (import cross 
 sectional table, generate stats data table, import aseg volume, set 
 longitudinal dependent variables and pick continuous variable.
 
 1) the first problem I am having is that when I go to process the 
 longitudinal 
 group results through QDEC it makes me pick a continuous variable when I just 
 want to analyze the dependent variable The symmetrized percent change. So I 
 have tried picking different continuous variables ( such as age or importing 
 rhcortex volume etc...) with choosing symmetrized percent change as the 
 dependent variable. No matter what continuous variable I pick the question: 
 ``does the average symmetrized percent change differ from zero? always comes 
 up, the problem is depending on what continuous variable I pick the results 
 change. Is there a way to just look at the longitudinal thickness changes 
 across a group alone, because I first want to look at the atrophy across the 
 whole group over 6 months and then compare the differences in atrophy against 
 the diagnosed and non diagnosed group. 
 
 2) another thing I don't quite understand is it seems like the longitudinal 
 qdec tables are made with the cross of the subjects under fsid, but why 
 wouldn't you use the longitudinals under the fsid for the longitudinal table 
 instead? Also it seems like in the cross sectional qdec table the base is the 
 subject being analyzed under fsid, which also doesn't make sense to me 
 because 
 in the tutorial it says base should not be used directly for analysis. 
 
 thanks for the help!
 
 Taylor 
  
  
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Re: [Freesurfer] longitudinal QDEC help

[Taylor North]

Hi Martin 
 
Yes I that definitely clears things up, thanks very much for the help. 
 
As for the QCAHCE we did use the long_mris_slopes described in the tutorial you 
linked in your email. Just to confirm I believe I should be using the 
mri_glmfit -osgm model for my one sample group mean analysis and then when I 
want to compare against my continuous/dependent variables I should be using 
QDEC? Also it looks like mri_glmfit -osgm calculates % change, so should I be 
analyzing % change, not symmetrized percent change on my QDEC analysis as well, 
even though it say symmetrized percent change is the more robust result?
 
Thanks again for your help
 
Taylor 
From: mreu...@nmr.mgh.harvard.edu
Date: Thu, 4 Sep 2014 22:44:16 -0400
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] longitudinal QDEC help

Hi Taylor,
first, in your description you mention 'base and 6 month'. Better call it 
'baseline' or 'first and second time points at 0 and 6 months' in order to not 
confuse the first time point with the 'base' = within-subject template created 
as the second step. I think you did not confuse it, but just want to make sure.
From your description it is not clear how you computed the symmetrized percent 
change. You say you ran QCACHE, but how? Did you use long_mris_slopes as 
described here:http://freesurfer.net/fswiki/LongitudinalTwoStageModel 
http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial 
That step computes slopes for each subject and (instead of having 2 thickness 
maps) reduces the information to a single map (here the symmetrized percent 
change is simply: 100 * tp2-tp1/(0.5*(tp1+tp2)) ) . These maps are stored in 
the base directories (one for each subject and of corse each hemisphere that 
you run).
Now to your questions:1) I think a 'one sample group mean' analysis is not 
possible in QDEC. For that you have to use mri_glmfit -osgm …. I wish we had 
this functionality and I'll see how hard it would be to implement it in future 
versions of QDEC (this came up frequently and it should not be too hard).
2) a) the longitudinal qdec table use the cross id's in the fsid column for 
simplicity. When it is used in many programs (e.g. long_mris_slopes, 
long_stats_slopes and other scripts with the long-qdec option) the scripts 
knows that it is a longitudinal qdec table (because of the existing fsid-base 
column) and internally use the longitudinal directories for processing. The 
cross sectional directories are never used.b) as mentioned above, the results 
from the first stage analysis (creation of the within subject slopes and 
percent changes) are stored in the base directories. They are used in this step 
and found there. (and you are right, the recon-all results from the base should 
not be analyzed directly, but here the data that is used is derived from the 
longitudinal directories and just placed in the base so that it can be found 
for each subject).
Hope that explains it.Best, Martin
On Sep 4, 2014, at 9:33 PM, Taylor North taylornorth...@hotmail.ca 
wrote:Hello, 

I am having some troubles using QDEC to analyze the cortical thickness changes 
in my 
group study and I was hoping someone may be able to give me a hand. The steps I 
have done are as follows: 

I am working on a study looking at 40 subjects scanned at two time points (base 
and 6 months after). I have followed all the steps for longitudinal processing 
for each subject (cross,base, and longitudinals) and made edits where they were 
necessary to the base. I then entered all 40 subjects into a QDEC table as 
follows 

fsid fsid-base time gender age
crosstpN1 base1 0 female 20
crosstpN2 base1 6 female 20 
.. continues for rest of the subjects


then I ran the QCHACHE on the data, made a Qdecrc. file in the subject DIR, and 
then transformed the longitudinal QDEC table into a QDEC table which looks like:

fsid time gender age 
Base1 3 female 20 
.. continues for the rest of the subjects. 

I then followed the QDEC steps outlined In the group tutorial. (import cross 
sectional table, generate stats data table, import aseg volume, set 
longitudinal dependent variables and pick continuous variable.

1) the first problem I am having is that when I go to process the longitudinal 
group results through QDEC it makes me pick a continuous variable when I just 
want to analyze the dependent variable The symmetrized percent change. So I 
have tried picking different continuous variables ( such as age or importing 
rhcortex volume etc...) with choosing symmetrized percent change as the 
dependent variable. No matter what continuous variable I pick the question: 
``does the average symmetrized percent change differ from zero? always comes 
up, the problem is depending on what continuous variable I pick the results 
change. Is there a way to just look at the longitudinal thickness changes 
across a group alone, because I first want to look at the atrophy across the 
whole group over 6 months and then compare

Re: [Freesurfer] longitudinal QDEC help

[Martin Reuter]

Hi Taylor,

You can do the glmfit osgm on whatever you like (rate, percentchange pc1, or 
symm. percent change spc). I recommend SPC. The 2stage model page shows an 
example of glmfit with osgm flag and explains how to stack your data first. 
Best Martin


Sent via my smartphone, please excuse brevity.

div Original message /divdivFrom: Taylor North 
taylornorth...@hotmail.ca /divdivDate:09/04/2014  11:14 PM  (GMT-05:00) 
/divdivTo: Freesurfer support list freesurfer@nmr.mgh.harvard.edu 
/divdivSubject: Re: [Freesurfer] longitudinal QDEC help /divdiv
/divHi Martin 
 
Yes I that definitely clears things up, thanks very much for the help. 
 
As for the QCAHCE we did use the long_mris_slopes described in the tutorial you 
linked in your email. Just to confirm I believe I should be using the 
mri_glmfit -osgm model for my one sample group mean analysis and then when I 
want to compare against my continuous/dependent variables I should be using 
QDEC? Also it looks like mri_glmfit -osgm calculates % change, so should I be 
analyzing % change, not symmetrized percent change on my QDEC analysis as well, 
even though it say symmetrized percent change is the more robust result?
 
Thanks again for your help
 
Taylor 
From: mreu...@nmr.mgh.harvard.edu
Date: Thu, 4 Sep 2014 22:44:16 -0400
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] longitudinal QDEC help

Hi Taylor,

first, in your description you mention 'base and 6 month'. Better call it 
'baseline' or 'first and second time points at 0 and 6 months' in order to not 
confuse the first time point with the 'base' = within-subject template created 
as the second step. I think you did not confuse it, but just want to make sure.

From your description it is not clear how you computed the symmetrized percent 
change. You say you ran QCACHE, but how? Did you use long_mris_slopes as 
described here:
http://freesurfer.net/fswiki/LongitudinalTwoStageModel 
http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial 

That step computes slopes for each subject and (instead of having 2 thickness 
maps) reduces the information to a single map (here the symmetrized percent 
change is simply: 100 * tp2-tp1/(0.5*(tp1+tp2)) ) . These maps are stored in 
the base directories (one for each subject and of corse each hemisphere that 
you run).

Now to your questions:
1) I think a 'one sample group mean' analysis is not possible in QDEC. For that 
you have to use mri_glmfit -osgm …. 
I wish we had this functionality and I'll see how hard it would be to implement 
it in future versions of QDEC (this came up frequently and it should not be too 
hard).

2) a) the longitudinal qdec table use the cross id's in the fsid column for 
simplicity. When it is used in many programs (e.g. long_mris_slopes, 
long_stats_slopes and other scripts with the long-qdec option) the scripts 
knows that it is a longitudinal qdec table (because of the existing fsid-base 
column) and internally use the longitudinal directories for processing. The 
cross sectional directories are never used.
b) as mentioned above, the results from the first stage analysis (creation of 
the within subject slopes and percent changes) are stored in the base 
directories. They are used in this step and found there. (and you are right, 
the recon-all results from the base should not be analyzed directly, but here 
the data that is used is derived from the longitudinal directories and just 
placed in the base so that it can be found for each subject).

Hope that explains it.
Best, Martin

On Sep 4, 2014, at 9:33 PM, Taylor North taylornorth...@hotmail.ca wrote:

Hello, 

I am having some troubles using QDEC to analyze the cortical thickness changes 
in my 
group study and I was hoping someone may be able to give me a hand. The steps I 
have done are as follows: 

I am working on a study looking at 40 subjects scanned at two time points (base 
and 6 months after). I have followed all the steps for longitudinal processing 
for each subject (cross,base, and longitudinals) and made edits where they were 
necessary to the base. I then entered all 40 subjects into a QDEC table as 
follows 

fsid fsid-base time gender age
crosstpN1 base1 0 female 20
crosstpN2 base1 6 female 20 
.. continues for rest of the subjects


then I ran the QCHACHE on the data, made a Qdecrc. file in the subject DIR, and 
then transformed the longitudinal QDEC table into a QDEC table which looks like:

fsid time gender age 
Base1 3 female 20 
.. continues for the rest of the subjects. 

I then followed the QDEC steps outlined In the group tutorial. (import cross 
sectional table, generate stats data table, import aseg volume, set 
longitudinal dependent variables and pick continuous variable.

1) the first problem I am having is that when I go to process the longitudinal 
group results through QDEC it makes me pick a continuous variable when I just 
want to analyze the dependent variable The symmetrized percent change

[Freesurfer] longitudinal QDEC question

[Salil Soman]

Hi,

I have been following the steps for longitudinal processing from here (
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), and
was hoping for some advice on how to setup the GLM.

I have a set of data where I have 2 time points for all subjects, have run
recon-all, qcache, the base and cross steps of processing. I also ran the
long mri_slopes step, created my long.qdec table, then created the
simplified table for qdec.

I would like to perform a whole brain analysis where I identify any brain
regions that changed (volume or cortical thickness) from time point 1 and
time point 2. I am a little unclear on what the explanatory variable should
be performing this analysis. Any suggestions on how best to structure the
analysis would be greatly appreciated.

Best wishes,

Salil Soman, MD, MS
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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.

Re: [Freesurfer] longitudinal QDEC question

[Martin Reuter]

Hi salil, the command for that are on the wiki. You'd do a one sample group 
mean (-osgm) . This asks if the variable of interest is significantly different 
from zero. Since you ran long mris slopes, that variable would be for example 
the rate of change or the percent change (one measure per subject).
Best Martin


Sent via my smartphone, please excuse brevity.

 Original message 
From: Salil Soman salso...@stanford.edu 
Date:07/01/2014  9:40 PM  (GMT+01:00) 
To: free surfer freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] longitudinal QDEC question 

Hi,

I have been following the steps for longitudinal processing from here 
(https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), and was 
hoping for some advice on how to setup the GLM. 

I have a set of data where I have 2 time points for all subjects, have run 
recon-all, qcache, the base and cross steps of processing. I also ran the long 
mri_slopes step, created my long.qdec table, then created the simplified table 
for qdec.

I would like to perform a whole brain analysis where I identify any brain 
regions that changed (volume or cortical thickness) from time point 1 and time 
point 2. I am a little unclear on what the explanatory variable should be 
performing this analysis. Any suggestions on how best to structure the analysis 
would be greatly appreciated.

Best wishes,

Salil Soman, MD, MS___
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