Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

[Shatil, Anwar Shahadat]

External Email - Use Caution

Hi Martin/Doug:

Still looking for an answer. Could not find a way to list the percentage change 
values for each subject in a tabular form.

Thanks,

Anwar

On 2018-08-30, 12:15 PM, "Shatil, Anwar Shahadat"  
wrote:

External Email - Use Caution

Hello Martin:

I am using freesurfer 6.0.0 and the long_mris_slopes version 1.42 (that 
came with it by default).

If I omit --out-pc1 but keep --do-pc1 still do not get any output as a .dat 
or .stats file. I only get .mgh file in surf folder.

I need percentage change values of tp2 from tp1 for each subject in a 
tabular form.

Best,

Anwar

On 2018-08-30, 3:22 AM, "Martin Reuter"  
wrote:

Hi Anwar,

what FS version are you using?

Also what happens if you omit the --out-pc1 but keep the --do-pc1 ?
Also no output with that ending? It should write it to the default
location.

Best, Martin





On Wed, 2018-08-29 at 16:45 +, Shatil, Anwar Shahadat wrote:
> External Email - Use Caution
> Dear Doug:
>
> I am trying to get a table containing pc1 values for each subject in
> a longitudinal study and failed to extract this. I use the code
> below:
>
> long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label
> --time years --qcache fsaverage --sd
> /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-pc1.dat
>
> It says
> long_mris_slopes: error: no such option: --out-pc1
>
>
> However in the --help file it says:
>
> Within-Subject Output:
> Pass these to overwrite the default names:
>
> --out-avg=OUT_AVG   filename to store temporal average in
> /stats/ (default:
> long..-avg.dat)
> --out-rate=OUT_RATE
> filename to store rate in
> /stats/
> (default: long..-rate.dat)
> --out-pc1fit=OUT_PC1FIT
> filename to store pct. change (to tp1fit) in
> /stats/ (default:
> long..-pc1fit.dat)
> --out-pc1=OUT_PC1   filename to store pct. change (to tp1) in
> /stats/ (default:
> long..-pc1.dat)
> --out-spc=OUT_SPC   filename to store sym. pct. change in
> /stats/ (default:
> long..-spc.dat)
> --out-resid=OUT_RESID
> filename to store residual in
> /stats/ (default:
> long..-resid.dat),
> requires
> --resid 
> --out-stack=OUT_STACK
> filename to store stacked measure file
> /stats/ (default:
> long..-stack.dat)
>
>   Stacked Tables:
> To output tables with results from all subjects
>
> --stack-avg=STACK_AVG
> full filename to stack temporal average
> tables
> (default no stacking)
> --stack-rate=STACK_RATE
> full filename to stack rate tables (default
> no
> stacking)
> --stack-pc1fit=STACK_PC1FIT
> full filename to stack pct. change to tp1fit
> tables
> (default no stacking)
> --stack-pc1=STACK_PC1
> full filename to stack pct. change to tp1
> tables
> (default no stacking)
> --stack-spc=STACK_SPC
> full filename to stack sym. pct. tables
> (default no
> stacking)
> --stack-resid=STACK_RESID
> full filename to stack residual tables
> (default no
> stacking)
>
>
> Am I writing the code wrong?? I never got any long..-
> pc1.dat file in /stats/ folder except bunch of mgh files
> in /surf/ folder.
>
> Thanks,
>
> Anwar
> --
   

Re: [Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

[Shatil, Anwar Shahadat]

External Email - Use Caution

Hello Martin:

I am using freesurfer 6.0.0 and the long_mris_slopes version 1.42 (that came 
with it by default).

If I omit --out-pc1 but keep --do-pc1 still do not get any output as a .dat or 
.stats file. I only get .mgh file in surf folder.

I need percentage change values of tp2 from tp1 for each subject in a tabular 
form.

Best,

Anwar

On 2018-08-30, 3:22 AM, "Martin Reuter"  wrote:

Hi Anwar,

what FS version are you using?

Also what happens if you omit the --out-pc1 but keep the --do-pc1 ?
Also no output with that ending? It should write it to the default
location.

Best, Martin





On Wed, 2018-08-29 at 16:45 +0000, Shatil, Anwar Shahadat wrote:
> External Email - Use Caution
> Dear Doug:
>
> I am trying to get a table containing pc1 values for each subject in
> a longitudinal study and failed to extract this. I use the code
> below:
>
> long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label
> --time years --qcache fsaverage --sd
> /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 out-pc1.dat
>
> It says
> long_mris_slopes: error: no such option: --out-pc1
>
>
> However in the --help file it says:
>
> Within-Subject Output:
> Pass these to overwrite the default names:
>
> --out-avg=OUT_AVG   filename to store temporal average in
> /stats/ (default:
> long..-avg.dat)
> --out-rate=OUT_RATE
> filename to store rate in
> /stats/
> (default: long..-rate.dat)
> --out-pc1fit=OUT_PC1FIT
> filename to store pct. change (to tp1fit) in
> /stats/ (default:
> long..-pc1fit.dat)
> --out-pc1=OUT_PC1   filename to store pct. change (to tp1) in
> /stats/ (default:
> long..-pc1.dat)
> --out-spc=OUT_SPC   filename to store sym. pct. change in
> /stats/ (default:
> long..-spc.dat)
> --out-resid=OUT_RESID
> filename to store residual in
> /stats/ (default:
> long..-resid.dat),
> requires
> --resid 
> --out-stack=OUT_STACK
> filename to store stacked measure file
> /stats/ (default:
> long..-stack.dat)
>
>   Stacked Tables:
> To output tables with results from all subjects
>
> --stack-avg=STACK_AVG
> full filename to stack temporal average
> tables
> (default no stacking)
> --stack-rate=STACK_RATE
> full filename to stack rate tables (default
> no
> stacking)
> --stack-pc1fit=STACK_PC1FIT
> full filename to stack pct. change to tp1fit
> tables
> (default no stacking)
> --stack-pc1=STACK_PC1
> full filename to stack pct. change to tp1
> tables
> (default no stacking)
> --stack-spc=STACK_SPC
> full filename to stack sym. pct. tables
> (default no
> stacking)
> --stack-resid=STACK_RESID
> full filename to stack residual tables
> (default no
> stacking)
>
>
> Am I writing the code wrong?? I never got any long..-
> pc1.dat file in /stats/ folder except bunch of mgh files
> in /surf/ folder.
>
> Thanks,
>
> Anwar
> --
>
> Anwar S. Shatil
>
> Research Assistant
> Department of Medical Imaging
> Sunnybrook Health Sciences Centre
> Room AB204, 2075 Bayview Avenue
> Toronto, ON M4N 3M5
> Tel: 416.480.6100 ext. 89617
> Email: anwar.sha...@sunnybrook.ca
> This e-mail is intended only for the named recipient(s) and may
> contain confidential, personal and/or health information (information
> which may be subject to legal restrictions on use, retention and/or
> disclosure).  No waiver of confidence is intended by virtue of
> communication via the internet.  Any review or distribution 

[Freesurfer] long_mris_slopes: error: cannot create a table with longitudinal pc1

[Shatil, Anwar Shahadat]

External Email - Use Caution

?Dear Doug:


I am trying to get a table containing pc1 values for each subject in a 
longitudinal study and failed to extract this. I use the code below:


long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness --hemi lh 
--do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years 
--qcache fsaverage --sd /Users/richardaviv/Desktop/Longitudinal_FS --out-pc1 
out-pc1.dat

It says

long_mris_slopes: error: no such option: --out-pc1


However in the --help file it says:


Within-Subject Output:

Pass these to overwrite the default names:


--out-avg=OUT_AVG   filename to store temporal average in

/stats/ (default:

long..-avg.dat)

--out-rate=OUT_RATE

filename to store rate in /stats/

(default: long..-rate.dat)

--out-pc1fit=OUT_PC1FIT

filename to store pct. change (to tp1fit) in

/stats/ (default:

long..-pc1fit.dat)

--out-pc1=OUT_PC1   filename to store pct. change (to tp1) in

/stats/ (default:

long..-pc1.dat)

--out-spc=OUT_SPC   filename to store sym. pct. change in

/stats/ (default:

long..-spc.dat)

--out-resid=OUT_RESID

filename to store residual in

/stats/ (default:

long..-resid.dat), requires

--resid 

--out-stack=OUT_STACK

filename to store stacked measure file

/stats/ (default:

long..-stack.dat)


  Stacked Tables:

To output tables with results from all subjects


--stack-avg=STACK_AVG

full filename to stack temporal average tables

(default no stacking)

--stack-rate=STACK_RATE

full filename to stack rate tables (default no

stacking)

--stack-pc1fit=STACK_PC1FIT

full filename to stack pct. change to tp1fit tables

(default no stacking)

--stack-pc1=STACK_PC1

full filename to stack pct. change to tp1 tables

(default no stacking)

--stack-spc=STACK_SPC

full filename to stack sym. pct. tables (default no

stacking)

--stack-resid=STACK_RESID

full filename to stack residual tables (default no

stacking)?



Am I writing the code wrong?? I never got any long..-pc1.dat file 
in /stats/ folder except bunch of mgh files in /surf/ 
folder.


Thanks,


Anwar

--

Anwar S. Shatil

Research Assistant
Department of Medical Imaging
Sunnybrook Health Sciences Centre
Room AB204, 2075 Bayview Avenue
Toronto, ON M4N 3M5
Tel: 416.480.6100 ext. 89617
Email: anwar.sha...@sunnybrook.ca
This e-mail is intended only for the named recipient(s) and may contain 
confidential, personal and/or health information (information which may be 
subject to legal restrictions on use, retention and/or disclosure).  No waiver 
of confidence is intended by virtue of communication via the internet.  Any 
review or distribution by anyone other than the person(s) for whom it was 
originally intended is strictly prohibited.  If you have received this e-mail 
in error, please contact the sender and destroy all copies.

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Re: [Freesurfer] Extracting number of vertices in Yeo's 7Networks from significant clusters

[Shatil, Anwar Shahadat]

External Email - Use Caution

Hi Doug:


Thanks for your reply. I think you are correct.


Is there any way to extract the number of vertices from the cluster spanning 
each of Yeo's 7 networks? I tried to overlay Yeo2011_7Networks_N1000.annot on 
the .mgh file and use my cursor to get information, but that does not give me 
the number of vertices.


Thanks,

Anwar




Date: Wed, 15 Aug 2018 11:18:50 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] Extracting number of vertices in Yeo's
7Networks from significant clusters
To: 
Message-ID: <0870c8a6-0a29-b748-500a-3cbfbc39b...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"; format=flowed

The input (--i) only supplies information for use in computing the Mean,
StdDev, etc. The number of vertices willcome from the annot. Or am I
misunderstanding something?
________
From: Shatil, Anwar Shahadat
Sent: August 15, 2018 10:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Extracting number of vertices in Yeo's 7Networks from significant 
clusters


Hello Doug and other experts:


I have done QDEC analysis between two groups (healthy controls vs disease) and 
obtained different .mgh and .annot files. I got one big cluster covering most 
part of the brain. I wanted to extract the number of vertices for Yeo's 7 
Networks in that big cluster and therefore I ran this:


mri_segstats --i cache.th30.pos.sig.masked.mgh --annot fsaverage rh 
Yeo2011_7Networks_N1000 --excludeid 0 --sum network_param.dat

The result was:

Col Headers  Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range
  1   1 2251914950.0  7Networks_11.4816 
1.8126 0. 3.6990 3.6990
  2   2 3020712514.7  7Networks_22.6658 
1.6596 0. 3.6990 3.6990
  3   3 17604 8224.3  7Networks_32.6278 
1.6778 0. 3.6990 3.6990
  4   4 19402 8357.2  7Networks_43.3453 
1.0877 0. 3.6990 3.6990
  5   5 11614 6205.0  7Networks_52.1434 
1.7750 0. 3.6990 3.6990
  6   6 2233012170.7  7Networks_62.6315 
1.6761 0. 3.6990 3.6990
  7   7 2605613826.2  7Networks_73.0249 
1.4229 0. 3.6990 3.6990

I ran the same code for different --i (input) .mgh files and everytime the 
NVertices were the same, which means this is not the one I am looking for.

Can you please help me in getting the number of vertices of Yeo's each network 
that fall in that big cluster?

Thanks.

Anwar



--

Anwar S. Shatil

Research Assistant
Department of Medical Imaging
Sunnybrook Health Sciences Centre
Room AB204, 2075 Bayview Avenue
Toronto, ON M4N 3M5
Tel: 416.480.6100 ext. 89617
Email: anwar.sha...@sunnybrook.ca
This e-mail is intended only for the named recipient(s) and may contain 
confidential, personal and/or health information (information which may be 
subject to legal restrictions on use, retention and/or disclosure).  No waiver 
of confidence is intended by virtue of communication via the internet.  Any 
review or distribution by anyone other than the person(s) for whom it was 
originally intended is strictly prohibited.  If you have received this e-mail 
in error, please contact the sender and destroy all copies.

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[Freesurfer] Extracting number of vertices in Yeo's 7Networks from significant clusters

[Shatil, Anwar Shahadat]

External Email - Use Caution

Hello Doug and other experts:


I have done QDEC analysis between two groups (healthy controls vs disease) and 
obtained different .mgh and .annot files. I got one big cluster covering most 
part of the brain. I wanted to extract the number of vertices for Yeo's 7 
Networks in that big cluster and therefore I ran this:


mri_segstats --i cache.th30.pos.sig.masked.mgh --annot fsaverage rh 
Yeo2011_7Networks_N1000 --excludeid 0 --sum network_param.dat

The result was:

Col Headers  Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range
  1   1 2251914950.0  7Networks_11.4816 
1.8126 0. 3.6990 3.6990
  2   2 3020712514.7  7Networks_22.6658 
1.6596 0. 3.6990 3.6990
  3   3 17604 8224.3  7Networks_32.6278 
1.6778 0. 3.6990 3.6990
  4   4 19402 8357.2  7Networks_43.3453 
1.0877 0. 3.6990 3.6990
  5   5 11614 6205.0  7Networks_52.1434 
1.7750 0. 3.6990 3.6990
  6   6 2233012170.7  7Networks_62.6315 
1.6761 0. 3.6990 3.6990
  7   7 2605613826.2  7Networks_73.0249 
1.4229 0. 3.6990 3.6990

I ran the same code for different --i (input) .mgh files and everytime the 
NVertices were the same, which means this is not the one I am looking for.

Can you please help me in getting the number of vertices of Yeo's each network 
that fall in that big cluster?

Thanks.

Anwar



--

Anwar S. Shatil

Research Assistant
Department of Medical Imaging
Sunnybrook Health Sciences Centre
Room AB204, 2075 Bayview Avenue
Toronto, ON M4N 3M5
Tel: 416.480.6100 ext. 89617
Email: anwar.sha...@sunnybrook.ca
This e-mail is intended only for the named recipient(s) and may contain 
confidential, personal and/or health information (information which may be 
subject to legal restrictions on use, retention and/or disclosure).  No waiver 
of confidence is intended by virtue of communication via the internet.  Any 
review or distribution by anyone other than the person(s) for whom it was 
originally intended is strictly prohibited.  If you have received this e-mail 
in error, please contact the sender and destroy all copies.

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[Freesurfer] How to extract stats of the regions that is covered by large clusters

[Shatil, Anwar Shahadat]

Hello Experts:

After running mri_glmfit sim, I got below clusters:

ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxsWghtVtx   Annot
   1   16.567   56197  13752.71-36.8  -15.5   55.0  0.00020  0.0  
0.00040  30900   180209.80  precentral
   29.630   57862   3018.98-29.7  -72.0  -10.1  0.00020  0.0  
0.00040   462023119.05  fusiform
   39.488  162470   2465.82-16.0  -79.37.4  0.00020  0.0  
0.00040   410819097.47  pericalcarine
   48.845   35506   1860.62-24.5  -79.0   23.1  0.00020  0.0  
0.00040   337515122.28  superiorparietal
   56.223   84246   1019.33 -4.8   15.4   -6.3  0.00020  0.0  
0.00040   1760 6950.26  rostralanteriorcingulate

However, Cluster-1 area is large compared to others and it actually 
postcentral, and some portion of paracentral region. How can I extract the 
stats for these regions?

Thanks,
Anwar


Anwar S. Shatil

Research Assistant, Medical Imaging
Sunnybrook Health Sciences Centre
Toronto, ON, M4N 3M5
Email: anwar.sha...@sunnybrook.ca

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[Freesurfer] Does paracentral include precentral area

[Shatil, Anwar Shahadat]

Hi Doug:

I am confused about the visualisation of “Paracentral” and “precentral” 
clusters after running mri_glmfit-sim command. I used two cache values (3 pos 
and 4 pos) to see if the area changes. Each time the “Paracentral” cluster 
appears to be the largest significant area, but, the area shrinks during the 
cache value of 4 pos.

It seems that paracentral and precentral areas are not mutually exclusive. I.e. 
paracentral seems to include precentral. Is that true? If not, then how can I 
visualize the actual significant area despite seeing a large “Paracentral” or 
“Precentral” area.


Thanks,
Anwar
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[Freesurfer] Finding correlation between Cth and clinical data

[Shatil, Anwar Shahadat]

Dear Experts:

I am very new to freesurfer glmfit and this post may seem dumb. I want to find 
the correlation between Cth and Education for each of HC and RRMS group 
regressing out the effect of gender and (demeaned) age. My fsgd file is 
something like below.

GroupDescriptorFile   1
Title   Group-Edu-Correlation
MeasurementName   thickness
Class  FemaleHC
Class  FemaleRRMS
Class  MaleHC
Class  MaleRRMS
Variables AgeEducation
Input 1  FemaleRRMS -7.97  0.243
Input 2  MaleRRMS  -2.97  -1.300
Input 3  FemaleHC   -12.97-0.914
Input 5  Male HC   4.03-1.686
………..
I used DODS method.
For HC, I set the correlation matrix as: 0  0  0  0  0  0  0  0  0.5  0  0.5  0
And for RRMS, I set the matrix as:  0  0  0  0  0  0  0  0  0  0.5  0  0.5


  1.  Are my DODS contrasts correct?
  2.  To get better DOF, should I create two different FSGD file for each group 
(i.e. one for HC and one for RRMS)?
  3.  If I create two different FSGD file for each group then can I use DOSS 
method and use the contrast: 0 0 0 1 ?

Thanks,
Anwar

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[Freesurfer] Correlation between CTh and Clinical Data

[Shatil, Anwar Shahadat]

Dear Experts:

I am very new to freesurfer glmfit and this post may seem dumb. I wanted to 
find the correlation between Cth and Education for each of HC and RRMS group 
regressing out the effect of gender and (demeaned) age. My fsgd file is 
something like below.

GroupDescriptorFile   1
Title   Group-Edu-Correlation
MeasurementName   thickness
Class  FemaleHC
Class  FemaleRRMS
Class  MaleHC
Class  MaleRRMS
Variables AgeEducation
Input 1  FemaleRRMS -7.97  0.243
Input 2  MaleRRMS  -2.97  -1.300
Input 3  FemaleHC   -12.97-0.914
Input 5  Male HC   4.03-1.686
………..
I used DODS method.
For HC, I set the correlation matrix as: 0  0  0  0  0  0  0  0  0.5  0  0.5  0
And for RRMS, I set the matrix as:  0  0  0  0  0  0  0  0  0  0.5  0  0.5


  1.  I am wondering, if my DODS contrasts are correct.
  2.  To get better DOF, should I create two different FSGD file for each group 
(i.e. one for HC and one for RRMS)?
  3.  If I create two different FSGD file for each group then can I use DOSS 
method and use the contrast: 0 0 0 1 ?

Thanks,
Anwar


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[Freesurfer] How to calculate WM lobar volumes

[Shatil, Anwar Shahadat]

Dear All:

I want to find the WM lobar volumes in a set of MS patients. I also have the 
processed images from freesurfer. To extract the lobar volumes I used below 
codes from one of the previous threads of Freesurfer 
(https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2012-April/023232.html):

1. mri_annotation2label --s  --hemi rh --lobesStrict lobesfile
2. mri_aparc2aseg —s  --labelwm --annot lobesfile
3.  mri_segstats --seg mri/lobesfile+aseg.mgz --sum wmparc.lobar.stats --pv 
mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/norm.mgz --in 
mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject  
--surf-wm-vol --ctab /Applications/freesurfer/WMParcStatsLUT.txt —etiv

Now, I don’t know how to get the volumes or which LUT table to use in the 
overlay.

Please correct me if I used the correct LUT file in --ctab.

Your guidance would be highly appreciated.

Thanks,
Anwar
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