[Freesurfer] mri_glmfit error - matrix ill-conditioned. no solution from archive.

[miracle ozzoude]

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Hello,

Any idea how to solve this problem? I have tried the suggested solutions on
the archive, that's Demean and Rescale but to no avail.

I have attached the necessary files in the email below.

Many thanks,
Miracle

mri_glmfit command: mri_glmfit --y
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh
--fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf
fsaverage lh --cortex --glmdir
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
bash-3.2$ mri_glmfit --y 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh 
--fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf 
fsaverage lh --cortex --glmdir 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
gdfRead(): reading thickness_DHI_Emotional_edit.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 47.0476 9.22459
1 Sports 0.619048 1.13289
2 Days_TBI 1734.1 919.571
3 Emotional 13.5238 7.19536
Class Size and Means of each Continuous Variable
1 PPCS_male  5  39.8000   1.6000 1557.8000  12.8000 
2 PPCS_female 16  49.3125   0.3125 1789.1875  13.7500 
WARNING: Class PPCS_male has 5 members. With 4 variables and using DODS, This 
is the bare minimum which may cause problems with the design matrix.
INFO: gd2mtx_method is dods
Reading source surface 
/Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65417.00
AvgVtxArea   0.399269
AvgVtxDist   0.721953
StdVtxDist   0.195472

7.2.0
cwd /Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness
cmdline mri_glmfit --y 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh 
--fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf 
fsaverage lh --cortex --glmdir 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir 
sysname  Darwin
hostname ip-130-63-40-126.dynamic.yorku.ca
machine  x86_64
user sergiolab
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh
logyflag 0
usedti  0
FSGD thickness_DHI_Emotional_edit.fsgd
labelmask  
/Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/fsaverage/label/lh.cortex.label
maskinv 0
glmdir results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
Loading y from 
/Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh
   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 653034
Design matrix --
 1.0   0.0   30.0   0.0   4.0   0.0   1687.0   
0.0   10.0   0.0;
 0.0   1.0   0.0   46.0   0.0   0.0   0.0   
2149.0   0.0   12.0;
 1.0   0.0   41.0   0.0   0.0   0.0   2148.0   
0.0   6.0   0.0;
 0.0   1.0   0.0   49.0   0.0   0.0   0.0   
2257.0   0.0   18.0;
 0.0   1.0   0.0   51.0   0.0   0.0   0.0   
1939.0   0.0   28.0;
 0.0   1.0   0.0   61.0   0.0   0.0   0.0   
3404.0   0.0   8.0;
 0.0   1.0   0.0   53.0   0.0   0.0   0.0   
2368.95825   0.0   6.0;
 0.0   1.0   0.0   60.0   0.0   2.0   0.0   
1407.0   0.0   10.0;
 0.0   1.0   0.0   48.0   0.0   0.0   0.0   
1670.95837   0.0   6.0;
 0.0   1.0   0.0   38.0   0.0   0.0   0.0   
12.0   0.0   26.0;
 0.0   1.0   0.0   63.0   0.0   0.0   0.0   
796.0   0.0   18.0;
 0.0   1.0   0.0   40.0   0.0   0.0   0.0   
476.0   0.0   6.0;
 0.0   1.0   0.0   44.0   0.0   2.0   0.0   
1980.0   0.0   14.0;
 0.0   1.0   0.0   50.0   0.0   1.0   0.0   
3517.04175   0.0   6.0;
 1.0   0.0   29.0   0.0   1.0   0.0   177.04167   
0.0   18.0   0.0;
 0.0   1.0   0.0   39.0   0.0   0.0   0.0   
2571.0   0.0   22.0;
 0.0   1.0   0.0   53.0   0.0   0.0   0.0   
1872.0   0.0   18.0;
 1.0   0.0   59.0   0.0   0.0   0.0   1148.0   
0.0   24.0   0.0;
 

[Freesurfer] Along- tract multiple comparison result visualisation and summary interpretation

[miracle ozzoude]

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Hello,

Please, can someone answer my questions regarding the along-tract stats
using mri_glmfit and mri_glmfit-sim with permutation for version 7.2.

1) I ran it and I found a significant negative association between FA and
clinical score (see attached summary file). how do I know the entire length
of the tract and how much was affected based on the summary file; should I
be interpreting the results from the summary file differently?

2) Also when performing clusterwise correction for multiple comparison for
along-tract analyses, should the bonferroni flag (--2spaces) be included?
This is because it wasn't mentioned/included in the tracula statistics
tutorial nor the publication "Using diffusion MRI data acquired with
ultra-high gradient strength to improve tractography in routine-quality
data".

3) Lastly, is it appropriate to embed the perm.th13.neg.sig.cluster.mgh
from mri_glmfit-sim in dmri_trk2trk?


Many thanks,
Paul


perm.th13.abs.sig.cluster.summary
Description: Binary data
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[Freesurfer] Along- tract multiple comparison result visualisation and summary interpretation

[miracle ozzoude]

External Email - Use Caution

Hello,

I have questions regarding the along-tract stats using mri_glmfit and
mri_glmfit-sim with permutation for version 7.2.

1) I ran it and I found a significant result (see attached summary file)
where I expected/found a negative association between FA and clinical
score. how do I know the entire length of the tract and how much was
affected based on the summary file; should I be interpreting the results
from the summary file differently?

2) Also when performing clusterwise correction for multiple comparison for
along-tract analyses, should the bonferroni flag (--2spaces) be included?
This is because it wasn't mentioned/included in the tracula statistics
tutorial nor the publication "Using diffusion MRI data acquired with
ultra-high gradient strength to improve tractography in routine-quality data
".

3) Lastly, is it appropriate to embed the perm.th13.neg.sig.cluster.mgh from
mri_glmfit-sim in dmri_trk2trk?


Many thanks,
Paul


perm.th13.abs.sig.cluster.summary
Description: Binary data
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[Freesurfer] TRACULA cluster statistics visualization

[miracle ozzoude]

External Email - Use Caution

I have a similar question to this unanswer one (see link)
https://secure-web.cisco.com/1TPpYYjX_nTrm6lqczxoG15eSKbWRPZCXEekOMWT-xtyurpqfBqaFyz4aiSqrY42eu_2JI_dWX-HNfM9jWT5eTLES0zDZCVeGrslztLwHYrbkr_R08eoTG2wWnG2Be3lJlA5KOn3C00RFTWSpD7jyXDn6V0cmzukr2a1BZ66xTC3yOB_AAERXQC7DBDBNJDlDlTkg6iRJu8DlOzJUmIUSISa13MhDz7w6b4oF-97h09B4FeeO-GescFCpFpBxd8OvjZgQVzb9_ok9K4yzL79Rx0r6nqi_I-8maz_cpd4zCpITmOtKAPtXatUA-N9L0Di7HUO_3hEUmJaGqxQN__cqEg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74147.html
*Also*
1) If I run along-tract stats with mri_glmfit/mri_glmfit-sim and I found a
significant result, how do I know the entire length of the tract and how
much was affected? Also, is it measured in mm?

2) When performing clusterwise correction for multiple comparison for
along-tract analyses, should the bonferroni flag (--2spaces) be included?
This is because it wasn't mentioned/included in the tracula statistics
tutorial nor the publication "Using diffusion MRI data acquired with
ultra-high gradient strength to improve tractography in routine-quality data
".

Many thanks,
Paul
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Re: [Freesurfer] mri_glmfit with doss isn't working. v7.2

[miracle ozzoude]

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Hello Doug,

Do you mean like this?

GroupDescriptorFile 1

Title Rivermead cluster 2

DOSS

Class PPCS_Male

Class PPCS_Female

Variables Age Sports Games Days_TBI RPQ_13


If yes, i did but still getting similar area


Best,

Paul

On Tue, Jan 3, 2023 at 11:51 AM miracle ozzoude 
wrote:

> Hello Doug,
>
> Thanks for the quick response. I did see the error. However, I specified
> doss in the mri_glmfit command and my mtx looks accurate as indicated
> above. Does that mean it can only work with dods? The reason I'm using 2
> groups is because I want to regress out the effect of sex. However, the
> recommended way to do it in fsgd is to create a class for it and I only
> have 3 males.
>
> Is there a workaround for this?
>
> Many thanks.
>
> On Fri, Dec 30, 2022 at 6:37 PM miracle ozzoude 
> wrote:
>
>> Hello,
>>
>> I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did
>> like to regress out the effects of groups + other variables by using doss.
>> However, whenever I specify doss with the mri_glmfit command, it gives me
>> an error message (see below). I saw that others have experienced similar
>> issues without any solutions. How can we solve this? Any insight is
>> appreciated.
>>
>> Best,
>> Paul
>>
>> mri_glmfit command:
>>
>> mri_glmfit --y
>> ../../freesurfer/subjects/tracula_output/stats/mcp.avg16_syn_bbr.FA.nii.gz
>> --fsgd dti_RPQ_3.fsgd doss --C dti_RPQ.mtx --o mcp_FA.glmdir --save-eres
>> --nii.gz
>>
>>
>> design.mtx:
>>
>> 0 0 0 0 0 0 0.5
>>
>>
>> Terminal output:
>>
>> gdfRead(): reading dti_RPQ_3.fsgd
>>
>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>>
>> Continuous Variable Means (all subjects)
>>
>> 0 Age 46.9333 9.86216
>>
>> 1 Sports 0.067 0.249444
>>
>> 2 Games 1.1 1.62754
>>
>> 3 Days_TBI 1903.2 907.81
>>
>> 4 RPQ_3 7 2.28035
>>
>> Class Size and Means of each Continuous Variable
>>
>> 1 PPCS_Male  3  33.   0.   2. 1337.3472   6.6667
>>
>> 2 PPCS_Female 12  50.   0.   0.8333 2044.6632   7.0833
>>
>> ERROR: Class PPCS_Male has 3 members. With 5 variables and using DODS,
>> you need at least 6 members
>>
>
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Re: [Freesurfer] mri_glmfit with doss isn't working. v7.2

[miracle ozzoude]

External Email - Use Caution

Hello Doug,

Thanks for the quick response. I did see the error. However, I specified
doss in the mri_glmfit command and my mtx looks accurate as indicated
above. Does that mean it can only work with dods? The reason I'm using 2
groups is because I want to regress out the effect of sex. However, the
recommended way to do it in fsgd is to create a class for it and I only
have 3 males.

Is there a workaround for this?

Many thanks.

On Fri, Dec 30, 2022 at 6:37 PM miracle ozzoude 
wrote:

> Hello,
>
> I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did like
> to regress out the effects of groups + other variables by using doss.
> However, whenever I specify doss with the mri_glmfit command, it gives me
> an error message (see below). I saw that others have experienced similar
> issues without any solutions. How can we solve this? Any insight is
> appreciated.
>
> Best,
> Paul
>
> mri_glmfit command:
>
> mri_glmfit --y
> ../../freesurfer/subjects/tracula_output/stats/mcp.avg16_syn_bbr.FA.nii.gz
> --fsgd dti_RPQ_3.fsgd doss --C dti_RPQ.mtx --o mcp_FA.glmdir --save-eres
> --nii.gz
>
>
> design.mtx:
>
> 0 0 0 0 0 0 0.5
>
>
> Terminal output:
>
> gdfRead(): reading dti_RPQ_3.fsgd
>
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>
> Continuous Variable Means (all subjects)
>
> 0 Age 46.9333 9.86216
>
> 1 Sports 0.067 0.249444
>
> 2 Games 1.1 1.62754
>
> 3 Days_TBI 1903.2 907.81
>
> 4 RPQ_3 7 2.28035
>
> Class Size and Means of each Continuous Variable
>
> 1 PPCS_Male  3  33.   0.   2. 1337.3472   6.6667
>
> 2 PPCS_Female 12  50.   0.   0.8333 2044.6632   7.0833
>
> ERROR: Class PPCS_Male has 3 members. With 5 variables and using DODS, you
> need at least 6 members
>
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[Freesurfer] mri_glmfit with doss isn't working. v7.2

[miracle ozzoude]

External Email - Use Caution

Hello,

I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did like
to regress out the effects of groups + other variables by using doss.
However, whenever I specify doss with the mri_glmfit command, it gives me
an error message (see below). I saw that others have experienced similar
issues without any solutions. How can we solve this? Any insight is
appreciated.

Best,
Paul

mri_glmfit command:

mri_glmfit --y
../../freesurfer/subjects/tracula_output/stats/mcp.avg16_syn_bbr.FA.nii.gz
--fsgd dti_RPQ_3.fsgd doss --C dti_RPQ.mtx --o mcp_FA.glmdir --save-eres
--nii.gz


design.mtx:

0 0 0 0 0 0 0.5


Terminal output:

gdfRead(): reading dti_RPQ_3.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 Age 46.9333 9.86216

1 Sports 0.067 0.249444

2 Games 1.1 1.62754

3 Days_TBI 1903.2 907.81

4 RPQ_3 7 2.28035

Class Size and Means of each Continuous Variable

1 PPCS_Male  3  33.   0.   2. 1337.3472   6.6667

2 PPCS_Female 12  50.   0.   0.8333 2044.6632   7.0833

ERROR: Class PPCS_Male has 3 members. With 5 variables and using DODS, you
need at least 6 members
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Re: [Freesurfer] intrareg: Undefined variable

[miracle ozzoude]

External Email - Use Caution

Never mind. Solved it.



On Mon, Sep 26, 2022 at 1:16 PM miracle ozzoude 
wrote:

> Hello,
>
> I am trying to run TRACULA using FreeSurfer version7.2. I followed the
> instructions on the tutorial website for cross-sectional study with 1 scan
> (see link below). However, I keep getting "intrareg:Undefined variable"
> error whenever I run the first step "trac-all -prep -c tracula.file".
>
> I checked my config file and I did set intrareg = 3. Any suggestions on
> what the issue is/how to fix it? I have attached my config file in the
> email below, in addition to the log file. The participants' recon-all were
> processed using freesurfer v6.0
>
> Many thanks,
> Paul
>
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[Freesurfer] intrareg: Undefined variable

[miracle ozzoude]

External Email - Use Caution

Hello,

I am trying to run TRACULA using FreeSurfer version7.2. I followed the
instructions on the tutorial website for cross-sectional study with 1 scan
(see link below). However, I keep getting "intrareg:Undefined variable"
error whenever I run the first step "trac-all -prep -c tracula.file".

I checked my config file and I did set intrareg = 3. Any suggestions on
what the issue is/how to fix it? I have attached my config file in the
email below, in addition to the log file. The participants' recon-all were
processed using freesurfer v6.0

Many thanks,
Paul


tracula.file
Description: Binary data


trac-all.local-copy
Description: Binary data
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Re: [Freesurfer] Is hypointensities part of lh/rh cerebral white matter from aparc+aseg.mgz using mri_segstats

[miracle ozzoude]

External Email - Use Caution

Great. thanks Doug. I appreciate it

On Thu, Jun 24, 2021 at 12:07 PM miracle ozzoude 
wrote:

> Hello,
> I was wondering if anyone has an answer to my question.
>
> Cheers
>
> On Wed, Jun 23, 2021 at 5:42 PM miracle ozzoude 
> wrote:
>
>> Hello All,
>>
>> I was wondering if the  Right/Left-Cerebral-White-Matter in the
>> aparc+aseg.mgz contains WM hypointensities.
>>
>> mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats
>> --ctab FreeSurferColorLUT.txt
>>
>> Best,
>> Paul
>>
>>
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Re: [Freesurfer] Is hypointensities part of lh/rh cerebral white matter from aparc+aseg.mgz using mri_segstats

[miracle ozzoude]

External Email - Use Caution

Hello,
I was wondering if anyone has an answer to my question.

Cheers

On Wed, Jun 23, 2021 at 5:42 PM miracle ozzoude 
wrote:

> Hello All,
>
> I was wondering if the  Right/Left-Cerebral-White-Matter in the
> aparc+aseg.mgz contains WM hypointensities.
>
> mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats
> --ctab FreeSurferColorLUT.txt
>
> Best,
> Paul
>
>
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[Freesurfer] Is hypointensities part of lh/rh cerebral white matter from aparc+aseg.mgz using mri_segstats

[miracle ozzoude]

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Hello All,

I was wondering if the  Right/Left-Cerebral-White-Matter in the
aparc+aseg.mgz contains WM hypointensities.

mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats
--ctab FreeSurferColorLUT.txt

Best,
Paul
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[Freesurfer] (no subject)

[miracle ozzoude]

External Email - Use Caution

Hello All,

I was wondering if the  Right/Left-Cerebral-White-Matter in the
aparc+aseg.mgz contains WM hypointensities.

mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats
--ctab FreeSurferColorLUT.txt

Best,
Paul
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[Freesurfer] mri_segstats to report empty and non-empty segmentation

[miracle ozzoude]

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Hello Experts,

I am using mri_segstats with the --ctab flag to extract dti and suvr values
from a white matter hyperintensities parcellation. Running mri_segstats on
the image and parcellation with --ctab only reports on non-empty
segmentations. I want it to also report on the empty segmentations.

Is there a flag or any other freesurfer commands that i can use?

Summary: I want mri_segstats to report on non-empty and empty
segmentations, not just the former.

Cheers.

cmdline mri_segstats --seg wmh_lobar.nii.gz --i
subj_rescaled_wholecere_PET2T1_smooth.nii.gz --sum SUVR_WMH_lobar.stats
--ctab WMColorLUT.ctab --pv norm.mgz
Loading wmh_lobar.nii.gz
INFO: using NIfTI-1 qform
Loading subj_rescaled_wholecere_PET2T1_smooth.nii.gz
Loading norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 13 segmentations
Computing statistics for each segmentationReporting on 11 segmentations
Using PrintSegStat
mri_segstats done
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[Freesurfer] retaining label ids

[miracle ozzoude]

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Hello Experts,

I did like to extract wm whilst retaining the label ids. I tried
mri_extract_labels but it didn't work.

Any help would be appreciated.

Many thanks,
Paul
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Re: [Freesurfer] mri_glmfit dependent variable

[miracle ozzoude]

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Thanks Doug. I appreciate it. I have more questions.

1) Aren't both models answering the same question regardless of which side
of the equation cortical thickness or syndromes is placed?

2) Also, I noticed in the mri_glmfit --help, it said that forward model 2
is inverted to solve for the regressor of interest. Correct if I'm wrong,
does it mean if my matrix is 0 0 0 1 where 1 represents neuropsych
syndrome, it will solve for it?

The forward model is given by:


y = W*X*B + n


where X is the Ns-by-Nb design matrix, y is the Ns-by-Nv input data

set, B is the Nb-by-Nv regression parameters, and n is noise. Ns is

the number of inputs, Nb is the number of regressors, and Nv is the

number of voxels/vertices (all cols/rows/slices). y may be surface

or volume data and may or may not have been spatially smoothed. W

is a diagonal weighing matrix.


During the estimation stage, the forward model is inverted to

solve for B:


B = inv(X'W'*W*X)*X'W'y


3) Lastly, how do I extract the beta-values after running mri_glmfit-sim
without matlab?

Many thanks,
Paul

On Tue, Feb 23, 2021 at 12:37 AM miracle ozzoude 
wrote:

> Hello Experts,
>
> I've a question about mri_glmfit. I want to investigate the association
> between thickness and neuropsychiatric syndromes, controlling for age and
> cognition. Which model below is mri_glmfit performing?
>
> Model 1
> neuropsych syndromes ~ age + cognition + cortical thickness
> or
> Model 2
> cortical thickness ~ age + cognition + neuropsych syndrome
>
> Many thanks,
> Paul
>
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[Freesurfer] mri_glmfit dependent variable

[miracle ozzoude]

External Email - Use Caution

Hello Experts,

I've a question about mri_glmfit. I want to investigate the association
between thickness and neuropsychiatric syndromes, controlling for age and
cognition. Which model below is mri_glmfit performing?

Model 1
neuropsych syndromes ~ age + cognition + cortical thickness
or
Model 2
cortical thickness ~ age + cognition + neuropsych syndrome

Many thanks,
Paul
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Re: [Freesurfer] non-pvc processing error

[miracle ozzoude]

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Thanks Doug for your answer.
However, I got the same error when I tried replacing 29 with 3. I also
tried --replace 29 2 but gave a similar error.
I've attached the gtmseg.ctab and seg.replace.list

Replacing 19
Pruning ctab
ERROR: CTABpruneCTab(): ctab does not have segid 3
Checking tissue type
/users/surface-based_analyses/pet_base_SUVR_fromcoregstep_nopvc.sh: line
98: 16610 Segmentation fault  mri_gtmpvc --i ${pet} --reg ${reg_lta}
--psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask
${var_automask} ${mgx} --mgx ${mgx} --o ${gtm_out_nopvc} --rescale ${nr}
--replace 29 3



On Fri, Feb 5, 2021 at 1:45 PM miracle ozzoude  wrote:

> Hi Doug,
>
> I followed the processing workflow as described on the PETSurfer wiki and
> gtmseg.mgz was created, but included a warning for only one of my subjects:
>
> WARNING: segid  29 Left-undetermined tissue type is not set
> Writing output file to /ID/mri/gtmseg.mgz
> Writing colortable to /ID/mri/gtmseg.ctab
> Writing lta file to /ID/mri/gtmseg.lta
>
> Next, I ran both pvc and non-pvc. However, the non-pvc failed, whereas the
> pvc did not. These are the commands I ran and the error I got for non-pvc:
>
> mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg
> gtmseg.mgz --default-seg-merge --auto-mask PSF 0.01 --mgx 0.01 --o
> /gtmnopvc.output.ref --rescale 8 47
> vgthresh 0.001000
> nReplace 18
> 0. 0. 0. 0. 0. 0.
> 24 avail.processors, using 1
> Creating output directory /gtmnopvc.output.ref
> Loading seg for gtm /ID/mri/gtmseg.mgz
> Loading seg ctab /ID/mri/gtmseg.ctab
> Reading /ID/mri/gtmseg.lta
> Replacing 18
> Pruning ctab
> Checking tissue type
> ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not
> set
> Failed tissue type check
>
> Also , in the aux folder of non-pvc, only limited amount of files were
> created, including:
> Mask.nii, seg.ctab, seg.nii, seg.replace.list, seg.vol.nii
> Any idea why only the non-pvc failed ? Any help would be greatly
> appreciated!
>
> Many thanks
>


seg.replace.list
Description: Binary data


gtmseg.ctab
Description: Binary data
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[Freesurfer] non-pvc processing error

[miracle ozzoude]

External Email - Use Caution

Hi Doug,

I followed the processing workflow as described on the PETSurfer wiki and
gtmseg.mgz was created, but included a warning for only one of my subjects:

WARNING: segid  29 Left-undetermined tissue type is not set
Writing output file to /ID/mri/gtmseg.mgz
Writing colortable to /ID/mri/gtmseg.ctab
Writing lta file to /ID/mri/gtmseg.lta

Next, I ran both pvc and non-pvc. However, the non-pvc failed, whereas the
pvc did not. These are the commands I ran and the error I got for non-pvc:

mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg
gtmseg.mgz --default-seg-merge --auto-mask PSF 0.01 --mgx 0.01 --o
/gtmnopvc.output.ref --rescale 8 47
vgthresh 0.001000
nReplace 18
0. 0. 0. 0. 0. 0.
24 avail.processors, using 1
Creating output directory /gtmnopvc.output.ref
Loading seg for gtm /ID/mri/gtmseg.mgz
Loading seg ctab /ID/mri/gtmseg.ctab
Reading /ID/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set
Failed tissue type check

Also , in the aux folder of non-pvc, only limited amount of files were
created, including:
Mask.nii, seg.ctab, seg.nii, seg.replace.list, seg.vol.nii
Any idea why only the non-pvc failed ? Any help would be greatly
appreciated!

Many thanks
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Re: [Freesurfer] extracting mask for basal ganglia, deep grey, and centrum semiovale

[miracle ozzoude]

External Email - Use Caution

Nevermind. I didn't see your initial reply Doug. Thanks alot.

Best,
Paul

On Wed, Dec 2, 2020 at 1:35 PM miracle ozzoude  wrote:

> Any help with this will be greatly appreciated.
> Thanks.
>
> -- Forwarded message -----
> From: miracle ozzoude 
> Date: Fri, Nov 27, 2020 at 9:28 AM
> Subject: extracting mask for basal ganglia, deep grey, and centrum
> semiovale
> To: Douglas N Greve 
>
>
> Hello Experts,
>
> I did like to create a mask for basal ganglia, deep grey matter, and
> centrum semiovale. I know how to extract the mask for the first 2 (using
> aseg.mgz) however, how do I extract the last one. What mask should I use to
> extract the centrum semiovale? I don't want to include the cerebellar white
> matter.
>
> Thanks.
>
> Best,
> Paul
>
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[Freesurfer] Fwd: extracting mask for basal ganglia, deep grey, and centrum semiovale

[miracle ozzoude]

External Email - Use Caution

Any help with this will be greatly appreciated.
Thanks.

-- Forwarded message -
From: miracle ozzoude 
Date: Fri, Nov 27, 2020 at 9:28 AM
Subject: extracting mask for basal ganglia, deep grey, and centrum semiovale
To: Douglas N Greve 


Hello Experts,

I did like to create a mask for basal ganglia, deep grey matter, and
centrum semiovale. I know how to extract the mask for the first 2 (using
aseg.mgz) however, how do I extract the last one. What mask should I use to
extract the centrum semiovale? I don't want to include the cerebellar white
matter.

Thanks.

Best,
Paul
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[Freesurfer] extracting mask for basal ganglia, deep grey, and centrum semiovale

[miracle ozzoude]

External Email - Use Caution

Hello Experts,

I did like to create a mask for basal ganglia, deep grey matter, and
centrum semiovale. I know how to extract the mask for the first 2 (using
aseg.mgz) however, how do I extract the last one. What mask should I use to
extract the centrum semiovale? I don't want to include the cerebellar white
matter.

Thanks.

Best,
Paul
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Re: [Freesurfer] grey matter thickness map and SNR

[miracle ozzoude]

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Hello Doug,

Any advantages of surface-based smoothing of the gm thickness maps beside
increasing signal to noise ratio? I read the paper and based on the results
and conclusion, mcz with higher threshold and fwhm should be fine (though
permutation is recommended) for thickness.

best,
paul


On Wed, Sep 30, 2020 at 10:37 AM miracle ozzoude 
wrote:

> Thank you very much Doug. I appreciate it. I guess we will have to redo
> our analyses based using permutation and hope the results are the same
>
>
> On Wed, Sep 30, 2020 at 10:22 AM Douglas N. Greve 
> wrote:
>
>>
>> For statistical analysis, the reviewer is right, see
>> https://pubmed.ncbi.nlm.nih.gov/29288131
>> We are recommending permutation analysis, see
>>
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>> or
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
>>
>> On 9/30/2020 9:23 AM, miracle ozzoude wrote:
>>
>> External Email - Use Caution
>> Hello Experts,
>>
>> I have a question regarding grey matter thickness map and signal to noise
>> ratio. Does smoothing of the map increase signal to noise during surface
>> based cortical thickness analyses? if yes or no, why? This question was
>> asked by a reviewer in one of our manuscript because he/she thinks that one
>> of the reasons to perform smoothing is to comply with random field theory
>> hypotheses, when controlling for multiple testing.
>>
>> We did apply multiple comparison corrections using monte carlo simulation
>> with cluster threshold of 2, 5000 iterations, and bonferroni.
>>
>> Thanks alot.
>>
>> best,
>> Paul
>>
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>
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Re: [Freesurfer] grey matter thickness map and SNR

[miracle ozzoude]

External Email - Use Caution

Thank you very much Doug. I appreciate it. I guess we will have to redo our
analyses based using permutation and hope the results are the same


On Wed, Sep 30, 2020 at 10:22 AM Douglas N. Greve 
wrote:

>
> For statistical analysis, the reviewer is right, see
> https://pubmed.ncbi.nlm.nih.gov/29288131
> We are recommending permutation analysis, see
>
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
> or
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
>
> On 9/30/2020 9:23 AM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Hello Experts,
>
> I have a question regarding grey matter thickness map and signal to noise
> ratio. Does smoothing of the map increase signal to noise during surface
> based cortical thickness analyses? if yes or no, why? This question was
> asked by a reviewer in one of our manuscript because he/she thinks that one
> of the reasons to perform smoothing is to comply with random field theory
> hypotheses, when controlling for multiple testing.
>
> We did apply multiple comparison corrections using monte carlo simulation
> with cluster threshold of 2, 5000 iterations, and bonferroni.
>
> Thanks alot.
>
> best,
> Paul
>
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[Freesurfer] grey matter thickness map and SNR

[miracle ozzoude]

External Email - Use Caution

Hello Experts,

I have a question regarding grey matter thickness map and signal to noise
ratio. Does smoothing of the map increase signal to noise during surface
based cortical thickness analyses? if yes or no, why? This question was
asked by a reviewer in one of our manuscript because he/she thinks that one
of the reasons to perform smoothing is to comply with random field theory
hypotheses, when controlling for multiple testing.

We did apply multiple comparison corrections using monte carlo simulation
with cluster threshold of 2, 5000 iterations, and bonferroni.

Thanks alot.

best,
Paul
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Re: [Freesurfer] extracting clusters for each timepoints for longitudinal analyses

[miracle ozzoude]

External Email - Use Caution

Lovely. Thank you very much Doug. I appreciate your help.

Best,
Paul

On Tue, Jun 16, 2020 at 12:41 PM Douglas N. Greve 
wrote:

> ok, still  pretty easy
>
> mri_segstats --seg ocn.mgh --exclude 0 --i timepoint1.mgh --avgwf
> timepoint1.table.dat
>
> where
> ocn.mgh is something like cache.th13.abs.sig.ocn.mgh
> timepoint1.mgh is the stack of timepoint 1 for all subjects
> The output will be a table with subjects on the rows and clusters on the
> columns
>
> On 6/16/2020 12:28 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Thanks Doug.
>
> I ran multiple comparisons to get the clusters. However, I want to extract
> the clusters values for the individual timepoints. The paired t-test does a
> paired-difference (timepoint1 - timepoint2) and I presume the significant
> clusters come from the difference image used in mri_glmfit. My goal is to
> extract the clusters values for each of the timepoints not
> paired-difference. This is a surface-based analysis.
>
> Best,
> Paul
>
> On Tue, Jun 16, 2020 at 11:35 AM Douglas N. Greve 
> wrote:
>
>> did you run the correction for multiple comparisons to get your
>> clusters? If so, then there should be a table with a row for each subject
>> and a column for each cluster.
>>
>> On 6/16/2020 11:03 AM, miracle ozzoude wrote:
>>
>> External Email - Use Caution
>> Hello,
>>
>> I ran a pet longitudinal paired t-test analysis with 2 timepoints using
>> mri_glmfit and I found significant clusters. I want to extract the values
>> of these significant clusters for each timepoints. How do I go about doing
>> this?
>>
>> Thank you.
>>
>> Best,
>> Paul.
>>
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Re: [Freesurfer] extracting clusters for each timepoints for longitudinal analyses

[miracle ozzoude]

External Email - Use Caution

Thanks Doug.

I ran multiple comparisons to get the clusters. However, I want to extract
the clusters values for the individual timepoints. The paired t-test does a
paired-difference (timepoint1 - timepoint2) and I presume the significant
clusters come from the difference image used in mri_glmfit. My goal is to
extract the clusters values for each of the timepoints not
paired-difference. This is a surface-based analysis.

Best,
Paul

On Tue, Jun 16, 2020 at 11:35 AM Douglas N. Greve 
wrote:

> did you run the correction for multiple comparisons to get your  clusters?
> If so, then there should be a table with a row for each subject and a
> column for each cluster.
>
> On 6/16/2020 11:03 AM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Hello,
>
> I ran a pet longitudinal paired t-test analysis with 2 timepoints using
> mri_glmfit and I found significant clusters. I want to extract the values
> of these significant clusters for each timepoints. How do I go about doing
> this?
>
> Thank you.
>
> Best,
> Paul.
>
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[Freesurfer] extracting clusters for each timepoints for longitudinal analyses

[miracle ozzoude]

External Email - Use Caution

Hello,

I ran a pet longitudinal paired t-test analysis with 2 timepoints using
mri_glmfit and I found significant clusters. I want to extract the values
of these significant clusters for each timepoints. How do I go about doing
this?

Thank you.

Best,
Paul.
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Re: [Freesurfer] negative SUVr using PETsurfer

[miracle ozzoude]

External Email - Use Caution

Thanks Doug. we double checked the registration with gtm.seg.mgz and it
looks good. Also the uptake in Acc is not much smaller than other regions
and is pretty similar on both hemispheres so we are not sure what could be
causing this. Any suggestions much appreciated.

Many thanks

Paul

On Mon, Dec 2, 2019 at 5:15 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> It may or may not be something that needs to be fixed. The PVC is just a
> linear model where the regression coefficients are the uptake in each ROI.
> As with any model, it adjusts the regression coefs to minimize the error in
> the fit. If some end up being less than zero when you really expect all to
> be > 0, then this probably indicates an error in the (linear) model. This
> error could come from several sources. For example, the registration could
> be off. The PSF might not be right. Or the uptake might not be constant
> across the ROIs. You should definitely start by checking the registration.
> If the uptake in Nuc Acc is very small relative to other ROIs, then I would
> just leave it the way it is, ie, DON'T just set it to 0 when you go to a
> group analysis.
>
> On 12/2/2019 4:48 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Hello Experts,
>
> I ran the PETsurfer pipeline using AV45 pet and performed pvc using pons
> as reference point. When i looked at the gtm.stats.dat file for one of my
> subjects, the SUVr for right and left nucleus-accumbens areas were in the
> negative (left = -0.361; right = -0.046).
>
> This is strange because SUVR shouldn't be negative. How do i go about
> fixing this error? Below, is my pvc command.
> mri_gtmpvc --i pet.nii --reg register.lta --psf 6 --seg gtmseg.mgz
> --default--seg-merge --auto-mask PSF .01 --mgx .01 --o subject_gtmpvc
> --rescale 174
>
> Thanks.
>
> Best,
> Paul
>
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[Freesurfer] negative SUVr using PETsurfer

[miracle ozzoude]

External Email - Use Caution

Hello Experts,

I ran the PETsurfer pipeline using AV45 pet and performed pvc using pons as
reference point. When i looked at the gtm.stats.dat file for one of my
subjects, the SUVr for right and left nucleus-accumbens areas were in the
negative (left = -0.361; right = -0.046).

This is strange because SUVR shouldn't be negative. How do i go about
fixing this error? Below, is my pvc command.
mri_gtmpvc --i pet.nii --reg register.lta --psf 6 --seg gtmseg.mgz
--default--seg-merge --auto-mask PSF .01 --mgx .01 --o subject_gtmpvc
--rescale 174

Thanks.

Best,
Paul
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[Freesurfer] subcortical volume-based pet analysis

[miracle ozzoude]

External Email - Use Caution

Hello Experts,

I do have couple questions about using mri_glmfit and mri_glmfit-sim for
this analysis based on the tutorial page.
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
 1) Do i have to add any other flags when using mri_glmfit for this
analysis?
mri_glmfit --y ${results_dir}/all.mgx.subctxgm.mni305.sm05.nii.gz --fsgd
$pet_fsgd --C $matrix1 \
--mask ${SUBJECTS_DIR}/fsaverage/mri.2mm/subcort.mask.mgz --glmdir
${results_dir}/sub.pet.B6.glmdir
2) When correcting for multiple comparisons, should i use --2spaces or
--3spaces?
3) I ran a paired ttest analysis using age as regressor of no interest for
amyloid uptake. My contrast is  "1 0" based on the tutorial
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis.
How do i interpret the direction of contrast if I get a result from
mri_glmfit-sim (see below)? This is because it doesn't have the Max column
for surface based analysis
# Cluster   Size(n)   Size(mm^3) MNIX   MNIYMNIZ  Max
 CWPCWPLowCWPHi
  112709  101672.0  26.00  -69.00  -41.00   5.46844
 0.01037  0.00798  0.01316  Right-Cerebellum-White-Matter


Thank you.
best,
Paul
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[Freesurfer] covariate with repeated anova

[miracle ozzoude]

External Email - Use Caution

Hello Experts,

I would like to include covariates in the freesurfer repeated anova steps
https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. When i
tried including 3 covariates, mri_glmfit complained about "martix is
ill-conditioned".

How do i fix it?

Below is an example my fsgd file. I've also attached the matrix design in
the email.

GroupDescriptorFile 1
Class PsyDis1
Class PsyDis2
Variables TP1vsTP2 Age Llesion Rlesion
Input Psy1_Pre.long.Psy1 PsyDis1 1 68 96 61
Input Psy1_6mos.long.Psy1 PsyDis1 -1 68 96 61
Input Psy2_Pre.long.Psy2 PsyDis2 1 39 217 140
Input Psy2_6mos.long.Psy2 PsyDis2 -1 39 217 140

contrast: 0 0 1 0 0

Best,
Paul


Xg.dat
Description: Binary data
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[Freesurfer] paired t-test for pet surface analysis

[miracle ozzoude]

External Email - Use Caution

Hello Freesurfer,

I am trying to run a surface based paired ttest for pet. I started by
running mri_vol2surf for each pet longitudinal subject. However, when i use
mri_concat with --f, --prune, and --paired-diff i get an error
" --paired-xxx specified but there are an odd number of frames". I have 4
subjects, 3 has 3 timepoints and 1 has 2 timepoints (total of 11 frames).
Below are my commands and full errors.

How do I solve this problem?

best,
Paul


*COMMANDS* mri_vol2surf --mov
$in_dir/${session}.gtmpvc.output/mgx.ctxgm.nii.gz --reg
$in_dir/${session}.gtmpvc.output/aux/bbpet2anat.lta --hemi lh --projfrac
0.5 \
 --o $in_dir/lh.mgx.ctxgm.${session}.fsaverage.sm00.nii.gz --cortex
--trgsubject fsaverage

{ echo $in_dir/lh.mgx.ctxgm.${session}.fsaverage.sm00.nii.gz; } >> $lhmgxctx

#concatenate the surface pets
mri_concat --f "$lhmgxctxgm" --o
${results_dir}/all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --prune --paired-diff

session=subject_basline.long.baseid (e.g. 001_baseline.long.001,
001_12mon.long.001 etc)

lhmgxctx = text file containing the pet volumes mapped to the surface for
each timepoints. (e.g.
/Analysis/001_baseline.long.001/lh.mgx.ctxgm.001_baseline.long.001.fsaverage.sm00.nii.gz
/Analysis/001_12mon.long.001/lh.mgx.ctxgm.001_12mon.long.001.fsaverage.sm00.nii.gz
etc.)

*ERRORS*
+ mri_concat --f Analysis/lh_hemi_ctxgm.txt --o
Analysis/results/all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz --prune
--paired-diff-norm1
ninputs = 11
Checking inputs
nframestot = 11
ERROR: --paired-xxx specified but there are an odd number of frames
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Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr

[miracle ozzoude]

External Email - Use Caution

Thanks Doug. Another question, how do i find the p-values for voxel-wise
map corrected for multiple comparisons at a voxel (rather than cluster)
level (perm.th40.abs.sig.voxel.mgh). There is no summary file for it.
Best,
Paul

On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> The 3 spaces is for left hemi, right hemi, and subcortical, so, if you
> are using all three then correct for all 3
>
> On 8/7/19 9:26 AM, miracle ozzoude wrote:
> >
> > External Email - Use Caution
> >
> > Got it. Thanks a lot doug. If i have to correct for multiple
> > comparison in surface based pet analysis and mutlimodal analysis (pet
> > and thickness), should i use --3spaces?
> > Thank you.
> >
> > best,
> > Paul
> >
> > On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > I think there is still something not right. You should just have
> > one mri_glmfit command for each hemisphere in which the input is
> > ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then
> > specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz
> > --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The
> > second is the same as the first but with a reversed sign, but it
> >     is not necessary since we always use unsigned tests and show both
> > signs (but you can still do it).
> >
> > On 8/5/2019 8:14 PM, miracle ozzoude wrote:
> >>
> >> External Email - Use Caution
> >>
> >> I think i got it now. Something like this:
> >>
> >> ## group1 comes first in my fsgd file. removing the effects of
> >> age and education
> >> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2.
> >> mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c
> >> pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \
> >> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz  -surf
> >> fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir
> >> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c
> >> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \
> >> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage
> >> lh --cortex --glmdir rh.pet.thickness.glmdir
> >>
> >> contrast =  0 0 0 0 0 0 1 -1
> >>
> >> ##group 2 is second in my fsgd file. removing the effects of age
> >> and education
> >> ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2
> >>  mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c
> >> pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \
> >> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
> >> rh.pet.thickness.glmdir
> >> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c
> >> pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \
> >> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
> >> rh.pet.thickness.glmdir
> >>
> >> contrast = 0 0 0 0 0 0 -1 1
> >>
> >> On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D.
> >> mailto:dgr...@mgh.harvard.edu>> wrote:
> >>
> >> It still looks like you are using a group specific input
> >> (--y). The input should be a simple file with both groups
> >> (same input as you would use without pvr)
> >>
> >> On 8/5/2019 4:39 PM, miracooloz wrote:
> >>>
> >>> External Email - Use Caution
> >>>
> >>> Thanks Doug. How about the mri_glmfit commands? Since the
> >>> contrasts are correct, I think the commands should be right.
> >>>
> >>> Best,
> >>> Paul.
> >>>
> >>>
> >>>
> >>> Sent from my Samsung Galaxy smartphone.
> >>>
> >>>  Original message 
> >>> From: "Greve, Douglas N.,Ph.D." 
> >>> <mailto:dgr...@mgh.harvard.edu>
> >>> Date: 2019-08-05 15:52 (GMT-05:00)
> >>> To: freesurfer@nmr.mgh.harvard.edu
> >>> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >>> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and
> >>> cortical thicknes

Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr

[miracle ozzoude]

External Email - Use Caution

Got it. Thanks a lot doug. If i have to correct for multiple comparison in
surface based pet analysis and mutlimodal analysis (pet and thickness),
should i use --3spaces?
Thank you.

best,
Paul

On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> I think there is still something not right. You should just have one
> mri_glmfit command for each hemisphere in which the input is
> ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then specify the
> pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz --pvr
> ?h.pvr_grp2_pet.niigz) and then use that first contrast. The second is the
> same as the first but with a reversed sign, but it is not necessary since
> we always use unsigned tests and show both signs (but you can still do it).
>
> On 8/5/2019 8:14 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> I think i got it now. Something like this:
>
> ## group1 comes first in my fsgd file. removing the effects of age and
> education
> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2.
> mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx
> --pvr  lh.pvr_grp1_pet.nii.gz \
> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz  -surf fsaverage lh
> --cortex --glmdir lh.pet.thickness.glmdir
> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx
> --pvr rh.pvr_grp1_pet.nii.gz \
> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh
> --cortex --glmdir rh.pet.thickness.glmdir
>
> contrast =  0 0 0 0 0 0 1 -1
>
> ##group 2 is second in my fsgd file. removing the effects of age and
> education
> ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2
>  mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx
> --pvr  allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \
> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
> rh.pet.thickness.glmdir
> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx
> --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \
> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
> rh.pet.thickness.glmdir
>
> contrast = 0 0 0 0 0 0 -1 1
>
> On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> It still looks like you are using a group specific input (--y). The input
>> should be a simple file with both groups (same input as you would use
>> without pvr)
>>
>> On 8/5/2019 4:39 PM, miracooloz wrote:
>>
>> External Email - Use Caution
>> Thanks Doug. How about the mri_glmfit commands? Since the contrasts are
>> correct, I think the commands should be right.
>>
>> Best,
>> Paul.
>>
>>
>>
>> Sent from my Samsung Galaxy smartphone.
>>
>>  Original message 
>> From: "Greve, Douglas N.,Ph.D." 
>> 
>> Date: 2019-08-05 15:52 (GMT-05:00)
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical
>> thickness relationship) using --pvr
>>
>> Yes, that contrast is correct.
>>
>> On 8/5/2019 3:11 PM, miracle ozzoude wrote:
>>
>> External Email - Use Caution
>> Hello Doug,
>>
>> Thanks very much for your help. Your assumption was right in that i want
>> to run a group comparison (i.e. test for a difference in amyloid-thickness
>> slopes between the two groups). However, I am having a hard time creating
>> the correct mri_glmfit and contrasts in this case. Based on your advice and
>> searching through the forum (
>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html),
>>  i
>> need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it
>> another shot below. Please let me know if i am correct.
>>
>> Thank you.
>> Paul.
>>
>> ## group1 comes first in my fsgd file. removing the effects of age and
>> education
>> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2.
>> mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c
>> pvr1.mtx --pvr  lh.pvr_grp1_pet.nii.gz \
>> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz  -surf fsaverage lh
>> --cortex --glmdir lh.pet.thickness.glmdir
>> mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c
>> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \
>> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh
>> --cortex --glmdir rh.pet.thickness.glmdir
>>
>> contrast =  0 0 0 0 0 0 1 -1
>>
>> ##group 2 is secon

Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr

[miracle ozzoude]

External Email - Use Caution

I think i got it now. Something like this:

## group1 comes first in my fsgd file. removing the effects of age and
education
##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2.
mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx
--pvr  lh.pvr_grp1_pet.nii.gz \
--pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz  -surf fsaverage lh
--cortex --glmdir lh.pet.thickness.glmdir
mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr1.mtx
--pvr rh.pvr_grp1_pet.nii.gz \
--pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh
--cortex --glmdir rh.pet.thickness.glmdir

contrast =  0 0 0 0 0 0 1 -1

##group 2 is second in my fsgd file. removing the effects of age and
education
##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2
 mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx
--pvr  allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \
--pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
rh.pet.thickness.glmdir
mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c pvr2.mtx
--pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \
--pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
rh.pet.thickness.glmdir

contrast = 0 0 0 0 0 0 -1 1

On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> It still looks like you are using a group specific input (--y). The input
> should be a simple file with both groups (same input as you would use
> without pvr)
>
> On 8/5/2019 4:39 PM, miracooloz wrote:
>
> External Email - Use Caution
> Thanks Doug. How about the mri_glmfit commands? Since the contrasts are
> correct, I think the commands should be right.
>
> Best,
> Paul.
>
>
>
> Sent from my Samsung Galaxy smartphone.
>
>  Original message 
> From: "Greve, Douglas N.,Ph.D." 
> 
> Date: 2019-08-05 15:52 (GMT-05:00)
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical
> thickness relationship) using --pvr
>
> Yes, that contrast is correct.
>
> On 8/5/2019 3:11 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Hello Doug,
>
> Thanks very much for your help. Your assumption was right in that i want
> to run a group comparison (i.e. test for a difference in amyloid-thickness
> slopes between the two groups). However, I am having a hard time creating
> the correct mri_glmfit and contrasts in this case. Based on your advice and
> searching through the forum (
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html),
>  i
> need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it
> another shot below. Please let me know if i am correct.
>
> Thank you.
> Paul.
>
> ## group1 comes first in my fsgd file. removing the effects of age and
> education
> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2.
> mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c
> pvr1.mtx --pvr  lh.pvr_grp1_pet.nii.gz \
> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz  -surf fsaverage lh
> --cortex --glmdir lh.pet.thickness.glmdir
> mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c
> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \
> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh
> --cortex --glmdir rh.pet.thickness.glmdir
>
> contrast =  0 0 0 0 0 0 1 -1
>
> ##group 2 is second in my fsgd file. removing the effects of age and
> education
> ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2
>  mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c
> pvr2.mtx --pvr  allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \
> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
> rh.pet.thickness.glmdir
> mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c
> pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \
> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
> rh.pet.thickness.glmdir
>
> contrast = 0 0 0 0 0 0 -1 1
>
>
> On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> That  mostly looks good.
>>
>> I would suggest is to change your smoothing command to something like
>> mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune
>> --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz
>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz
>> The only difference will be that any vertices that are 0 in the input
>> will be excluded (pruned) from the smoothing mask.
>>
>> The mri_glmfit command is not right. That command looks like it is f

Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr

[miracle ozzoude]

External Email - Use Caution

Hello Doug,

Thanks very much for your help. Your assumption was right in that i want to
run a group comparison (i.e. test for a difference in amyloid-thickness
slopes between the two groups). However, I am having a hard time creating
the correct mri_glmfit and contrasts in this case. Based on your advice and
searching through the forum (
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html),
i
need 2 PVRs for each hemisphere in the mri_glmfit command. I gave it
another shot below. Please let me know if i am correct.

Thank you.
Paul.

## group1 comes first in my fsgd file. removing the effects of age and
education
##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2.
mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c
pvr1.mtx --pvr  lh.pvr_grp1_pet.nii.gz \
--pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz  -surf fsaverage lh
--cortex --glmdir lh.pet.thickness.glmdir
mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd project.fsgd dods --c
pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \
--pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage lh
--cortex --glmdir rh.pet.thickness.glmdir

contrast =  0 0 0 0 0 0 1 -1

##group 2 is second in my fsgd file. removing the effects of age and
education
##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2
 mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c
pvr2.mtx --pvr  allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \
--pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
rh.pet.thickness.glmdir
mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd project.fsgd dods --c
pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \
--pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir
rh.pet.thickness.glmdir

contrast = 0 0 0 0 0 0 -1 1


On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> That  mostly looks good.
>
> I would suggest is to change your smoothing command to something like
> mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm 5 --cortex --prune
> --i allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz
> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz
> The only difference will be that any vertices that are 0 in the input will
> be excluded (pruned) from the smoothing mask.
>
> The mri_glmfit command is not right. That command looks like it is for
> analyzing each group separately and independently. If that is what you want
> to do, then you don't need to go through all the extra stuff of creating
> zero files, etc. I had assumed that you wanted to do some kind of
> comparison between groups. If so, then you would use a single file with all
> your data in it (probably what you were using before), and your fsgd file
> would have both groups.
>
> 1) will my fsgd file contain both groups?
> yes, see above
> 2) If the answer from question is yes, i should have 2 contrasts (pvr1.mtx
> for group1 and pvr2.mtx for group2). yes/no?
> Again, if all you want to do is to test the pvr for each group separately,
> then you don't need to go through the processes of creating zero files,
> etc. In any event, if you want to test a pvr, then you need a contrast for
> it.
> 3) below is a sample of my fsgd file. are the constrasts correct?
> hard to say without resolving the questions above. You will need to have a
> value in the contrast for each pvr.
>
>
>
> On 8/2/2019 3:56 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Hello Doug,
>
> Thanks for answering. Based on your explanation, i wrote out a series of
> command needed to execute this. Please let me know if i made any
> mistakes/correct.
> ##step1 concatenating the 10 amyloid pet volumes files projected to
> surface using mri_vol2surf for group1
> mri_concat --f grp1.lhmgxctx --o allgrp1.lhmgxctx.fsaverage.sm00.nii.gz
> --prune
> mri_concat --f grp2.rhmgxctx --o allgrp1.rhmgxctx.fsaverage.sm00.nii.gz
> --prune
>
> ##step2 concatenating the 20 amyloid pet volumes files projected to
> surface using mri_vol2surf for group2
> mri_concat --f grp2.lhmgxctx --o allgrp2.lhmgxctx.fsaverage.sm00.nii.gz
> --prune
> mri_concat --f grp2.rhmgxctx --o allgrp2.rhmgxctx.fsaverage.sm00.nii.gz
> --prune
>
> ##step3 smooth on the surface for each hemisphere for group1
> mri_surf2surf --hemi lh --s fsaverage --sval
> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval
> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz
> mri_surf2surf --hemi rh --s fsaverage --sval
> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --cortex --tval
> allgrp1.rhmgxctx.fsaverage.sm05.nii.gz
>
> ##step4 smooth on the surface for each hemisphere for group2
> mri_surf2surf --hemi lh --s fsaverage --sval
> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 --c

Re: [Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr

[miracle ozzoude]

h 10 frames the other 20 frames). Then create the file of zeros using
> fscalc group2.mgz mul 0 -o group2.zeros.mgz
> Then
> mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz
> Then create the contrast based on the FSGD, but then add two more numbers,
> one for PVR1 (which tests for the within group correlation), and one for
> PVR2
>
>
> On 8/1/2019 3:14 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Please, can anyone help me with this.
> Thank you
>
> Paul
>
> -- Forwarded message -
> From: miracle ozzoude 
> Date: Wed, Jul 31, 2019 at 2:11 PM
> Subject: multimodal analysis (pet and cortical thickness relationship)
> using --pvr
> To: Douglas N Greve 
>
>
> Hello Experts,
>
> I am performing an analysis looking at the relationship between amyloid
> uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups
> and 2 variables (age and education). I want to run a within group analysis
> while regressing out age and education (i.e. Within group 1, is there a
> negative relationship between amyloid uptake and cortical thickness
> regressing out the effects of age and education).
>
> However, i'm not sure how my pvr contrasts will look like. Below are my
> fsgd and an attempt at creating contrasts. Please, can you let me know if
> my contrasts are correct based on my questions.
>
> Thank you.
>
> Best,
> Paul
>
> The fsgd file lists:
> -
> GroupDescriptorFile 1
> Title Relationship Amy-thick reg out age and education
> Class g1
> Class g2
>
> Variable Age Education
> Input XX1 g1 60 16
> Input XX2 g1 58 14
>
> Input YY1 g2 62 20
>
> Input YY1 g2 62 20
>
> -
>
> matrix for group1:
>
> pvrgroup1= 1 0 0 0 0 0 0
>
> is there a relationship between amyloid-thickness in group1 regressing out age
>
> and education?
>
> matrix for group2:
>
> pvrgroup2= 0 1 0 0 0 0 0
>
> is there a relationship between amyloid-thickness in group2 regressing out age
>
> and education?
>
>
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[Freesurfer] Fwd: multimodal analysis (pet and cortical thickness relationship) using --pvr

[miracle ozzoude]

External Email - Use Caution

Please, can anyone help me with this.
Thank you

Paul

-- Forwarded message -
From: miracle ozzoude 
Date: Wed, Jul 31, 2019 at 2:11 PM
Subject: multimodal analysis (pet and cortical thickness relationship)
using --pvr
To: Douglas N Greve 


Hello Experts,

I am performing an analysis looking at the relationship between amyloid
uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups
and 2 variables (age and education). I want to run a within group analysis
while regressing out age and education (i.e. Within group 1, is there a
negative relationship between amyloid uptake and cortical thickness
regressing out the effects of age and education).

However, i'm not sure how my pvr contrasts will look like. Below are my
fsgd and an attempt at creating contrasts. Please, can you let me know if
my contrasts are correct based on my questions.

Thank you.

Best,
Paul

The fsgd file lists:
-
GroupDescriptorFile 1
Title Relationship Amy-thick reg out age and education
Class g1
Class g2

Variable Age Education
Input XX1 g1 60 16
Input XX2 g1 58 14

Input YY1 g2 62 20

Input YY1 g2 62 20

-

matrix for group1:

pvrgroup1= 1 0 0 0 0 0 0

is there a relationship between amyloid-thickness in group1 regressing out age

and education?

matrix for group2:

pvrgroup2= 0 1 0 0 0 0 0

is there a relationship between amyloid-thickness in group2 regressing out age

and education?
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[Freesurfer] multimodal analysis (pet and cortical thickness relationship) using --pvr

[miracle ozzoude]

External Email - Use Caution

Hello Experts,

I am performing an analysis looking at the relationship between amyloid
uptake and cortical thickness using --pvr flag in mri_glmfit. I've 2 groups
and 2 variables (age and education). I want to run a within group analysis
while regressing out age and education (i.e. Within group 1, is there a
negative relationship between amyloid uptake and cortical thickness
regressing out the effects of age and education).

However, i'm not sure how my pvr contrasts will look like. Below are my
fsgd and an attempt at creating contrasts. Please, can you let me know if
my contrasts are correct based on my questions.

Thank you.

Best,
Paul

The fsgd file lists:
-
GroupDescriptorFile 1
Title Relationship Amy-thick reg out age and education
Class g1
Class g2

Variable Age Education
Input XX1 g1 60 16
Input XX2 g1 58 14

Input YY1 g2 62 20

Input YY1 g2 62 20

-

matrix for group1:

pvrgroup1= 1 0 0 0 0 0 0

is there a relationship between amyloid-thickness in group1 regressing out age

and education?

matrix for group2:

pvrgroup2= 0 1 0 0 0 0 0

is there a relationship between amyloid-thickness in group2 regressing out age

and education?
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Re: [Freesurfer] Single SUVr for PETsurfer

[miracle ozzoude]

External Email - Use Caution

thanks doug

paul

On Wed, Jul 3, 2019 at 4:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> yes
>
> On 7/3/2019 4:03 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> E.g. if there are 68 ROIs, single SUVr for each subject will be:
>
> (# of voxels in ROI 1*(suvr of ROI1 ) + +  # of voxels in ROI
> 68*(suvr of ROI 68))
> _ __
> (# of voxels in ROI 1 + .. # of voxels in ROI 68)
>
> On Wed, Jul 3, 2019 at 3:45 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> You can look in the gtm.stats file for all the cortical ROIs. Multiply
>> the uptake value by the number of voxels in the ROI and then divide by the
>> sum of the number of voxels across all ROIs. See
>> https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer here for the
>> identity of the columns in the  gtm.stats file
>>
>> On 7/3/2019 3:36 PM, miracle ozzoude wrote:
>>
>> External Email - Use Caution
>> Over the cortex.
>>
>>
>> On Wed, Jul 3, 2019 at 2:59 PM Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> The mean over what area? Whole brain or just cortex?
>>>
>>> On 7/3/2019 2:15 PM, miracle ozzoude wrote:
>>>
>>> External Email - Use Caution
>>> Hello Expert,
>>>
>>> How do i get a single SUVr value for PETsurfer? Similar to
>>> Mean_Thickness from Freesurfer, I want to extract a global/Mean SUVr value
>>> for each of my subjects.
>>>
>>> Thank you.
>>>
>>> Paul
>>>
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>>>
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>>
>>
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>>
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>
>
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Re: [Freesurfer] Single SUVr for PETsurfer

[miracle ozzoude]

External Email - Use Caution

E.g. if there are 68 ROIs, single SUVr for each subject will be:

(# of voxels in ROI 1*(suvr of ROI1 ) + +  # of voxels in ROI
68*(suvr of ROI 68))
_ __
(# of voxels in ROI 1 + .. # of voxels in ROI 68)

On Wed, Jul 3, 2019 at 3:45 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> You can look in the gtm.stats file for all the cortical ROIs. Multiply the
> uptake value by the number of voxels in the ROI and then divide by the sum
> of the number of voxels across all ROIs. See
> https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer here for the identity
> of the columns in the  gtm.stats file
>
> On 7/3/2019 3:36 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Over the cortex.
>
>
> On Wed, Jul 3, 2019 at 2:59 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> The mean over what area? Whole brain or just cortex?
>>
>> On 7/3/2019 2:15 PM, miracle ozzoude wrote:
>>
>> External Email - Use Caution
>> Hello Expert,
>>
>> How do i get a single SUVr value for PETsurfer? Similar to Mean_Thickness
>> from Freesurfer, I want to extract a global/Mean SUVr value for each of my
>> subjects.
>>
>> Thank you.
>>
>> Paul
>>
>> ___
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>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
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Re: [Freesurfer] Single SUVr for PETsurfer

[miracle ozzoude]

External Email - Use Caution

Over the cortex.


On Wed, Jul 3, 2019 at 2:59 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> The mean over what area? Whole brain or just cortex?
>
> On 7/3/2019 2:15 PM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Hello Expert,
>
> How do i get a single SUVr value for PETsurfer? Similar to Mean_Thickness
> from Freesurfer, I want to extract a global/Mean SUVr value for each of my
> subjects.
>
> Thank you.
>
> Paul
>
> ___
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>
>
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> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Single SUVr for PETsurfer

[miracle ozzoude]

External Email - Use Caution

Hello Expert,

How do i get a single SUVr value for PETsurfer? Similar to Mean_Thickness
from Freesurfer, I want to extract a global/Mean SUVr value for each of my
subjects.

Thank you.

Paul
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Re: [Freesurfer] mri_gtmpvc on Tau and FDG PET

[miracle ozzoude]

External Email - Use Caution

Hello Doug,

Thanks for replying. Anything I should watch out for when using it for Tau
processing?

Thanks.

Best,
Paul

On Mon, Mar 25, 2019 at 11:19 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> It is certainly good for FDG. Tau is a little trickier, but I think it has
> been used. I think the reference region for tau is still an open question.
> For FDG, people often use pons.
>
> On 3/25/19 10:33 AM, miracle ozzoude wrote:
>
> External Email - Use Caution
> Hello FreeSurfer,
>
> I would like to know if mri_gtmpvc for PetSurfer is appropriate for Tau
> (AV_1451) and FDG pet imaging. Also, is cerebellum a good reference point
> for both tracers?
>
> Thanks.
> Paul
>
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[Freesurfer] mri_gtmpvc on Tau and FDG PET

[miracle ozzoude]

External Email - Use Caution

Hello FreeSurfer,

I would like to know if mri_gtmpvc for PetSurfer is appropriate for Tau
(AV_1451) and FDG pet imaging. Also, is cerebellum a good reference point
for both tracers?

Thanks.
Paul
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[Freesurfer] mri_gtmpvc for partial volume

[miracle ozzoude]

External Email - Use Caution

Hello,

Can i specify a lookup table when using mri_gtmpvc? This is because I have
a non-freesurfer segmentation (MALPEM) and i would like to perform partial
volume on it without having to run freesurfer on the subject for PET
analysis. I have a lookup table for the segmentation.

I know mri_gtmpvc expects (?.ctab) file from the segmentation however, it
will require processing the subject with freesurfer and petsurfer. I only
want to use the partial volume command. How do I make it use the lookup
table i made rather than  ?.ctab file?

Thank you.

Best,
Paul
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[Freesurfer] converting a color lookup table in csv to freesurfer format (.ctab)

[miracle ozzoude]

External Email - Use Caution

Hello,

How can I convert a csv color lookup table to freesurfer format (.ctab)? My
end goal is to use it to perform partial volume correction for an
atlas/segmentation different from default freesurfer atlas. The atlas has a
color lookup table however, mri_gtmpvc can't read it. The atlas is in nifti
format and is based on MAPLEM.
https://web.gin.g-node.org/doi/MALPEM_ADNI_data

Thanks.

best,
Paul
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[Freesurfer] recon-all with mri_ca_normalize (longitudinal)

[miracle ozzoude]

External Email - Use Caution

Hello FreeSurfer team,

In order to create the longitudinal base after norm.mgz, Is the command
below the right way to end recon-all after creating norm.mgz?

recon-all -s subjectID -autorecon1 -autorecon2  -i T1image -canorm.

Thank you.

Best,
Paul
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[Freesurfer] Fwd: error with mri_ca_register in long

[miracle ozzoude]

External Email - Use Caution

Hello,
Can anyone help me with this? I think it got lost in the pool of email.

Best,
Paul
-- Forwarded message --
From: miracle ozzoude 
Date: Thu, Jul 5, 2018 at 12:23 PM
Subject: error with mri_ca_register in long
To: Douglas N Greve 


Hello All,

When running the longitudinal pipeline for version 6, i encountered this
error " TransformSample: gcam has not been inverted!; Numerical result out
of range". I found a thread with similar error but the problem wasn't
solved. https://mail.nmr.mgh.harvard.edu/pipermail/
freesurfer/2017-April/051240.html.
Just like the previous thread, it happens whenever I include the
"-bigventricle" flag. Below is a sample of my recon-all scripts from
cross-sectional to longitudinal. The error.log and recon.log files are too
large to send. Thank you.

Best,
Paul

Cross-sectional
recon-all -s ${SUBJECTS_DIR}/$session -autorecon-all -i ${filename}
-hippocampal-subfields-T1 -parallel -openmp 20 -bigventricles -3T -time

Longitudinal
recon-all -base ${session} -tp "${tp1}" -tp "${tp2}" -all -parallel -openmp
20 -bigventricles -3T -time

recon-all -long ${tp1} ${session} -all -parallel -openmp 20 -bigventricles
-3T -time
recon-all -long ${tp2} ${session} -all -parallel -openmp 20 -bigventricles
-3T -time
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[Freesurfer] error with mri_ca_register in long

[miracle ozzoude]

External Email - Use Caution

Hello All,

When running the longitudinal pipeline for version 6, i encountered this
error " TransformSample: gcam has not been inverted!; Numerical result out
of range". I found a thread with similar error but the problem wasn't
solved.
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-April/051240.html
.
Just like the previous thread, it happens whenever I include the
"-bigventricle" flag. Below is a sample of my recon-all scripts from
cross-sectional to longitudinal. The error.log and recon.log files are too
large to send. Thank you.

Best,
Paul

Cross-sectional
recon-all -s ${SUBJECTS_DIR}/$session -autorecon-all -i ${filename}
-hippocampal-subfields-T1 -parallel -openmp 20 -bigventricles -3T -time

Longitudinal
recon-all -base ${session} -tp "${tp1}" -tp "${tp2}" -all -parallel -openmp
20 -bigventricles -3T -time

recon-all -long ${tp1} ${session} -all -parallel -openmp 20 -bigventricles
-3T -time
recon-all -long ${tp2} ${session} -all -parallel -openmp 20 -bigventricles
-3T -time
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Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

[miracle ozzoude]

External Email - Use Caution

My freesurfer home is /opt/freesurfer-6.0.0 which contains all the
necessary freesurfer binaries, .sh files etc in order for freesurfer to
run. I always include this in my shell script
export FREESURFER_HOME=/opt/freesurfer-6.0.0
source $FREESURFER_HOME/SetUpFreeSurfer.sh

On Thu, May 31, 2018 at 3:33 PM, miracle ozzoude 
wrote:

> Hello,
>
> I was able to solve the previous error (not finding the sources.sh)
> however, i have encountered another error (please find the attached
> hippocampal-subfileds-T1.log file). In this case, line 3 of kvlAutoCrop has
> a problem with kvlAutoCrop.bin
>
> Thanks,
> Best,
> Miracle
>
> On Wed, May 30, 2018 at 6:03 PM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
>> External Email - Use Caution
>>
>> Hard to tell without seeing the contents of the directories, but I'd put
>> my money on:
>>
>> export FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer
>>
>> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>>
>> recon-all ...
>>
>>
>> Juan Eugenio Iglesias
>>
>> Centre for Medical Image Computing (CMIC)
>>
>> University College London
>>
>> http://www.jeiglesias.com
>>
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <
>> miracoo...@gmail.com>
>> *Sent:* Wednesday, May 30, 2018 9:21:19 PM
>> *To:* Freesurfer support list
>>
>> *Subject:* Re: [Freesurfer] hippocampal subfield segmentation error
>> (fsv6.0)
>>
>>
>> External Email - Use Caution
>>
>> Thanks.
>>
>> So I changed it to " export FREESURFER_HOME=/opt/freesurfer-6.0.0;
>> source $FREESURFER_HOME/freesurfer/SetUpFreeSurfer.sh" (based on
>> printenv). However, when i tried to run my script i got another error
>> (/opt/freesurfer-6.0.0/freesurfer/SetUpFreeSurfer.sh: line 42:
>> /opt/freesurfer-6.0.0/FreeSurferEnv.sh: No such file or directory). This
>> is  line 42 "source $FREESURFER_HOME/FreeSurferEnv.sh".
>>
>> Do you think it's wise if i add another line (line 43) with the command
>> "source $FREESURFER_HOME/freesurfer/FreeSurferEnv.sh" and comment  line
>> 42? It might solve the problem.
>>
>> Best,
>> Miracle
>>
>>
>> On Wed, May 30, 2018 at 2:43 PM, Iglesias Gonzalez, Eugenio <
>> e.igles...@ucl.ac.uk> wrote:
>>
>> External Email - Use Caution
>>
>> Hi again,
>>
>>
>>
>> The two following statements are inconsistent! I believe that’s the root
>> of the problem:
>>
>>
>>
>> a. When i type "printenv FREESURFER_HOME" I get "
>> /opt/freesurfer-6.0.0".
>>
>> b. I always insert this lines " export FREESURFER_HOME=/opt/freesurfe
>> r-6.0.0/freesurfer
>>
>>
>>
>> Cheers,
>>
>>
>>
>> /E
>>
>>
>>
>>
>>
>> --
>>
>> Juan Eugenio Iglesias
>>
>> ERC Senior Research Fellow
>>
>> Centre for Medical Image Computing (CMIC)
>>
>> University College London
>>
>> http://www.jeiglesias.com
>>
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>>
>>
>>
>> *From: * on behalf of miracle
>> ozzoude 
>> *Reply-To: *Freesurfer support list 
>> *Date: *Wednesday, 30 May 2018 at 18:57
>>
>> *To: *Freesurfer support list 
>> *Subject: *Re: [Freesurfer] hippocampal subfield segmentation error
>> (fsv6.0)
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Yes, because I processed all my subjects with v6.0 without any issue.
>> When i type "printenv FREESURFER_HOME" I get " /opt/freesurfer-6.0.0".
>>
>> I always insert this lines " export 
>> FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer;
>> source $FREESURFER_HOME/SetUpFreeSurfer.sh" in all my bash scripts for
>> freesurfer.
>>
>>
>>
>> Best,
>>
>> Miracle
>>
>>
>>
>> On Wed, May 30, 2018 at 12:47 PM, Iglesias Gonzalez, Eugenio <
>> e.igles...@ucl.ac.uk> wrote:
>>
>> *External Email - Use Caution*
>>
>> No, the contents of kvlAutoCrop are what they should be. What I don’t
>> understand is why the code is looking for /opt/freesurfer-6.0.0/sources.sh
>> (this

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

[miracle ozzoude]

External Email - Use Caution

Hello,

I was able to solve the previous error (not finding the sources.sh)
however, i have encountered another error (please find the attached
hippocampal-subfileds-T1.log file). In this case, line 3 of kvlAutoCrop has
a problem with kvlAutoCrop.bin

Thanks,
Best,
Miracle

On Wed, May 30, 2018 at 6:03 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> External Email - Use Caution
>
> Hard to tell without seeing the contents of the directories, but I'd put
> my money on:
>
> export FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer
>
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> recon-all ...
>
>
> Juan Eugenio Iglesias
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of miracle ozzoude <
> miracoo...@gmail.com>
> *Sent:* Wednesday, May 30, 2018 9:21:19 PM
> *To:* Freesurfer support list
>
> *Subject:* Re: [Freesurfer] hippocampal subfield segmentation error
> (fsv6.0)
>
>
> External Email - Use Caution
>
> Thanks.
>
> So I changed it to " export FREESURFER_HOME=/opt/freesurfer-6.0.0; source
> $FREESURFER_HOME/freesurfer/SetUpFreeSurfer.sh" (based on printenv).
> However, when i tried to run my script i got another error
> (/opt/freesurfer-6.0.0/freesurfer/SetUpFreeSurfer.sh: line 42:
> /opt/freesurfer-6.0.0/FreeSurferEnv.sh: No such file or directory). This
> is  line 42 "source $FREESURFER_HOME/FreeSurferEnv.sh".
>
> Do you think it's wise if i add another line (line 43) with the command
> "source $FREESURFER_HOME/freesurfer/FreeSurferEnv.sh" and comment  line
> 42? It might solve the problem.
>
> Best,
> Miracle
>
>
> On Wed, May 30, 2018 at 2:43 PM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
> External Email - Use Caution
>
> Hi again,
>
>
>
> The two following statements are inconsistent! I believe that’s the root
> of the problem:
>
>
>
> a. When i type "printenv FREESURFER_HOME" I get "
> /opt/freesurfer-6.0.0".
>
> b. I always insert this lines " export FREESURFER_HOME=/opt/freesurfe
> r-6.0.0/freesurfer
>
>
>
> Cheers,
>
>
>
> /E
>
>
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 30 May 2018 at 18:57
>
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] hippocampal subfield segmentation error
> (fsv6.0)
>
>
>
> *External Email - Use Caution*
>
> Yes, because I processed all my subjects with v6.0 without any issue. When
> i type "printenv FREESURFER_HOME" I get " /opt/freesurfer-6.0.0".
>
> I always insert this lines " export 
> FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer;
> source $FREESURFER_HOME/SetUpFreeSurfer.sh" in all my bash scripts for
> freesurfer.
>
>
>
> Best,
>
> Miracle
>
>
>
> On Wed, May 30, 2018 at 12:47 PM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
> *External Email - Use Caution*
>
> No, the contents of kvlAutoCrop are what they should be. What I don’t
> understand is why the code is looking for /opt/freesurfer-6.0.0/sources.sh
> (this is what your log says). Are you sure FREESURFER_HOME is properly
> defined?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 30 May 2018 at 17:39
>
>
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] hippocampal subfield segmentation error
> (fsv6.0)
>
>
>
> *External Email - Use Caution*
>
> Hello,
>
>
>
> I checked and my sources.sh is located in  
> /opt/freesurfer-6.0.0/freesurfer/sources.sh
> not  /opt/freesurfer-6.0.0/sources.sh.  I opened the kvlAutoCropt file
> and it found 

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

[miracle ozzoude]

External Email - Use Caution

Thanks.

So I changed it to " export FREESURFER_HOME=/opt/freesurfer-6.0.0; source
$FREESURFER_HOME/freesurfer/SetUpFreeSurfer.sh" (based on printenv).
However, when i tried to run my script i got another error
(/opt/freesurfer-6.0.0/freesurfer/SetUpFreeSurfer.sh: line 42:
/opt/freesurfer-6.0.0/FreeSurferEnv.sh: No such file or directory). This
is  line 42 "source $FREESURFER_HOME/FreeSurferEnv.sh".

Do you think it's wise if i add another line (line 43) with the command
"source $FREESURFER_HOME/freesurfer/FreeSurferEnv.sh" and comment  line 42?
It might solve the problem.

Best,
Miracle


On Wed, May 30, 2018 at 2:43 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> External Email - Use Caution
>
> Hi again,
>
>
>
> The two following statements are inconsistent! I believe that’s the root
> of the problem:
>
>
>
> a. When i type "printenv FREESURFER_HOME" I get "
> /opt/freesurfer-6.0.0".
>
> b. I always insert this lines " export FREESURFER_HOME=/opt/
> freesurfer-6.0.0/freesurfer
>
>
>
> Cheers,
>
>
>
> /E
>
>
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 30 May 2018 at 18:57
>
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] hippocampal subfield segmentation error
> (fsv6.0)
>
>
>
> *External Email - Use Caution*
>
> Yes, because I processed all my subjects with v6.0 without any issue. When
> i type "printenv FREESURFER_HOME" I get " /opt/freesurfer-6.0.0".
>
> I always insert this lines " export 
> FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer;
> source $FREESURFER_HOME/SetUpFreeSurfer.sh" in all my bash scripts for
> freesurfer.
>
>
>
> Best,
>
> Miracle
>
>
>
> On Wed, May 30, 2018 at 12:47 PM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
> *External Email - Use Caution*
>
> No, the contents of kvlAutoCrop are what they should be. What I don’t
> understand is why the code is looking for /opt/freesurfer-6.0.0/sources.sh
> (this is what your log says). Are you sure FREESURFER_HOME is properly
> defined?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 30 May 2018 at 17:39
>
>
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] hippocampal subfield segmentation error
> (fsv6.0)
>
>
>
> *External Email - Use Caution*
>
> Hello,
>
>
>
> I checked and my sources.sh is located in  
> /opt/freesurfer-6.0.0/freesurfer/sources.sh
> not  /opt/freesurfer-6.0.0/sources.sh.  I opened the kvlAutoCropt file
> and it found this
>
> source $FREESURFER_HOME/sources.sh
>
> kvlAutoCrop.bin "$@"
>
> Can I edit the  kvlAutoCrop file to point the correct? or something else
>
>
>
> Best,
>
> Miracle
>
>
>
> On Wed, May 30, 2018 at 11:55 AM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
> *    External Email - Use Caution*
>
> Hey so kvlAutoCrop is looking for sources.sh in  /opt/freesurfer-6.0.0/
> which seems to be FREESURFER_HOME at that point. However, from the rest of
> your code, it seems that FREESURFER_HOME is /opt/freesurfer-6.0.0/
> freesurfer/
>
> Please double check.
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 30 May 2018 at 16:46
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] hippocampal subfield segmentation error
> (fsv6.0)
>
>
>
> *External Email - Use Caution*
>
> Hello Eugenio,
>
>
>
> Thanks for the response. All my processing w

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

[miracle ozzoude]

External Email - Use Caution

Yes, because I processed all my subjects with v6.0 without any issue. When
i type "printenv FREESURFER_HOME" I get " /opt/freesurfer-6.0.0".
I always insert this lines " export
FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer; source
$FREESURFER_HOME/SetUpFreeSurfer.sh" in all my bash scripts for freesurfer.

Best,
Miracle

On Wed, May 30, 2018 at 12:47 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> External Email - Use Caution
>
> No, the contents of kvlAutoCrop are what they should be. What I don’t
> understand is why the code is looking for /opt/freesurfer-6.0.0/sources.sh
> (this is what your log says). Are you sure FREESURFER_HOME is properly
> defined?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 30 May 2018 at 17:39
>
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] hippocampal subfield segmentation error
> (fsv6.0)
>
>
>
> *External Email - Use Caution*
>
> Hello,
>
>
>
> I checked and my sources.sh is located in  
> /opt/freesurfer-6.0.0/freesurfer/sources.sh
> not  /opt/freesurfer-6.0.0/sources.sh.  I opened the kvlAutoCropt file
> and it found this
>
> source $FREESURFER_HOME/sources.sh
>
> kvlAutoCrop.bin "$@"
>
> Can I edit the  kvlAutoCrop file to point the correct? or something else
>
>
>
> Best,
>
> Miracle
>
>
>
> On Wed, May 30, 2018 at 11:55 AM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
> *External Email - Use Caution*
>
> Hey so kvlAutoCrop is looking for sources.sh in  /opt/freesurfer-6.0.0/
> which seems to be FREESURFER_HOME at that point. However, from the rest of
> your code, it seems that FREESURFER_HOME is /opt/freesurfer-6.0.0/
> freesurfer/
>
> Please double check.
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 30 May 2018 at 16:46
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] hippocampal subfield segmentation error
> (fsv6.0)
>
>
>
> *External Email - Use Caution*
>
> Hello Eugenio,
>
>
>
> Thanks for the response. All my processing was done with FreeSurfer v6.0
> although, we have version 5.3 installed on the server too. I always set my
> environment to version 6 ( export 
> FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer;
> source $FREESURFER_HOME/SetUpFreeSurfer.sh) before running any
> processing.
>
>
>
> Also, our server has matlab2008b installed but, it expired hence, i don't
> think that will interfere with the processing because we installed the
> correct/recent matlab runtime.
>
>
>
> Best,
>
> Miracle
>
>
>
> On Wed, May 30, 2018 at 11:35 AM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
> *    External Email - Use Caution*
>
> Hi Miracle,
>
> I believe Doug (CCed) ran into a similar problem recently, and I think the
> problem had to do with mixing versions.
>
> What exact version are you using?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 30 May 2018 at 16:11
> *To: *Douglas N Greve 
> *Subject: *[Freesurfer] hippocampal subfield segmentation error (fsv6.0)
>
>
>
> *External Email - Use Caution*
>
> Hello,
>
>
>
> I am using v6.0 installed on a linux server (via PUTTY) to segment
> hippocampal subfields. I downloaded the runtime from this link (
> https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime) and followed the
> instructions on how to install it ( it was installed on the same server as
> v6.0). The installation process wor

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

[miracle ozzoude]

External Email - Use Caution

Hello,

I checked and my sources.sh is located in
/opt/freesurfer-6.0.0/freesurfer/sources.sh
not  /opt/freesurfer-6.0.0/sources.sh.  I opened the kvlAutoCropt file and
it found this
source $FREESURFER_HOME/sources.sh
kvlAutoCrop.bin "$@"
Can I edit the  kvlAutoCrop file to point the correct? or something else

Best,
Miracle

On Wed, May 30, 2018 at 11:55 AM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> External Email - Use Caution
>
> Hey so kvlAutoCrop is looking for sources.sh in  /opt/freesurfer-6.0.0/
> which seems to be FREESURFER_HOME at that point. However, from the rest of
> your code, it seems that FREESURFER_HOME is /opt/freesurfer-6.0.0/
> freesurfer/
>
> Please double check.
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 30 May 2018 at 16:46
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] hippocampal subfield segmentation error
> (fsv6.0)
>
>
>
> *External Email - Use Caution*
>
> Hello Eugenio,
>
>
>
> Thanks for the response. All my processing was done with FreeSurfer v6.0
> although, we have version 5.3 installed on the server too. I always set my
> environment to version 6 ( export 
> FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer;
> source $FREESURFER_HOME/SetUpFreeSurfer.sh) before running any
> processing.
>
>
>
> Also, our server has matlab2008b installed but, it expired hence, i don't
> think that will interfere with the processing because we installed the
> correct/recent matlab runtime.
>
>
>
> Best,
>
> Miracle
>
>
>
> On Wed, May 30, 2018 at 11:35 AM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
> *External Email - Use Caution*
>
> Hi Miracle,
>
> I believe Doug (CCed) ran into a similar problem recently, and I think the
> problem had to do with mixing versions.
>
> What exact version are you using?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 30 May 2018 at 16:11
> *To: *Douglas N Greve 
> *Subject: *[Freesurfer] hippocampal subfield segmentation error (fsv6.0)
>
>
>
> *External Email - Use Caution*
>
> Hello,
>
>
>
> I am using v6.0 installed on a linux server (via PUTTY) to segment
> hippocampal subfields. I downloaded the runtime from this link (
> https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime) and followed the
> instructions on how to install it ( it was installed on the same server as
> v6.0). The installation process worked fine.
>
>
>
> However, when I wanted to run recon-all on already processed FS data (
> e.g. recon-all -s ${SUBJECTS_DIR}/$session -hippocampal-subfields-T1
> -parallel -openmp 6 -bigventricles -3T -time), I encountered an error. I
> have attached the log for your viewing. Thank you.
>
>
>
> Best,
>
> Miracle
>
>
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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> HelpLine at
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Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

[miracle ozzoude]

External Email - Use Caution

Hello Eugenio,

Thanks for the response. All my processing was done with FreeSurfer v6.0
although, we have version 5.3 installed on the server too. I always set my
environment to version 6 ( export
FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer; source
$FREESURFER_HOME/SetUpFreeSurfer.sh) before running any processing.

Also, our server has matlab2008b installed but, it expired hence, i don't
think that will interfere with the processing because we installed the
correct/recent matlab runtime.

Best,
Miracle

On Wed, May 30, 2018 at 11:35 AM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> External Email - Use Caution
>
> Hi Miracle,
>
> I believe Doug (CCed) ran into a similar problem recently, and I think the
> problem had to do with mixing versions.
>
> What exact version are you using?
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of miracle
> ozzoude 
> *Reply-To: *Freesurfer support list 
> *Date: *Wednesday, 30 May 2018 at 16:11
> *To: *Douglas N Greve 
> *Subject: *[Freesurfer] hippocampal subfield segmentation error (fsv6.0)
>
>
>
> *External Email - Use Caution*
>
> Hello,
>
>
>
> I am using v6.0 installed on a linux server (via PUTTY) to segment
> hippocampal subfields. I downloaded the runtime from this link (
> https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime) and followed the
> instructions on how to install it ( it was installed on the same server as
> v6.0). The installation process worked fine.
>
>
>
> However, when I wanted to run recon-all on already processed FS data (
> e.g. recon-all -s ${SUBJECTS_DIR}/$session -hippocampal-subfields-T1
> -parallel -openmp 6 -bigventricles -3T -time), I encountered an error. I
> have attached the log for your viewing. Thank you.
>
>
>
> Best,
>
> Miracle
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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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.
>
>
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[Freesurfer] hippocampal subfield segmentation error (fsv6.0)

[miracle ozzoude]

External Email - Use Caution

Hello,

I am using v6.0 installed on a linux server (via PUTTY) to segment
hippocampal subfields. I downloaded the runtime from this link (
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime) and followed the
instructions on how to install it ( it was installed on the same server as
v6.0). The installation process worked fine.

However, when I wanted to run recon-all on already processed FS data ( e.g.
recon-all -s ${SUBJECTS_DIR}/$session -hippocampal-subfields-T1 -parallel
-openmp 6 -bigventricles -3T -time), I encountered an error. I have
attached the log for your viewing. Thank you.

Best,
Miracle


hippocampal-subfields-T1.log
Description: Binary data
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dispose of the e-mail.

[Freesurfer] Installing different versions of FreeSurfer on Same computer (error)

[miracle ozzoude]

External Email - Use Caution

Hello, 

My Mac has v5.3 installed in the default location ( application). However, 
whenever I try to install v6.0 in a different location ( desktop) it deletes 
the existing v5.3 from application. Any solution to this? I’m trying to run the 
brainstem and hippo&amygdala subfields on v5.3 processed data. Thank you. 

Best, 
Paul

Sent from my iPhone

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Re: [Freesurfer] mri_watershed error/global region of the brain empty

[miracle ozzoude]

External Email - Use Caution

Hello Bruce,

Thanks. Can I use tkregisterfv to visualize it?

Best,
Paul


On Fri, Apr 27, 2018 at 11:37 AM, Bruce Fischl 
wrote:

> Hi Paul
>
> that usually means something went wrong before the watershed. Check the
> input image to make sure that it and the talairach_with_skull.lta are ok
>
> cheers
> Bruce
>
>
> On Fri, 27 Apr 2018, miracle ozzoude wrote:
>
>
>> External Email - Use Caution
>>
>>
>> Hello FreeSurfer,
>> While running recon-all on a subject, i got encountered an error during
>> the watershed step
>> (mri_watershed). How do i fix this problem? I have attached the
>> recon-all.log and
>> recon-all-status.log files. Thank you
>>
>> Best,
>> Paul
>>
>>
> ___
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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.
>
>
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[Freesurfer] mri_watershed error/global region of the brain empty

[miracle ozzoude]

External Email - Use Caution

Hello FreeSurfer,

While running recon-all on a subject, i got encountered an error during the
watershed step (mri_watershed). How do i fix this problem? I have attached
the recon-all.log and recon-all-status.log files. Thank you

Best,
Paul


recon-all.log
Description: Binary data


recon-all-status.log
Description: Binary data
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Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Doug,

Thank you. How do i got about fixing? Do you think it's a good idea to
start afresh on this subject (i.e. recon-all and longitudinal pipeline)?

Best,
Paul

On Mon, Feb 5, 2018 at 12:20 PM, Douglas Greve 
wrote:

> The first frame in your input file is all 0s, so something is wrong with
> the fist subject
>
> On 2/3/18 3:03 PM, miracle ozzoude wrote:
>
> Hello Doug,
>
> I have uploaded the files you requested. Thank you for your help.
>
> Best,
> Paul
>
> On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve 
> wrote:
>
>> Can you upload the glmfit folders and the glmfit input (--y file) to our
>> filedrop?
>>
>> https://gate.nmr.mgh.harvard.edu/filedrop2/
>>
>> On 2/1/18 7:46 PM, miracle ozzoude wrote:
>>
>> Hello Doug,
>>
>> I have attached a screen shot of the mask.mgh for both right and left
>> hemispheres. Everything looks yellow. I followed the paired t-test tutorial
>> on the wiki page (included my scripts, fsgd files, and matrix in email
>> thread). How do i go about fixing it? Thanks you
>>
>> Best,
>> Paul
>>
>> On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve > > wrote:
>>
>>> that usually means that something has gone wrong with the analysis. Do
>>> the maps look ok? In particular, look at the mask
>>>
>>>
>>>
>>> On 1/20/18 1:56 PM, miracle ozzoude wrote:
>>>
>>> Hello Doug,
>>>
>>> I tried using the MC tables that FS distributed. However, i got an error
>>> about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no
>>> fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and
>>> cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3
>>> on mac. Thank you.
>>>
>>> Best,
>>> Paul
>>>
>>> mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
>>> $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos
>>> --cwpvalthresh 0.05 --2spaces --overwrite
>>> mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
>>> $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos
>>> --cwpvalthresh 0.05 --2spaces --overwrite
>>>
>>> On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve <
>>> gr...@nmr.mgh.harvard.edu> wrote:
>>>
>>>> Why are you doing your own MC simulation? You can just use the tables
>>>> that we distribute ...
>>>>
>>>> On 1/17/18 6:12 PM, miracle ozzoude wrote:
>>>>
>>>> Hello Experts,
>>>>
>>>> I am running a paired t-test cortical thickness analysis based on the
>>>> instruction on the wiki page (https://surfer.nmr.mgh.harvar
>>>> d.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't
>>>> not created when i corrected for multiple comparisons. Below are my script,
>>>> fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z
>>>> maps. Please can you help me figure out why the error is happening. Thank
>>>> you.
>>>>
>>>> Best,
>>>> Paul
>>>>
>>>> *Script*:
>>>> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
>>>> martrix2=age.mtx
>>>> #resample each subjects's left and right hemisphere data to fsavarage.
>>>> mris_preproc --target fsaverage --hemi lh --meas thickness --out
>>>> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
>>>> mris_preproc --target fsaverage --hemi rh --meas thickness --out
>>>> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
>>>> # #smoothen the concatenated file by 5mm FWHM. --cortex means only
>>>> smooth areas in the cortex. N:B. FWHM changes based on study type.
>>>> mri_surf2surf --hemi lh --s fsaverage --sval
>>>> lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
>>>> lh.paired-diff.thickness.sm05.mgh
>>>> mri_surf2surf --hemi rh --s fsaverage --sval
>>>> rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
>>>> rh.paired-diff.thickness.sm05.mgh
>>>> # #Run GLM analysis
>>>> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
>>>> $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
>>>> lh.paired-diff.glmdirir
>>>> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
>>>> $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
>>>>

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Doug,

I have uploaded the files you requested. Thank you for your help.

Best,
Paul

On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve 
wrote:

> Can you upload the glmfit folders and the glmfit input (--y file) to our
> filedrop?
>
> https://gate.nmr.mgh.harvard.edu/filedrop2/
>
> On 2/1/18 7:46 PM, miracle ozzoude wrote:
>
> Hello Doug,
>
> I have attached a screen shot of the mask.mgh for both right and left
> hemispheres. Everything looks yellow. I followed the paired t-test tutorial
> on the wiki page (included my scripts, fsgd files, and matrix in email
> thread). How do i go about fixing it? Thanks you
>
> Best,
> Paul
>
> On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve 
> wrote:
>
>> that usually means that something has gone wrong with the analysis. Do
>> the maps look ok? In particular, look at the mask
>>
>>
>>
>> On 1/20/18 1:56 PM, miracle ozzoude wrote:
>>
>> Hello Doug,
>>
>> I tried using the MC tables that FS distributed. However, i got an error
>> about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no
>> fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and
>> cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3
>> on mac. Thank you.
>>
>> Best,
>> Paul
>>
>> mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
>> $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos
>> --cwpvalthresh 0.05 --2spaces --overwrite
>> mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
>> $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos
>> --cwpvalthresh 0.05 --2spaces --overwrite
>>
>> On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve > > wrote:
>>
>>> Why are you doing your own MC simulation? You can just use the tables
>>> that we distribute ...
>>>
>>> On 1/17/18 6:12 PM, miracle ozzoude wrote:
>>>
>>> Hello Experts,
>>>
>>> I am running a paired t-test cortical thickness analysis based on the
>>> instruction on the wiki page (https://surfer.nmr.mgh.harvar
>>> d.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't
>>> not created when i corrected for multiple comparisons. Below are my script,
>>> fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z
>>> maps. Please can you help me figure out why the error is happening. Thank
>>> you.
>>>
>>> Best,
>>> Paul
>>>
>>> *Script*:
>>> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
>>> martrix2=age.mtx
>>> #resample each subjects's left and right hemisphere data to fsavarage.
>>> mris_preproc --target fsaverage --hemi lh --meas thickness --out
>>> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
>>> mris_preproc --target fsaverage --hemi rh --meas thickness --out
>>> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
>>> # #smoothen the concatenated file by 5mm FWHM. --cortex means only
>>> smooth areas in the cortex. N:B. FWHM changes based on study type.
>>> mri_surf2surf --hemi lh --s fsaverage --sval
>>> lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
>>> lh.paired-diff.thickness.sm05.mgh
>>> mri_surf2surf --hemi rh --s fsaverage --sval
>>> rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
>>> rh.paired-diff.thickness.sm05.mgh
>>> # #Run GLM analysis
>>> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
>>> $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
>>> lh.paired-diff.glmdirir
>>> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
>>> $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
>>> rh.paired-diff.glmdir
>>> # # #Run Clusterwise correction for multiple comparisons using MONTE
>>> CARLO. First create a table for of simulations
>>> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2
>>> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
>>> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2
>>> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
>>> *Fsgd file 1:pairs.fsgd*
>>>
>>> GroupDescriptorFile 1
>>>
>>> Class ADEX
>>>
>>> Input 1000_1 ADEX
>>>
>>> Input 1000_2 ADEX
>>>
>>> Input 1001_1 ADEX
>>>
>>> Input 1001_2 ADEX
>>>
>>> Input 1003_1 ADEX
>>

[Freesurfer] Fwd: Fwd: monte-carlo error in longitudinal pipeline

[miracle ozzoude]

-- Forwarded message --
From: miracle ozzoude 
Date: Fri, Jan 26, 2018 at 7:08 PM
Subject: Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline
To: Freesurfer support list 


Hello Doug,

Thanks for the patience. Here's the output from the terminal when I ran
mri_glmfit.

Best,
Paul

/Applications/freesurfer


 START: LONGITUDINAL CORTICAL THICKNESS

1000

1000_1

1000_1.long.1000

1000_2

1000_2.long.1000

1001

1001_1

1001_1.long.1001

1001_2

1001_2.long.1001

1003

1003_1

1003_1.long.1003

1003_2

1003_2.long.1003

1005

1005_1

1005_1.long.1005

1005_2

1005_2.long.1005

1008

1008_1

1008_1.long.1008

1008_2

1008_2.long.1008

1013

1013_1

1013_1.long.1013

1013_2

1013_2.long.1013

1014

1014_1

1014_1.long.1014

1014_2

1014_2.long.1014

gdfReadHeader: reading paired_diff.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 Age 76 3.70328

Class Means of each Continuous Variable

1 ADEX  76.

INFO: gd2mtx_method is doss

Reading source surface /Users/carm/Documents/Cas/
ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/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 /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018

cmdline mri_glmfit --y lh.paired.diff.thickness.10.mgh --fsgd
paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage lh --cortex
--glmdir lh.paired.diff.glmdir

sysname  Darwin

hostname opennet-33-172.uhnres.utoronto.ca

machine  x86_64

user carm

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh

logyflag 0

usedti  0

FSGD paired_diff.fsgd

labelmask  /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.paired.diff.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.paired.diff.glmdir

Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh

INFO: gd2mtx_method is doss

Saving design matrix to lh.paired.diff.glmdir/Xg.dat

Normalized matrix condition is 1686.7

Matrix condition is 2.46289e+06

Found 149955 points in label.

Pruning voxels by thr: 0.00

Found 0 voxels in mask

Saving mask to lh.paired.diff.glmdir/mask.mgh

Reshaping mriglm->mask...

search space = 0.00

DOF = 5

Starting fit and test

Fit completed in 8.3e-05 minutes

Computing spatial AR1 on surface

WARNING: ar1 = nan <= 0. Setting fwhm to 0.

Residual: ar1mn=nan, ar1std=nan, gstd=0.00, fwhm=0.00

Writing results

  mean

maxvox sig=0  F=0  at  index 0 0 0seed=1517221145

  age

maxvox sig=0  F=0  at  index 0 0 0seed=1517221145

mri_glmfit done

gdfReadHeader: reading paired_diff.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 Age 76 3.70328

Class Means of each Continuous Variable

1 ADEX  76.

INFO: gd2mtx_method is doss

Reading source surface /Users/carm/Documents/Cas/
ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/rh.white

Number of vertices 163842

Number of faces327680

Total area 65020.765625

AvgVtxArea   0.396850

AvgVtxDist   0.717994

StdVtxDist   0.193566


$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $

cwd /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018

cmdline mri_glmfit --y rh.paired.diff.thickness.10.mgh --fsgd
paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage rh --cortex
--glmdir rh.paired.diff.glmdir

sysname  Darwin

hostname opennet-33-172.uhnres.utoronto.ca

machine  x86_64

user carm

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh

logyflag 0

usedti  0

FSGD paired_diff.fsgd

labelmask  /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/fsaverage/label/rh.cortex.label

maskinv 0

glmdir rh.paired.diff.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory rh.paired.diff.glmdir

Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh

INFO: gd2mtx_method is doss

Saving design matrix to rh.paired.diff.glmdir/Xg.dat

Normalized matrix condition is 1686.7

Matrix condition is 2.46289e+06

Found 149926 points in label.

Pruning voxels by thr: 0.00

Found 0 voxels in mask

Saving mask to rh.paired.diff.glmdir/mask.mgh

Reshaping mriglm->mask...

search space = 0.00

DOF = 5

Starting fit and test

Fit compl

Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline

[miracle ozzoude]

dex 0 0 0seed=1517884366

  age

maxvox sig=0  F=0  at  index 0 0 0seed=1517884366

mri_glmfit done



On Wed, Jan 24, 2018 at 2:59 PM, Douglas N Greve 
wrote:

> can you send the terminal output of mri_glmfit?
>
>
> On 01/24/2018 02:52 PM, miracle ozzoude wrote:
> > Hello Doug,
> >
> > I looked at the fwhm.dat and fwhm value =  0. I have attached the
> > mri_glmfit.log file. How do i solve this problem?
> >
> > Best,
> > Paul
> >
> > On Mon, Jan 22, 2018 at 11:57 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > If your fwhm is 0, then something is wrong. Look in the fwhm.dat
> > file in
> > the glmfit output to see what the value is. Also, send the terminal
> > output from mri_glmfit (not mri_glmfit-sim)
> >
> >
> > On 01/22/2018 11:43 AM, miracle ozzoude wrote:
> > >
> > > -- Forwarded message --
> > > From: *miracle ozzoude*  miracoo...@gmail.com>
> > > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>>
> > > Date: Sat, Jan 20, 2018 at 1:56 PM
> > > Subject: Re: [Freesurfer] monte-carlo error in longitudinal
> pipeline
> > > To: Freesurfer support list  > <mailto:freesurfer@nmr.mgh.harvard.edu>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > >
> > >
> > > Hello Doug,
> > >
> > > I tried using the MC tables that FS distributed. However, i got an
> > > error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked
> and
> > > there's no fwhm00, the table starts from fwhm01 to fwhm30. Below
> are
> > > my script and cache.mri_glmfi-sim.log files. My FreeSurfer
> > version is
> > > stable version 5.3 on mac. Thank you.
> > >
> > > Best,
> > > Paul
> > >
> > > mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
> > > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache
> > 3 pos
> > > --cwpvalthresh 0.05 --2spaces --overwrite
> > > mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
> > > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache
> > 3 pos
> > > --cwpvalthresh 0.05 --2spaces --overwrite
> > >
> > > On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve
> > > mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> > >
> > > Why are you doing your own MC simulation? You can just use the
> > > tables that we distribute ...
> > >
> > >
> > > On 1/17/18 6:12 PM, miracle ozzoude wrote:
> > >> Hello Experts,
> > >>
> > >> I am running a paired t-test cortical thickness analysis
> > based on
> > >> the instruction on the wiki page
> > >> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> > <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>
> > >> <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> > <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>>).
> > >> However, the monte carlo files weren't not created when i
> > >> corrected for multiple comparisons. Below are my script, fsgd
> > >> files, mc-z log file, and a screenshot of contrast folder
> > missing
> > >> mc.z maps. Please can you help me figure out why the error is
> > >> happening. Thank you.
> > >>
> > >> Best,
> > >> Paul
> > >>
> > >> *Script*:
> > >> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
> > >> martrix2=age.mtx
> > >> #resample each subjects's left and right hemisphere data to
> > >> fsavarage.
> > >> mris_preproc --target fsaverage --hemi lh --meas thickness
> > --out
> > >> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
> > >> mris_preproc --target fsaverage --hemi rh --meas thickness
> > --out
> > >> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff

Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Doug,

I looked at the fwhm.dat and fwhm value =  0. I have attached the
mri_glmfit.log file. How do i solve this problem?

Best,
Paul

On Mon, Jan 22, 2018 at 11:57 AM, Douglas N Greve  wrote:

> If your fwhm is 0, then something is wrong. Look in the fwhm.dat file in
> the glmfit output to see what the value is. Also, send the terminal
> output from mri_glmfit (not mri_glmfit-sim)
>
>
> On 01/22/2018 11:43 AM, miracle ozzoude wrote:
> >
> > -- Forwarded message ------
> > From: *miracle ozzoude*  > <mailto:miracoo...@gmail.com>>
> > Date: Sat, Jan 20, 2018 at 1:56 PM
> > Subject: Re: [Freesurfer] monte-carlo error in longitudinal pipeline
> > To: Freesurfer support list  > <mailto:freesurfer@nmr.mgh.harvard.edu>>
> >
> >
> > Hello Doug,
> >
> > I tried using the MC tables that FS distributed. However, i got an
> > error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and
> > there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are
> > my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is
> > stable version 5.3 on mac. Thank you.
> >
> > Best,
> > Paul
> >
> > mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
> > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos
> > --cwpvalthresh 0.05 --2spaces --overwrite
> > mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
> > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos
> > --cwpvalthresh 0.05 --2spaces --overwrite
> >
> > On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Why are you doing your own MC simulation? You can just use the
> > tables that we distribute ...
> >
> >
> > On 1/17/18 6:12 PM, miracle ozzoude wrote:
> >> Hello Experts,
> >>
> >> I am running a paired t-test cortical thickness analysis based on
> >> the instruction on the wiki page
> >> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> >> <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>).
> >> However, the monte carlo files weren't not created when i
> >> corrected for multiple comparisons. Below are my script, fsgd
> >> files, mc-z log file, and a screenshot of contrast folder missing
> >> mc.z maps. Please can you help me figure out why the error is
> >> happening. Thank you.
> >>
> >> Best,
> >> Paul
> >>
> >> *Script*:
> >> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
> >> martrix2=age.mtx
> >> #resample each subjects's left and right hemisphere data to
> >> fsavarage.
> >> mris_preproc --target fsaverage --hemi lh --meas thickness --out
> >> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
> >> mris_preproc --target fsaverage --hemi rh --meas thickness --out
> >> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
> >> # #smoothen the concatenated file by 5mm FWHM. --cortex means
> >> only smooth areas in the cortex. N:B. FWHM changes based on study
> >> type.
> >> mri_surf2surf --hemi lh --s fsaverage --sval
> >> lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
> >> lh.paired-diff.thickness.sm05.mgh
> >> mri_surf2surf --hemi rh --s fsaverage --sval
> >> rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
> >> rh.paired-diff.thickness.sm05.mgh
> >> # #Run GLM analysis
> >> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired
> >> --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
> >> lh.paired-diff.glmdirir
> >> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired
> >> --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
> >> rh.paired-diff.glmdir
> >> # # #Run Clusterwise correction for multiple comparisons using
> >> MONTE CARLO. First create a table for of simulations
> >> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2
> >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
> >> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2
> >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
> >> *Fsgd file 1:pairs.fsgd*
> >>
> >> GroupDescriptorFile 1
> &g

[Freesurfer] Fwd: monte-carlo error in longitudinal pipeline

[miracle ozzoude]

-- Forwarded message --
From: miracle ozzoude 
Date: Sat, Jan 20, 2018 at 1:56 PM
Subject: Re: [Freesurfer] monte-carlo error in longitudinal pipeline
To: Freesurfer support list 


Hello Doug,

I tried using the MC tables that FS distributed. However, i got an error
about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no
fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and
cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3
on mac. Thank you.

Best,
Paul

mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos
--cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos
--cwpvalthresh 0.05 --2spaces --overwrite



On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve 
wrote:

> Why are you doing your own MC simulation? You can just use the tables that
> we distribute ...
>
> On 1/17/18 6:12 PM, miracle ozzoude wrote:
>
> Hello Experts,
>
> I am running a paired t-test cortical thickness analysis based on the
> instruction on the wiki page (https://surfer.nmr.mgh.harvar
> d.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't not
> created when i corrected for multiple comparisons. Below are my script,
> fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z
> maps. Please can you help me figure out why the error is happening. Thank
> you.
>
> Best,
> Paul
>
> *Script*:
> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx
> #resample each subjects's left and right hemisphere data to fsavarage.
> mris_preproc --target fsaverage --hemi lh --meas thickness --out
> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
> mris_preproc --target fsaverage --hemi rh --meas thickness --out
> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
> # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth
> areas in the cortex. N:B. FWHM changes based on study type.
> mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh
> --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh
> mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh
> --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh
> # #Run GLM analysis
> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
> $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
> lh.paired-diff.glmdirir
> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
> $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
> rh.paired-diff.glmdir
> # # #Run Clusterwise correction for multiple comparisons using MONTE
> CARLO. First create a table for of simulations
> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2
> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2
> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
> *Fsgd file 1:pairs.fsgd*
>
> GroupDescriptorFile 1
>
> Class ADEX
>
> Input 1000_1 ADEX
>
> Input 1000_2 ADEX
>
> Input 1001_1 ADEX
>
> Input 1001_2 ADEX
>
> Input 1003_1 ADEX
>
> Input 1003_2 ADEX
>
> Input 1005_1 ADEX
>
> Input 1005_2 ADEX
>
> Input 1008_1 ADEX
>
> Input 1008_2 ADEX
>
> Input 1013_1 ADEX
>
> Input 1013_2 ADEX
>
> Input 1014_1 ADEX
>
> Input 1014_2 ADEX
> *Fsgd file 2: paired_diff.fsgd*
>
> GroupDescriptorFile 1
>
> Class ADEX
>
> Variables Age
>
> Input 1000 ADEX 72
>
> Input 1001 ADEX 76
>
> Input 1003 ADEX 72
>
> Input 1005 ADEX 80
>
> Input 1008 ADEX 72
>
> Input 1013 ADEX 80
>
> Input 1014 ADEX 80
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> 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.
>
>


cache.mri_glmfit-sim.log
Description: B

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Doug,

I tried using the MC tables that FS distributed. However, i got an error
about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no
fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and
cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3
on mac. Thank you.

Best,
Paul

mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos
--cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos
--cwpvalthresh 0.05 --2spaces --overwrite



On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve 
wrote:

> Why are you doing your own MC simulation? You can just use the tables that
> we distribute ...
>
> On 1/17/18 6:12 PM, miracle ozzoude wrote:
>
> Hello Experts,
>
> I am running a paired t-test cortical thickness analysis based on the
> instruction on the wiki page (https://surfer.nmr.mgh.harvard.edu/fswiki/
> PairedAnalysis). However, the monte carlo files weren't not created when
> i corrected for multiple comparisons. Below are my script, fsgd files, mc-z
> log file, and a screenshot of contrast folder missing mc.z maps. Please can
> you help me figure out why the error is happening. Thank you.
>
> Best,
> Paul
>
> *Script*:
> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx
> #resample each subjects's left and right hemisphere data to fsavarage.
> mris_preproc --target fsaverage --hemi lh --meas thickness --out
> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
> mris_preproc --target fsaverage --hemi rh --meas thickness --out
> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
> # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth
> areas in the cortex. N:B. FWHM changes based on study type.
> mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh
> --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh
> mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh
> --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh
> # #Run GLM analysis
> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
> $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
> lh.paired-diff.glmdirir
> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
> $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
> rh.paired-diff.glmdir
> # # #Run Clusterwise correction for multiple comparisons using MONTE
> CARLO. First create a table for of simulations
> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2
> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2
> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
> *Fsgd file 1:pairs.fsgd*
>
> GroupDescriptorFile 1
>
> Class ADEX
>
> Input 1000_1 ADEX
>
> Input 1000_2 ADEX
>
> Input 1001_1 ADEX
>
> Input 1001_2 ADEX
>
> Input 1003_1 ADEX
>
> Input 1003_2 ADEX
>
> Input 1005_1 ADEX
>
> Input 1005_2 ADEX
>
> Input 1008_1 ADEX
>
> Input 1008_2 ADEX
>
> Input 1013_1 ADEX
>
> Input 1013_2 ADEX
>
> Input 1014_1 ADEX
>
> Input 1014_2 ADEX
> *Fsgd file 2: paired_diff.fsgd*
>
> GroupDescriptorFile 1
>
> Class ADEX
>
> Variables Age
>
> Input 1000 ADEX 72
>
> Input 1001 ADEX 76
>
> Input 1003 ADEX 72
>
> Input 1005 ADEX 80
>
> Input 1008 ADEX 72
>
> Input 1013 ADEX 80
>
> Input 1014 ADEX 80
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> 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.
>
>


cache.mri_glmfit-sim.log
Description: Binary data
___
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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] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Doug, 
Thanks for responding. I am running a whole brain analysis as result shouldn’t 
I build my own MC simulation? 
Best, 
Paul 

Sent from my iPhone

> On Jan 18, 2018, at 5:23 PM, Douglas Greve  wrote:
> 
> Why are you doing your own MC simulation? You can just use the tables that we 
> distribute ...
> 
>> On 1/17/18 6:12 PM, miracle ozzoude wrote:
>> Hello Experts, 
>> 
>> I am running a paired t-test cortical thickness analysis based on the 
>> instruction on the wiki page 
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However, the 
>> monte carlo files weren't not created when i corrected for multiple 
>> comparisons. Below are my script, fsgd files, mc-z log file, and a 
>> screenshot of contrast folder missing mc.z maps. Please can you help me 
>> figure out why the error is happening. Thank you.
>> 
>> Best, 
>> Paul
>> 
>> Script: 
>> pairs=pairs.fsgd
>> paired=paired_diff.fsgd
>> martrix1=mean.mtx
>> martrix2=age.mtx
>> 
>> #resample each subjects's left and right hemisphere data to fsavarage. 
>> mris_preproc --target fsaverage --hemi lh --meas thickness --out 
>> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
>> mris_preproc --target fsaverage --hemi rh --meas thickness --out 
>> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
>> 
>> 
>> # #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth 
>> areas in the cortex. N:B. FWHM changes based on study type.
>> mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh 
>> --fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh
>> mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh 
>> --fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh
>> 
>> # #Run GLM analysis
>> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C 
>> $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir 
>> lh.paired-diff.glmdirir
>> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C 
>> $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir 
>> rh.paired-diff.glmdir
>> 
>> # # #Run Clusterwise correction for multiple comparisons using MONTE CARLO. 
>> First create a table for of simulations 
>> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2 mc-z.abs.2 
>> --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
>> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2 mc-z.abs.2 
>> --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
>> 
>> Fsgd file 1:pairs.fsgd
>> GroupDescriptorFile 1
>> 
>> Class ADEX
>> 
>> Input 1000_1 ADEX
>> 
>> Input 1000_2 ADEX
>> 
>> Input 1001_1 ADEX
>> 
>> Input 1001_2 ADEX
>> 
>> Input 1003_1 ADEX
>> 
>> Input 1003_2 ADEX
>> 
>> Input 1005_1 ADEX
>> 
>> Input 1005_2 ADEX
>> 
>> Input 1008_1 ADEX
>> 
>> Input 1008_2 ADEX
>> 
>> Input 1013_1 ADEX
>> 
>> Input 1013_2 ADEX
>> 
>> Input 1014_1 ADEX
>> 
>> Input 1014_2 ADEX
>> 
>> Fsgd file 2: paired_diff.fsgd
>> 
>> GroupDescriptorFile 1
>> 
>> Class ADEX
>> 
>> Variables Age
>> 
>> Input 1000 ADEX 72
>> 
>> Input 1001 ADEX 76
>> 
>> Input 1003 ADEX 72
>> 
>> Input 1005 ADEX 80
>> 
>> Input 1008 ADEX 72
>> 
>> Input 1013 ADEX 80
>> 
>> Input 1014 ADEX 80
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> ___
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[Freesurfer] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Experts,

I am running a paired t-test cortical thickness analysis based on the
instruction on the wiki page (
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). However, the
monte carlo files weren't not created when i corrected for multiple
comparisons. Below are my script, fsgd files, mc-z log file, and a
screenshot of contrast folder missing mc.z maps. Please can you help me
figure out why the error is happening. Thank you.

Best,
Paul

*Script*:
pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx martrix2=age.mtx

#resample each subjects's left and right hemisphere data to fsavarage.
mris_preproc --target fsaverage --hemi lh --meas thickness --out
lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
mris_preproc --target fsaverage --hemi rh --meas thickness --out
rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff


# #smoothen the concatenated file by 5mm FWHM. --cortex means only smooth
areas in the cortex. N:B. FWHM changes based on study type.
mri_surf2surf --hemi lh --s fsaverage --sval lh.paired-diff.thickness.mgh
--fwhm 5 --cortex --tval lh.paired-diff.thickness.sm05.mgh
mri_surf2surf --hemi rh --s fsaverage --sval rh.paired-diff.thickness.mgh
--fwhm 5 --cortex --tval rh.paired-diff.thickness.sm05.mgh

# #Run GLM analysis
mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
$martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
lh.paired-diff.glmdirir
mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
$martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
rh.paired-diff.glmdir

# # #Run Clusterwise correction for multiple comparisons using MONTE CARLO.
First create a table for of simulations
mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2 mc-z.abs.2
--sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2 mc-z.abs.2
--sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite

*Fsgd file 1:pairs.fsgd*

GroupDescriptorFile 1

Class ADEX

Input 1000_1 ADEX

Input 1000_2 ADEX

Input 1001_1 ADEX

Input 1001_2 ADEX

Input 1003_1 ADEX

Input 1003_2 ADEX

Input 1005_1 ADEX

Input 1005_2 ADEX

Input 1008_1 ADEX

Input 1008_2 ADEX

Input 1013_1 ADEX

Input 1013_2 ADEX

Input 1014_1 ADEX

Input 1014_2 ADEX

*Fsgd file 2: paired_diff.fsgd*

GroupDescriptorFile 1

Class ADEX

Variables Age

Input 1000 ADEX 72

Input 1001 ADEX 76

Input 1003 ADEX 72

Input 1005 ADEX 80

Input 1008 ADEX 72

Input 1013 ADEX 80

Input 1014 ADEX 80


mc-z.abs.2.mri_glmfit-sim.log
Description: Binary data
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Re: [Freesurfer] longitudinal base error. (not a netCDF file)

[miracle ozzoude]

Hello Martin,

I tried your first suggestion (removing the flags) and I got the same
errors. Yes, I do have enough space on the disk and nu1.mnc file does
exist. Do you think my script is the problem? I have attached the new recon
log file and my script. Thanks.

Best,
Paul

On Thu, Nov 9, 2017 at 11:13 AM, Martin Reuter 
wrote:

> Hi Paul,
>
> you can try to re-run from scratch (ensure there is enough space on the
> disk) and if you can replicate the problem start dropping some of the flags
> (like the parallel and the bigventricles etc, to find out if this is caused
> by one of the flags.)
>
> Anyway it looks more like an IO problem
> ncopen: filename "./tmp.mri_nu_correct.mni.53099/nu1.mnc": Not a netCDF
> file
> miopen: MINC package entry point
> Error opening ./tmp.mri_nu_correct.mni.53099/nu1.mnc
> mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.
> 53099/nu1.mnc
>
> is that file even there?
>
> Best, Martin
>
>
> > On 8. Nov 2017, at 19:56, miracle ozzoude  wrote:
> >
> > Hello FreeSurfer,
> >
> > While running base step of the longitudinal pipeline, i got the
> following error (please see the rec-all.log file for more details). How do
> i solve this problem? Thank you
> >
> > Best,
> > Paul
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
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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 Compliance
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


recon-all.error
Description: Binary data


recon-all.log
Description: Binary data


FreeSurferLongitudinal.sh
Description: Bourne shell script
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[Freesurfer] longitudinal base error. (not a netCDF file)

[miracle ozzoude]

Hello FreeSurfer,

While running base step of the longitudinal pipeline, i got the following
error (please see the rec-all.log file for more details). How do i solve
this problem? Thank you

Best,
Paul


recon-all.log
Description: Binary data
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Re: [Freesurfer] Fwd: cortical/subcortical volume based analysis

[miracle ozzoude]

Hello Bruce,

I am still waiting on your response or Lilla's. Thank you.

Best,
Paul

On Wed, Oct 18, 2017 at 8:20 PM, Bruce Fischl 
wrote:

> Hi Paul
>
> I was waiting for Lilla to respond :)
> Bruce
>
> On Wed, 18 Oct 2017, miracle ozzoude wrote:
>
> Hello Bruce,
>>
>> I wasn't sure if you answered my previous message hence, I'm sending it
>> again. Thank you.
>>
>> Best,
>> Paul
>>
>> -- Forwarded message --
>> From: miracle ozzoude 
>> Date: Sat, Oct 14, 2017 at 3:32 PM
>> Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
>> To: Freesurfer support list 
>>
>>
>> Hello Bruce,
>> Thank you for the response. I was able to look into CVS command and I
>> wrote a command on how to
>> register each subjects to cvs_avg35_inMNI152 template using the
>> following: mri_cvs_register --mov
>> subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz
>> --step1 --step2 --step3
>> --outdir  $SUBJECTS_DIR/$subID/cvs  --asegfname aparc+aseg --openmp 8. Do
>> i need to use the T1 in
>> the mri folder or mri.2mm folder when performing mri_cvs_register?
>>
>> My next goals are to:
>> 1) sample the volumes created using mri_cvs_register to the
>> cvs_avg35_inMNI152 template using
>> mri_vol2vol -reg .
>> -which of the outputs from mri_cvs_register should i use
>> to 
>> achieve?final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z,
>> or
>> final_CVSmorphed_toTEMPLATE_aseg.mgz
>> 2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the
>> output from mri_vol2vol.
>>   - How can I create the cortical mask from the
>> cvs_avg35_inMNI152/mri.2mm folder? This is
>> because the folder already has a subcortical mask and I want to create a
>> cortical mask, combine both
>> (using mri_merge) and use it to smooth with 8mm.
>>
>> 3) Lastly, use mri_concat to combine the smoothened maps in order to
>> perform group level analysis on
>> them.
>>   - when performing mri_glmfit on the combined maps, i don't need to
>> specify the --surf
>> fsaverage and lh/rh flags because it is a volume based analysis and it
>> was done on MNI template not
>> fsaverage?
>>
>> Thank you very much
>>
>> Best,
>> Paul
>>
>>
>> On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>>   Hi Paul
>>
>>   I guess you could use CVS for this.
>>
>>   cheers
>>   Bruce
>>   On Sat, 14 Oct 2017, miracle ozzoude wrote:
>>
>> Hello Bruce,
>>
>> Thank you very much. Can I still general cortical and
>> subcortical maps with
>> the Spherical warp of r/lh.white surface?  If yes, please
>> what are the steps
>> to achieve this? can I still analyze it with mri_glm?
>>
>> Best,
>> Paul
>>
>> Sent from my BlackBerry 10 smartphone.
>>   Original Message
>> From: Bruce Fischl
>> Sent: Saturday, October 14, 2017 11:27 AM
>> To: Freesurfer support list
>> Reply To: Freesurfer support list
>> Subject: Re: [Freesurfer] cortical/subcortical volume based
>> analysis
>>
>> Hi Paul
>>
>> if you use a property (like gm) to drive intersubject
>> registration it then
>> becomes difficult to also analyze it. If your warp was truly
>> perfect you
>> could just analyze the properties of the warp, but even then
>> it is hard to
>> localize effects (e.g. if you changed the smoothness of the
>> warp field
>> would the effect move somewhere else?). If the warp is not
>> perfect then
>> some of the effect is in your warp and some in the residual
>> anatomical
>> differences. There are lots of caveats like this you have to
>> worry about.
>> It's the reason we drive our spherical warp with the ?h.white
>> surface. It
>> is invariant to gm atrophy and so can be used to assess it
>> without worrying
>> about this kind of thing
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Fri, 13 Oct 2017, miracle ozzoude wrote:
>>
>>   Hello Bruce,
>>
>>   Thank you for the res

[Freesurfer] mri_cvs_register error

[miracle ozzoude]

Hello,

I am trying to run mri_cvs_register on a subject and I got an error (please
see attached log file). Below was the command I used. Thank you.

mri_cvs_register --mov 01091p --mni --step1 --step2 --step3 --outdir
/Users/MiracleOz/Documents/improvervsdeclinermri/01091p/cvs --asegfname
aparc+aseg --openmp 1

Best,

Paul


01091p_to_cvs_avg35_inMNI152.mri_cvs_register.1710211726.log
Description: Binary data


summary.01091p_to_cvs_avg35_inMNI152.mri_cvs_register.1710211726.log
Description: Binary data
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Re: [Freesurfer] Fwd: cortical/subcortical volume based analysis

[miracle ozzoude]

Hello Bruce, 

Thank you very much for the update. 

Best 
Paul

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Wednesday, October 18, 2017 8:20 PM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] Fwd: cortical/subcortical volume based analysis

Hi Paul

I was waiting for Lilla to respond :)
Bruce
On Wed, 18 Oct 2017, miracle ozzoude 
wrote:

> Hello Bruce, 
> 
> I wasn't sure if you answered my previous message hence, I'm sending it 
> again. Thank you.  
> 
> Best, 
> Paul
> 
> -- Forwarded message --
> From: miracle ozzoude 
> Date: Sat, Oct 14, 2017 at 3:32 PM
> Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
> To: Freesurfer support list 
> 
> 
> Hello Bruce, 
> Thank you for the response. I was able to look into CVS command and I wrote a 
> command on how to
> register each subjects to cvs_avg35_inMNI152 template using the following: 
> mri_cvs_register --mov
> subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz 
> --step1 --step2 --step3
> --outdir  $SUBJECTS_DIR/$subID/cvs  --asegfname aparc+aseg --openmp 8. Do i 
> need to use the T1 in
> the mri folder or mri.2mm folder when performing mri_cvs_register?
> 
> My next goals are to: 
> 1) sample the volumes created using mri_cvs_register to the 
> cvs_avg35_inMNI152 template using
> mri_vol2vol -reg .
>     -which of the outputs from mri_cvs_register should i use
> to 
> achieve?final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or
> final_CVSmorphed_toTEMPLATE_aseg.mgz
> 2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the 
> output from mri_vol2vol. 
>       - How can I create the cortical mask from the 
> cvs_avg35_inMNI152/mri.2mm folder? This is
> because the folder already has a subcortical mask and I want to create a 
> cortical mask, combine both
> (using mri_merge) and use it to smooth with 8mm. 
> 
> 3) Lastly, use mri_concat to combine the smoothened maps in order to perform 
> group level analysis on
> them. 
>       - when performing mri_glmfit on the combined maps, i don't need to 
> specify the --surf
> fsaverage and lh/rh flags because it is a volume based analysis and it was 
> done on MNI template not
> fsaverage? 
> 
> Thank you very much
> 
> Best, 
> Paul
> 
> 
> On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl  
> wrote:
> Hi Paul
>
> I guess you could use CVS for this.
>
> cheers
> Bruce
> On Sat, 14 Oct 2017, miracle ozzoude wrote:
>
> Hello Bruce, 
>
> Thank you very much. Can I still general cortical and subcortical maps with
> the Spherical warp of r/lh.white surface?  If yes, please what are the steps
> to achieve this? can I still analyze it with mri_glm?
>
> Best, 
> Paul
>
> Sent from my BlackBerry 10 smartphone.
>   Original Message  
> From: Bruce Fischl
> Sent: Saturday, October 14, 2017 11:27 AM
> To: Freesurfer support list
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
>
> Hi Paul
>
> if you use a property (like gm) to drive intersubject registration it then
> becomes difficult to also analyze it. If your warp was truly perfect you
> could just analyze the properties of the warp, but even then it is hard to
> localize effects (e.g. if you changed the smoothness of the warp field
> would the effect move somewhere else?). If the warp is not perfect then
> some of the effect is in your warp and some in the residual anatomical
> differences. There are lots of caveats like this you have to worry about.
> It's the reason we drive our spherical warp with the ?h.white surface. It
> is invariant to gm atrophy and so can be used to assess it without worrying
> about this kind of thing
>
> cheers
> Bruce
> 
> 
>
> On Fri, 13 Oct 2017, miracle ozzoude wrote:
>
> Hello Bruce,  
>
> Thank you for the response. I meant the latter ( making maps
> etc). I want to do something similar to the subcortical volume
> based analysis on PETSurfer page however, on freesurfer T1.
> Freesurfer doesn't perform VBM hence, why should there be a
> problem with interpretation? 
>
> Best, 
> Miracle
>
> Sent from my BlackBerry 10 smartphone.
>   Original Message  
> From: Bruce Fischl
> Sent: Friday, October 13, 2017 6:53 PM
> To: Freesurfer support list
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] cortical/subcortical volume based
> analysis
>
> Hi Paul
>
> we typically do this type of analysis by looking at scatter
> plots of
> structure volumes (e.g. hippocampus). Alternatively, you can
> make

[Freesurfer] Fwd: cortical/subcortical volume based analysis

[miracle ozzoude]

Hello Bruce, I wasn't sure if you answered my previous message hence, I'm sending it again. Thank you.  Best, Paul -- Forwarded message --From: miracle ozzoude <miracoo...@gmail.com>Date: Sat, Oct 14, 2017 at 3:32 PMSubject: Re: [Freesurfer] cortical/subcortical volume based analysisTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Hello Bruce, Thank you for the response. I was able to look into CVS command and I wrote a command on how to register each subjects to cvs_avg35_inMNI152 template using the following: mri_cvs_register --mov subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz
--step1 --step2 --step3 --outdir  $SUBJECTS_DIR/$subID/cvs
 --asegfname aparc+aseg --openmp 8. Do i need to use the T1 in the mri folder or mri.2mm folder when performing mri_cvs_register?My next goals are to: 1) sample the volumes created using mri_cvs_register to the cvs_avg35_inMNI152 template using mri_vol2vol -reg .    -which of the outputs from mri_cvs_register should i use to achieve?final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or final_CVSmorphed_toTEMPLATE_aseg.mgz2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the output from mri_vol2vol.       - How can I create the cortical mask from the cvs_avg35_inMNI152/mri.2mm folder? This is because the folder already has a subcortical mask and I want to create a cortical mask, combine both (using mri_merge) and use it to smooth with 8mm. 3) Lastly, use mri_concat to combine the smoothened maps in order to perform group level analysis on them.       - when performing mri_glmfit on the combined maps, i don't need to specify the --surf fsaverage and lh/rh flags because it is a volume based analysis and it was done on MNI template not fsaverage? Thank you very muchBest, Paul


















On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:Hi Paul

I guess you could use CVS for this.

cheers
Bruce
On Sat, 14 Oct 2017, miracle ozzoude wrote:


Hello Bruce, 

Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface?  If yes, please what are the steps to achieve this? can I still analyze it with mri_glm?

Best, 
Paul

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Saturday, October 14, 2017 11:27 AM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis

Hi Paul

if you use a property (like gm) to drive intersubject registration it then
becomes difficult to also analyze it. If your warp was truly perfect you
could just analyze the properties of the warp, but even then it is hard to
localize effects (e.g. if you changed the smoothness of the warp field
would the effect move somewhere else?). If the warp is not perfect then
some of the effect is in your warp and some in the residual anatomical
differences. There are lots of caveats like this you have to worry about.
It's the reason we drive our spherical warp with the ?h.white surface. It
is invariant to gm atrophy and so can be used to assess it without worrying
about this kind of thing

cheers
Bruce



On Fri, 13 Oct 2017, miracle ozzoude wrote:


Hello Bruce,  

Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation? 

Best, 
Miracle

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Friday, October 13, 2017 6:53 PM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis

Hi Paul

we typically do this type of analysis by looking at scatter plots of
structure volumes (e.g. hippocampus). Alternatively, you can make maps,
but that opens up all the problems/difficulties of interpretation of VBM.
Which did you mean?
cheers
Bruce

On Fri, 13 Oct 2017, miracle ozzoude wrote:


Hello FreeSurfer experts, 
I want to perform a whole brain volume based group analysis for cortical and subcortical regions.
That's something very similar to surface based group analysis for cortical thickness however, for
volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can
someone direct me how to go about doing it? My goal is to perform a group comparison between control
and PD patients based on volume. Thank you very much. 

Best, 
Paul 




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[Freesurfer] Fwd: cortical/subcortical volume based analysis

[miracle ozzoude]

-- Forwarded message --
From: miracle ozzoude 
Date: Sat, Oct 14, 2017 at 3:32 PM
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
To: Freesurfer support list 


Hello Bruce,

Thank you for the response. I was able to look into CVS command and I wrote
a command on how to register each subjects to cvs_avg35_inMNI152 template
using the following: mri_cvs_register --mov subID --mni
/Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz --step1 --step2
--step3 --outdir  $SUBJECTS_DIR/$subID/cvs  --asegfname aparc+aseg --openmp
8. Do i need to use the T1 in the mri folder or mri.2mm folder when
performing mri_cvs_register?

My next goals are to:
1) sample the volumes created using mri_cvs_register to the
cvs_avg35_inMNI152 template using mri_vol2vol -reg .
-which of the outputs from mri_cvs_register should i use to achieve?
final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or
final_CVSmorphed_toTEMPLATE_aseg.mgz

2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the
output from mri_vol2vol.
  - How can I create the cortical mask from the
cvs_avg35_inMNI152/mri.2mm folder? This is because the folder already has a
subcortical mask and I want to create a cortical mask, combine both (using
mri_merge) and use it to smooth with 8mm.

3) Lastly, use mri_concat to combine the smoothened maps in order to
perform group level analysis on them.
  - when performing mri_glmfit on the combined maps, i don't need to
specify the --surf fsaverage and lh/rh flags because it is a volume based
analysis and it was done on MNI template not fsaverage?

Thank you very much

Best,
Paul


On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl 
wrote:

> Hi Paul
>
> I guess you could use CVS for this.
>
> cheers
> Bruce
>
> On Sat, 14 Oct 2017, miracle ozzoude wrote:
>
> Hello Bruce,
>>
>> Thank you very much. Can I still general cortical and subcortical maps
>> with the Spherical warp of r/lh.white surface?  If yes, please what are the
>> steps to achieve this? can I still analyze it with mri_glm?
>>
>> Best,
>> Paul
>>
>> Sent from my BlackBerry 10 smartphone.
>>   Original Message
>> From: Bruce Fischl
>> Sent: Saturday, October 14, 2017 11:27 AM
>> To: Freesurfer support list
>> Reply To: Freesurfer support list
>> Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
>>
>> Hi Paul
>>
>> if you use a property (like gm) to drive intersubject registration it then
>> becomes difficult to also analyze it. If your warp was truly perfect you
>> could just analyze the properties of the warp, but even then it is hard to
>> localize effects (e.g. if you changed the smoothness of the warp field
>> would the effect move somewhere else?). If the warp is not perfect then
>> some of the effect is in your warp and some in the residual anatomical
>> differences. There are lots of caveats like this you have to worry about.
>> It's the reason we drive our spherical warp with the ?h.white surface. It
>> is invariant to gm atrophy and so can be used to assess it without
>> worrying
>> about this kind of thing
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Fri, 13 Oct 2017, miracle ozzoude wrote:
>>
>> Hello Bruce,
>>>
>>> Thank you for the response. I meant the latter ( making maps etc). I
>>> want to do something similar to the subcortical volume based analysis on
>>> PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM
>>> hence, why should there be a problem with interpretation?
>>>
>>> Best,
>>> Miracle
>>>
>>> Sent from my BlackBerry 10 smartphone.
>>>   Original Message
>>> From: Bruce Fischl
>>> Sent: Friday, October 13, 2017 6:53 PM
>>> To: Freesurfer support list
>>> Reply To: Freesurfer support list
>>> Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
>>>
>>> Hi Paul
>>>
>>> we typically do this type of analysis by looking at scatter plots of
>>> structure volumes (e.g. hippocampus). Alternatively, you can make maps,
>>> but that opens up all the problems/difficulties of interpretation of VBM.
>>> Which did you mean?
>>> cheers
>>> Bruce
>>>
>>> On Fri, 13 Oct 2017, miracle ozzoude wrote:
>>>
>>> Hello FreeSurfer experts,
>>>> I want to perform a whole brain volume based group analysis for
>>>> cortical and subcortical regions.
>>>> That's something very similar to surface based group analysis for
>>>> cortical thickness however, for
>&g

[Freesurfer] Fw: cortical/subcortical volume based analysis

[miracle ozzoude]

  Sent from my BlackBerry 10 smartphone.From: miracle ozzoude Sent: Saturday, October 14, 2017 3:32 PMTo: Freesurfer support listSubject: Re: [Freesurfer] cortical/subcortical volume based analysisHello Bruce, Thank you for the response. I was able to look into CVS command and I wrote a command on how to register each subjects to cvs_avg35_inMNI152 template using the following: mri_cvs_register --mov subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz
--step1 --step2 --step3 --outdir  $SUBJECTS_DIR/$subID/cvs
 --asegfname aparc+aseg --openmp 8. Do i need to use the T1 in the mri folder or mri.2mm folder when performing mri_cvs_register?My next goals are to: 1) sample the volumes created using mri_cvs_register to the cvs_avg35_inMNI152 template using mri_vol2vol -reg .    -which of the outputs from mri_cvs_register should i use to achieve?final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or final_CVSmorphed_toTEMPLATE_aseg.mgz2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the output from mri_vol2vol.       - How can I create the cortical mask from the cvs_avg35_inMNI152/mri.2mm folder? This is because the folder already has a subcortical mask and I want to create a cortical mask, combine both (using mri_merge) and use it to smooth with 8mm. 3) Lastly, use mri_concat to combine the smoothened maps in order to perform group level analysis on them.       - when performing mri_glmfit on the combined maps, i don't need to specify the --surf fsaverage and lh/rh flags because it is a volume based analysis and it was done on MNI template not fsaverage? Thank you very muchBest, Paul


















On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:Hi Paul

I guess you could use CVS for this.

cheers
Bruce
On Sat, 14 Oct 2017, miracle ozzoude wrote:


Hello Bruce, 

Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface?  If yes, please what are the steps to achieve this? can I still analyze it with mri_glm?

Best, 
Paul

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Saturday, October 14, 2017 11:27 AM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis

Hi Paul

if you use a property (like gm) to drive intersubject registration it then
becomes difficult to also analyze it. If your warp was truly perfect you
could just analyze the properties of the warp, but even then it is hard to
localize effects (e.g. if you changed the smoothness of the warp field
would the effect move somewhere else?). If the warp is not perfect then
some of the effect is in your warp and some in the residual anatomical
differences. There are lots of caveats like this you have to worry about.
It's the reason we drive our spherical warp with the ?h.white surface. It
is invariant to gm atrophy and so can be used to assess it without worrying
about this kind of thing

cheers
Bruce



On Fri, 13 Oct 2017, miracle ozzoude wrote:


Hello Bruce,  

Thank you for the response. I meant the latter ( making maps etc). I want to do something similar to the subcortical volume based analysis on PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should there be a problem with interpretation? 

Best, 
Miracle

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Friday, October 13, 2017 6:53 PM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis

Hi Paul

we typically do this type of analysis by looking at scatter plots of
structure volumes (e.g. hippocampus). Alternatively, you can make maps,
but that opens up all the problems/difficulties of interpretation of VBM.
Which did you mean?
cheers
Bruce

On Fri, 13 Oct 2017, miracle ozzoude wrote:


Hello FreeSurfer experts, 
I want to perform a whole brain volume based group analysis for cortical and subcortical regions.
That's something very similar to surface based group analysis for cortical thickness however, for
volume. Is there a tutorial on how to do it? if yes, please can i get the link. If not, please can
someone direct me how to go about doing it? My goal is to 

Re: [Freesurfer] cortical/subcortical volume based analysis

[miracle ozzoude]

Hello Bruce,

Thank you for the response. I was able to look into CVS command and I wrote
a command on how to register each subjects to cvs_avg35_inMNI152 template
using the following: mri_cvs_register --mov subID --mni
/Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz --step1 --step2
--step3 --outdir  $SUBJECTS_DIR/$subID/cvs  --asegfname aparc+aseg --openmp
8. Do i need to use the T1 in the mri folder or mri.2mm folder when
performing mri_cvs_register?

My next goals are to:
1) sample the volumes created using mri_cvs_register to the
cvs_avg35_inMNI152 template using mri_vol2vol -reg .
-which of the outputs from mri_cvs_register should i use to achieve?
final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or
final_CVSmorphed_toTEMPLATE_aseg.mgz

2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the
output from mri_vol2vol.
  - How can I create the cortical mask from the
cvs_avg35_inMNI152/mri.2mm folder? This is because the folder already has a
subcortical mask and I want to create a cortical mask, combine both (using
mri_merge) and use it to smooth with 8mm.

3) Lastly, use mri_concat to combine the smoothened maps in order to
perform group level analysis on them.
  - when performing mri_glmfit on the combined maps, i don't need to
specify the --surf fsaverage and lh/rh flags because it is a volume based
analysis and it was done on MNI template not fsaverage?

Thank you very much

Best,
Paul


On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl 
wrote:

> Hi Paul
>
> I guess you could use CVS for this.
>
> cheers
> Bruce
>
> On Sat, 14 Oct 2017, miracle ozzoude wrote:
>
> Hello Bruce,
>>
>> Thank you very much. Can I still general cortical and subcortical maps
>> with the Spherical warp of r/lh.white surface?  If yes, please what are the
>> steps to achieve this? can I still analyze it with mri_glm?
>>
>> Best,
>> Paul
>>
>> Sent from my BlackBerry 10 smartphone.
>>   Original Message
>> From: Bruce Fischl
>> Sent: Saturday, October 14, 2017 11:27 AM
>> To: Freesurfer support list
>> Reply To: Freesurfer support list
>> Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
>>
>> Hi Paul
>>
>> if you use a property (like gm) to drive intersubject registration it then
>> becomes difficult to also analyze it. If your warp was truly perfect you
>> could just analyze the properties of the warp, but even then it is hard to
>> localize effects (e.g. if you changed the smoothness of the warp field
>> would the effect move somewhere else?). If the warp is not perfect then
>> some of the effect is in your warp and some in the residual anatomical
>> differences. There are lots of caveats like this you have to worry about.
>> It's the reason we drive our spherical warp with the ?h.white surface. It
>> is invariant to gm atrophy and so can be used to assess it without
>> worrying
>> about this kind of thing
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Fri, 13 Oct 2017, miracle ozzoude wrote:
>>
>> Hello Bruce,
>>>
>>> Thank you for the response. I meant the latter ( making maps etc). I
>>> want to do something similar to the subcortical volume based analysis on
>>> PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM
>>> hence, why should there be a problem with interpretation?
>>>
>>> Best,
>>> Miracle
>>>
>>> Sent from my BlackBerry 10 smartphone.
>>>   Original Message
>>> From: Bruce Fischl
>>> Sent: Friday, October 13, 2017 6:53 PM
>>> To: Freesurfer support list
>>> Reply To: Freesurfer support list
>>> Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
>>>
>>> Hi Paul
>>>
>>> we typically do this type of analysis by looking at scatter plots of
>>> structure volumes (e.g. hippocampus). Alternatively, you can make maps,
>>> but that opens up all the problems/difficulties of interpretation of VBM.
>>> Which did you mean?
>>> cheers
>>> Bruce
>>>
>>> On Fri, 13 Oct 2017, miracle ozzoude wrote:
>>>
>>> Hello FreeSurfer experts,
>>>> I want to perform a whole brain volume based group analysis for
>>>> cortical and subcortical regions.
>>>> That's something very similar to surface based group analysis for
>>>> cortical thickness however, for
>>>> volume. Is there a tutorial on how to do it? if yes, please can i get
>>>> the link. If not, please can
>>>> someone direct me how to go about doing it? My goal 

Re: [Freesurfer] cortical/subcortical volume based analysis

[miracle ozzoude]

Hello Bruce, 

Thank you very much. Can I still general cortical and subcortical maps with the 
Spherical warp of r/lh.white surface?  ‎If yes, please what are the steps to 
achieve this? can I still analyze it with mri_glm?

Best, 
Paul

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Saturday, October 14, 2017 11:27 AM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis

Hi Paul

if you use a property (like gm) to drive intersubject registration it then 
becomes difficult to also analyze it. If your warp was truly perfect you 
could just analyze the properties of the warp, but even then it is hard to 
localize effects (e.g. if you changed the smoothness of the warp field 
would the effect move somewhere else?). If the warp is not perfect then 
some of the effect is in your warp and some in the residual anatomical 
differences. There are lots of caveats like this you have to worry about. 
It's the reason we drive our spherical warp with the ?h.white surface. It 
is invariant to gm atrophy and so can be used to assess it without worrying 
about this kind of thing

cheers
Bruce



On Fri, 13 Oct 2017, miracle ozzoude wrote:

> Hello Bruce,  
>
> Thank you for the response. I meant the latter ( making maps etc). I want to 
> do something similar to the subcortical volume based analysis on PETSurfer 
> page however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why 
> should there be a problem with interpretation? 
>
> Best, 
> Miracle
>
> Sent from my BlackBerry 10 smartphone.
>   Original Message  
> From: Bruce Fischl
> Sent: Friday, October 13, 2017 6:53 PM
> To: Freesurfer support list
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
>
> Hi Paul
>
> we typically do this type of analysis by looking at scatter plots of
> structure volumes (e.g. hippocampus). Alternatively, you can make maps,
> but that opens up all the problems/difficulties of interpretation of VBM.
> Which did you mean?
> cheers
> Bruce
>
> On Fri, 13 Oct 2017, miracle ozzoude wrote:
>
>> Hello FreeSurfer experts, 
>> I want to perform a whole brain volume based group analysis for cortical and 
>> subcortical regions.
>> That's something very similar to surface based group analysis for cortical 
>> thickness however, for
>> volume. Is there a tutorial on how to do it? if yes, please can i get the 
>> link. If not, please can
>> someone direct me how to go about doing it? My goal is to perform a group 
>> comparison between control
>> and PD patients based on volume. Thank you very much. 
>>
>> Best, 
>> Paul 
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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Re: [Freesurfer] cortical/subcortical volume based analysis

[miracle ozzoude]

Hello Bruce,  

Thank you for the response. I meant the latter ( making maps etc). I want to do 
something similar to the subcortical volume based analysis on PETSurfer page 
however, on freesurfer T1. Freesurfer doesn't perform VBM hence, why should 
there be a problem with interpretation? 

Best, 
Miracle

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Friday, October 13, 2017 6:53 PM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis

Hi Paul

we typically do this type of analysis by looking at scatter plots of 
structure volumes (e.g. hippocampus). Alternatively, you can make maps, 
but that opens up all the problems/difficulties of interpretation of VBM. 
Which did you mean?
cheers
Bruce

On Fri, 13 Oct 2017, miracle ozzoude wrote:

> Hello FreeSurfer experts, 
> I want to perform a whole brain volume based group analysis for cortical and 
> subcortical regions.
> That's something very similar to surface based group analysis for cortical 
> thickness however, for
> volume. Is there a tutorial on how to do it? if yes, please can i get the 
> link. If not, please can
> someone direct me how to go about doing it? My goal is to perform a group 
> comparison between control
> and PD patients based on volume. Thank you very much. 
> 
> Best, 
> Paul 
> 
>

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The information in this e-mail is intended only for the person to whom it is
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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] cortical/subcortical volume based analysis

[miracle ozzoude]

Hello FreeSurfer experts,

I want to perform a whole brain volume based group analysis for cortical
and subcortical regions. That's something very similar to surface based
group analysis for cortical thickness however, for volume. Is there a
tutorial on how to do it? if yes, please can i get the link. If not, please
can someone direct me how to go about doing it? My goal is to perform a
group comparison between control and PD patients based on volume. Thank you
very much.

Best,
Paul
___
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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] Fw: sim-sign abs/ cluster summary results confirmation

[miracle ozzoude]

Hello Doug,

Thank you very much for the response. Any reason why I have a list of
clusters when none of them were significant (based on the CWP). I thought
clusters that appeared on the summary text file should always be
significant because they survived correction.

Best,
Paul

On Mon, Sep 25, 2017 at 6:01 PM, Douglas N Greve 
wrote:

>
>
> On 09/24/2017 02:17 PM, miracle ozzoude wrote:
> >
> >
> > Sent from my BlackBerry 10 smartphone.
> > *From: *miracle ozzoude 
> > *Sent: *Friday, September 22, 2017 9:37 PM
> > *To: *Douglas N Greve
> > *Subject: *sim-sign abs/ cluster summary results confirmation
> >
> >
> > Hello,
> >
> > I ran cortical thickness analyses using the following contrast and
> > fsgd. After that, I corrected for multiple comparison using monte
> > carlo 5000 with cluster forming threshold of 2 and unsigned/2-tailed
> > t-test (abs). I wanted to confirm my interpretation of the results.
> >
> > 1) Since my contrast is (-1 1 0 0 representing control>stroke), it
> > should be red/yellow and if blue, it should be control > However, I see clusters with colors different from the aformentioned
> > (see attached screenshot). How should I interpret them?
> That is a parcellation/segmentation of the clusters, and the colors
> don't have inherent value. Eg, when you look at the aparc, you see
> precentral and postcentral are red and blue, but those colors don't mean
> anything, they are just a way to distinguish between areas. You have
> chosen abs, so it is not possible to interpret the sign.
> >
> > 2) I want to view the uncorrected p-values, which of the columns in
> > the summary text file should I concentrate, and should the p < or > 0.05?
> The uncorrected p-values are the voxel-wise values. The stats file will
> have the maximum uncorrected p-value (actually, -log10(p)).
> >
> > 3) Looking at the CWP column in the summary text file, can I conclude
> > that the obtained regions/clusters are significant? This is because
> > non of the cluster-wise p-values are below 0.05 (--cwp 0.05).
> Not sure which column you are talking about. All the CWP values are
> close to 1, so nothing is significant
> >
> > 4) Which of the columns represent the sign of my contrast i.e. where
> > Control>Stroke and Control if you used abs, then you can't interpret sign. Having said that, the
> "Max" column will indicate the sign of the vertex with the maximum
> -log10(p), and that will probably be the sign of the entire cluster
> >
> > FSGD file
> > GroupDescriptorFile
> > Title StrokevsControl
> > Class1 Stroke
> > Class2 Control
> > Variable bmi
> > Input 6001 Stroke 20
> > Input 8001 Control 30
> >
> > Contrast:
> > -1 1 0 0 (Control>Stroke removing the effects of bmi)
> >
> > Thank you,
> > Paul
> >
> >
> >
> >
> > ___
> > 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/
>
> ___
> 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.
>
>
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] freesurfer longitudinal pipeline

[miracle ozzoude]

Thank you very much Martin for your response. I do understand the
statistical analysis ascept, my question was more in line with the last
step (i.e. step 4) of the work flow summary (
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing). You
suggested we calculate the difference between the timepoints. Is there a
command to perform this operation?

Also, will the "-qdec-long" flag replace the "--s" flag because the qdec
table will contain the names of the fsid?

Best,
Paul

On Wed, Sep 27, 2017 at 11:38 AM, Martin Reuter  wrote:

> Hi Paul,
>
> for the statistical analysis take a look at the available options here:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics
>
>
> for asegstats2table you can use the --qdec-long flag with an appropriate
> text file containing the columns fsid and fsid-base . This will convince
> the script to look for the stats in the *.long.basename directories.
>
> Best, Martin
>
> Am 26.09.2017 um 17:50 schrieb miracle ozzoude:
>
> Hello Freesurfer,
>
> For the longitudinal pipeline, the website/ recon-all -help suggested that
> I calculate the different on the results from the longitudinal command
> (e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were
> named 1001_Baseline.long.longbase and 1001_Followup.long.longbase; is there
> a command i can use to preform this?
>
> Second question, i want to extract the output of the longitudinal pipeline
> using asegstats2table and aparcstats2table commands. what flag/s should i
> include in  the original command to perform this?
>
> Thanks.
> Paul
>
>
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[Freesurfer] freesurfer longitudinal pipeline

[miracle ozzoude]

Hello Freesurfer,

For the longitudinal pipeline, the website/ recon-all -help suggested that
I calculate the different on the results from the longitudinal command
(e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were
named 1001_Baseline.long.longbase and 1001_Followup.long.longbase; is there
a command i can use to preform this?

Second question, i want to extract the output of the longitudinal pipeline
using asegstats2table and aparcstats2table commands. what flag/s should i
include in  the original command to perform this?

Thanks.
Paul
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[Freesurfer] Fwd: longtitudinal pipeline

[miracle ozzoude]

-- Forwarded message --
From: miracle ozzoude 
Date: Fri, Sep 22, 2017 at 2:17 PM
Subject: longtitudinal pipeline
To: Douglas N Greve 


Hello Freesurfer,

For the longitudinal pipeline, the website/ recon-all -help suggested that
I calculate the different  on the results from the longitudinal command
(e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were
named 0001a.long.0001.longbase and 0001b.long.0001.longbase. is there a
command i can use to preform this?

Second question, i want to extract the output of the longitudinal pipeline
using asegstats2table and aparcstats2table commands. what flag/s should i
include in  the original command to perform this?

Thanks.
Paul
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[Freesurfer] Fw: sim-sign abs/ cluster summary results confirmation

[miracle ozzoude]

  Sent from my BlackBerry 10 smartphone.From: miracle ozzoude Sent: Friday, September 22, 2017 9:40 PMTo: Douglas N GreveSubject: Re: sim-sign abs/ cluster summary results confirmationI forgot to send the cluster summary sheet. Here is it. 







# Input      lh.stroke.fsgd.glmdir/contrast/sig.mgh
# Frame Number      0
# srcsubj fsaverage
# hemi lh
# surface white
# annot aparc
# SUBJECTS_DIR /Users/CT/Documents/stroke
# SearchSpace_mm2 65416.6
# SearchSpace_vtx 149953
# Bonferroni 0
# Minimum Threshold 2
# Maximum Threshold infinity
# Threshold Sign    abs
# AdjustThreshWhenOneTail 1
# Area Threshold    0 mm^2
# CSD thresh  2.00
# CSD nreps    5000
# CSD simtype  mc-z
# CSD contrast contrast
# CSD confint  90.00
# Overall max 2.26504 at vertex 146861
# Overall min -2.73325 at vertex 144073
# NClusters          13
# Total Cortical Surface Area 65416.6 (mm^2)
# FixMNI = 0
#
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ    CWP    CWPLow    CWPHi   NVtxs   Annot
   1       -2.733  144073     70.23    -31.5  -61.0  -15.8  0.99400  0.99260  0.99540   101  fusiform
   2       -2.537  153213     28.08    -14.2   40.2   12.1  1.0  -0.00020  1.0    57  superiorfrontal
   3       -2.348   57351     30.35    -63.3  -39.6    8.0  1.0  -0.00020  1.0    77  bankssts
   4        2.265  146861     20.30    -38.8  -57.9   25.4  1.0  -0.00020  1.0    45  inferiorparietal
   5       -2.261  116880     21.63    -33.3  -48.7   60.5  1.0  -0.00020  1.0    45  superiorparietal
   6        2.248   83406     24.49     -5.2   28.6   18.6  1.0  -0.00020  1.0    47  caudalanteriorcingulate
   7       -2.182   90669     20.62    -50.9  -56.2  -12.6  1.0  -0.00020  1.0    28  inferiortemporal
   8        2.143   32579      5.79     -7.9  -10.3   40.1  1.0  -0.00020  1.0    14  posteriorcingulate
   9       -2.052  159218      3.21     -5.0  -33.8   32.9  1.0  -0.00020  1.0     7  isthmuscingulate
  10       -2.050  127337      7.16    -17.7    6.2  -15.5  1.0  -0.00020  1.0    16  lateralorbitofrontal
  11       -2.013   93626      1.61    -37.4  -13.7   54.8  1.0  -0.00020  1.0     3  precentral
  12       -2.006    9896      0.87    -27.3   -0.6  -35.9  1.0  -0.00020  1.0     2  entorhinal
  13       -2.001   75892      0.47    -22.0  -33.4  -11.8  1.0  -0.00020  1.0     1  parahippocampalOn Fri, Sep 22, 2017 at 9:37 PM, miracle ozzoude <miracoo...@gmail.com> wrote:Hello, I ran cortical thickness analyses using the following contrast and fsgd. After that, I corrected for multiple comparison using monte carlo 5000 with cluster forming threshold of 2 and unsigned/2-tailed t-test (abs). I wanted to confirm my interpretation of the results. 1) Since my contrast is (-1 1 0 0 representing control>stroke), it should be red/yellow and if blue, it should be control2) I want to view the uncorrected p-values, which of the columns in the summary text file should I concentrate, and should the p < or > 0.05? 3) Looking at the CWP column in the summary text file, can I conclude that the obtained regions/clusters are significant? This is because non of the cluster-wise p-values are below 0.05 (--cwp 0.05). 4) Which of the columns represent the sign of my contrast i.e. where Control>Stroke and ControlFSGD file GroupDescriptorFile Title StrokevsControlClass1 StrokeClass2 Control Variable bmi Input 6001 Stroke 20Input 8001 Control 30 Contrast: -1 1 0 0 (Control>Stroke removing the effects of bmi)Thank you, Paul


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Re: [Freesurfer] sim-sign abs/ cluster summary results confirmation

[miracle ozzoude]

I forgot to send the cluster summary sheet. Here is it.

# Input  lh.stroke.fsgd.glmdir/contrast/sig.mgh

# Frame Number  0

# srcsubj fsaverage

# hemi lh

# surface white

# annot aparc

# SUBJECTS_DIR /Users/CT/Documents/stroke

# SearchSpace_mm2 65416.6

# SearchSpace_vtx 149953

# Bonferroni 0

# Minimum Threshold 2

# Maximum Threshold infinity

# Threshold Signabs

# AdjustThreshWhenOneTail 1

# Area Threshold0 mm^2

# CSD thresh  2.00

# CSD nreps5000

# CSD simtype  mc-z

# CSD contrast contrast

# CSD confint  90.00

# Overall max 2.26504 at vertex 146861

# Overall min -2.73325 at vertex 144073

# NClusters  13

# Total Cortical Surface Area 65416.6 (mm^2)

# FixMNI = 0

#

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
  CWPHi   NVtxs   Annot

   1   -2.733  144073 70.23-31.5  -61.0  -15.8  0.99400  0.99260
0.99540   101  fusiform

   2   -2.537  153213 28.08-14.2   40.2   12.1  1.0
-0.00020  1.057  superiorfrontal

   3   -2.348   57351 30.35-63.3  -39.68.0  1.0
-0.00020  1.077  bankssts

   42.265  146861 20.30-38.8  -57.9   25.4  1.0
-0.00020  1.045  inferiorparietal

   5   -2.261  116880 21.63-33.3  -48.7   60.5  1.0
-0.00020  1.045  superiorparietal

   62.248   83406 24.49 -5.2   28.6   18.6  1.0
-0.00020  1.047  caudalanteriorcingulate

   7   -2.182   90669 20.62-50.9  -56.2  -12.6  1.0
-0.00020  1.028  inferiortemporal

   82.143   32579  5.79 -7.9  -10.3   40.1  1.0
-0.00020  1.014  posteriorcingulate

   9   -2.052  159218  3.21 -5.0  -33.8   32.9  1.0
-0.00020  1.0 7  isthmuscingulate

  10   -2.050  127337  7.16-17.76.2  -15.5  1.0
-0.00020  1.016  lateralorbitofrontal

  11   -2.013   93626  1.61-37.4  -13.7   54.8  1.0
-0.00020  1.0 3  precentral

  12   -2.0069896  0.87-27.3   -0.6  -35.9  1.0
-0.00020  1.0 2  entorhinal

  13   -2.001   75892  0.47-22.0  -33.4  -11.8  1.0
-0.00020  1.0 1  parahippocampal

On Fri, Sep 22, 2017 at 9:37 PM, miracle ozzoude 
wrote:

> Hello,
>
> I ran cortical thickness analyses using the following contrast and fsgd.
> After that, I corrected for multiple comparison using monte carlo 5000 with
> cluster forming threshold of 2 and unsigned/2-tailed t-test (abs). I wanted
> to confirm my interpretation of the results.
>
> 1) Since my contrast is (-1 1 0 0 representing control>stroke), it should
> be red/yellow and if blue, it should be control clusters with colors different from the aformentioned (see attached
> screenshot). How should I interpret them?
>
> 2) I want to view the uncorrected p-values, which of the columns in the
> summary text file should I concentrate, and should the p < or > 0.05?
>
> 3) Looking at the CWP column in the summary text file, can I conclude that
> the obtained regions/clusters are significant? This is because non of the
> cluster-wise p-values are below 0.05 (--cwp 0.05).
>
> 4) Which of the columns represent the sign of my contrast i.e. where
> Control>Stroke and Control
> FSGD file
> GroupDescriptorFile
> Title StrokevsControl
> Class1 Stroke
> Class2 Control
> Variable bmi
> Input 6001 Stroke 20
> Input 8001 Control 30
>
> Contrast:
> -1 1 0 0 (Control>Stroke removing the effects of bmi)
>
> Thank you,
> Paul
>
>
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[Freesurfer] longtitudinal pipeline

[miracle ozzoude]

Hello Freesurfer,

For the longitudinal pipeline, the website/ recon-all -help suggested that
I calculate the different  on the results from the longitudinal command
(e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were
named 0001a.long.0001.longbase and 0001b.long.0001.longbase. is there a
command i can use to preform this?

Second question, i want to extract the output of the longitudinal pipeline
using asegstats2table and aparcstats2table commands. what flag/s should i
include in  the original command to perform this?

Thanks.
Paul
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[Freesurfer] Fwd: nu_correct failure

[miracle ozzoude]

-- Forwarded message --
From: miracle ozzoude 
Date: Thu, Sep 21, 2017 at 11:20 AM
Subject: nu_correct failure
To: Douglas N Greve 


Hello expert,

I ran several subjects on FS v6  and they failed on the same stage
(mri_nu_correct.mni and nu_correct). How can I solve this problem? I have
attache the recon-all.log file for 2 subjects.

Best,
Paul


recon-all.log
Description: Binary data


recon-all.log
Description: Binary data
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[Freesurfer] nu_correct failure

[miracle ozzoude]

Hello expert,

I ran several subjects on FS v6  and they failed on the same stage
(mri_nu_correct.mni and nu_correct). How can I solve this problem? I have
attache the recon-all.log file for 2 subjects.

Best,
Paul


recon-all.log
Description: Binary data


recon-all.log
Description: Binary data
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[Freesurfer] Fw: Multiple comparison, color maps and contrast

[miracle ozzoude]

  Sent from my BlackBerry 10 smartphone.From: miracle ozzoude Sent: Sunday, September 17, 2017 11:01 AMTo: Freesurfer support listSubject: Multiple comparison, color maps and contrast  Hello, I want to run a whole brain cortical thickness analysis and I will like to confirm some steps. a) for correcting for multiple comparison, I want to use both Monte Carlo and permutations in order to compare the difference. Are these the right commands?  Monte Carlo : mri_glmfit-sim --glmdir lh.name.glmdir --sim mc-z 5000 2 mc-z.abs.2 --sm-sign abs --cwp 0.05 --overwrite Permutation: mri_glmfit-sim --glmdir lh.name.glmdir --sim perm 5000 2  permcsd --sim-sign abs --cwp 0.05 --perm-resid --overwriteb) I have 2 groups and a contrast of (1 -1 0 0) representing where group 1> group 2 removing the effect of age. If I correct for multiple comparisons using abs and while visualizing my result the color map for the surviving clusters is blue , this means areas where  group 1 < group 2. If the color map for the surviving clusters is red/yellow, this means areas where group 1> group 2. Thank you.   Best, Paul Sent from my BlackBerry 10 smartphone.

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[Freesurfer] Multiple comparison, color maps and contrast

[miracle ozzoude]

 Hello, I want to run a whole brain cortical thickness analysis and I will like to confirm some steps. a) for correcting for multiple comparison, I want to use both Monte Carlo and permutations in order to compare the difference. Are these the right commands?  Monte Carlo : mri_glmfit-sim --glmdir lh.name.glmdir --sim mc-z 5000 2 mc-z.abs.2 --sm-sign abs --cwp 0.05 --overwrite Permutation: mri_glmfit-sim --glmdir lh.name.glmdir --sim perm 5000 2  permcsd --sim-sign abs --cwp 0.05 --perm-resid --overwriteb) I have 2 groups and a contrast of (1 -1 0 0) representing where group 1> group 2 removing the effect of age. If I correct for multiple comparisons using abs and while visualizing my result the color map for the surviving clusters is blue , this means areas where  group 1 < group 2. If the color map for the surviving clusters is red/yellow, this means areas where group 1> group 2. Thank you.   Best, Paul Sent from my BlackBerry 10 smartphone.
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Re: [Freesurfer] control point and aseg edit

[miracle ozzoude]

Thank you very much Bruce.

Best,
Paul

On Thu, Sep 14, 2017 at 4:02 PM, Bruce Fischl 
wrote:

> I mean there will be no subsequent command that turn of the use of control
> points in the aseg
>
>
> cheers
> Bruce
>
>
> On Thu, 14 Sep 2017, miracle ozzoude wrote:
>
> Thanks Bruce. resetting means, all my changes will be incorporated into
>> the final output files?
>> Best,
>> Paul
>>
>> On Thu, Sep 14, 2017 at 3:52 PM, Bruce Fischl 
>> wrote:
>>   I'm not sure it matters, but if you put it at the end nothing will
>> reset it
>>   On Thu, 14 Sep 2017, miracle ozzoude wrote:
>>
>> Hello Bruce,
>> Yes, that is my end goal. I have a patient i edited the aseg
>> to include
>> left-cerebral white matter
>> and also, want to normalize the intensity using expert
>> option. Where should
>> I place the
>> "-canorm-usecps" flag ? After the command like " recon-all
>> -autorecon2
>> -autorecon3 -expert -parallel
>> -openmp 8 -bigventricles -3T time -canorm-usecps" or before
>> autorecon2 like
>> "recon-all -autorecon2
>> -canorm-usecps -autorecon3 -expert -parallel -openmp 8
>> -bigventricles -3T
>> time. Thank you.
>>
>> Best,
>> Paul
>>
>> On Thu, Sep 14, 2017 at 3:17 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   do you want the control points to be applied to the
>> aseg? If so, you
>> need to also
>>   specify -canorm-usecps
>>
>>   cheers
>>   Bruce
>>   On Thu, 14 Sep 2017, miracle ozzoude wrote:
>>
>> Thanks Bruce. Yes, I want to regenerate the aseg
>> and also use
>> the expert
>> option for control point.
>> That's recon-all -autorecon2 -autorecon3 -expert
>> -parallel
>> -openmp 8
>> -bigventricles -3T time.
>> Best,
>> Paul
>>
>> On Thu, Sep 14, 2017 at 2:48 PM, Bruce Fischl
>> 
>>     wrote:
>>   do you want it to regenerate the aseg? If
>> not, then a). If
>> so, then
>> you would just run
>>   autorecon2 (instead of autorecon2-cp)
>>
>>   cheers
>>   Bruce
>>   On Thu, 14 Sep 2017, miracle ozzoude wrote:
>>
>> I used the expert option for control
>> points and
>> manually edited
>> the
>> aseg.presurf.mgz. Which is the
>> proper flag to use in other to
>> incorporate the
>> respective
>> changes?
>> a) recon-all -autorecon2-cp
>> -autorecon2-noaseg
>> -autorecon3
>> -expert -parallel
>> -openmp 8
>> -bigventricles -3T -time
>>
>> or
>>
>> b) recon-all -autorecon2-cp
>> -autorecon3 -expert
>> -parallel
>> -openmp 8
>> -bigventricles -3T -time
>>
>> Thanks.
>>
>> Best,
>> Paul
>>
>>
>>
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.e
>> du/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
>>

Re: [Freesurfer] control point and aseg edit

[miracle ozzoude]

Thanks Bruce. resetting means, all my changes will be incorporated into the
final output files?

Best,
Paul

On Thu, Sep 14, 2017 at 3:52 PM, Bruce Fischl 
wrote:

> I'm not sure it matters, but if you put it at the end nothing will reset it
>
> On Thu, 14 Sep 2017, miracle ozzoude wrote:
>
> Hello Bruce,
>> Yes, that is my end goal. I have a patient i edited the aseg to include
>> left-cerebral white matter
>> and also, want to normalize the intensity using expert option. Where
>> should I place the
>> "-canorm-usecps" flag ? After the command like " recon-all -autorecon2
>> -autorecon3 -expert -parallel
>> -openmp 8 -bigventricles -3T time -canorm-usecps" or before autorecon2
>> like "recon-all -autorecon2
>> -canorm-usecps -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T
>> time. Thank you.
>>
>> Best,
>> Paul
>>
>> On Thu, Sep 14, 2017 at 3:17 PM, Bruce Fischl 
>> wrote:
>>   do you want the control points to be applied to the aseg? If so,
>> you need to also
>>   specify -canorm-usecps
>>
>>   cheers
>>   Bruce
>>   On Thu, 14 Sep 2017, miracle ozzoude wrote:
>>
>> Thanks Bruce. Yes, I want to regenerate the aseg and also use
>> the expert
>> option for control point.
>> That's recon-all -autorecon2 -autorecon3 -expert -parallel
>> -openmp 8
>> -bigventricles -3T time.
>> Best,
>> Paul
>>
>> On Thu, Sep 14, 2017 at 2:48 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>       do you want it to regenerate the aseg? If not, then a).
>> If so, then
>> you would just run
>>   autorecon2 (instead of autorecon2-cp)
>>
>>   cheers
>>   Bruce
>>   On Thu, 14 Sep 2017, miracle ozzoude wrote:
>>
>> I used the expert option for control points and
>> manually edited
>> the
>> aseg.presurf.mgz. Which is the
>> proper flag to use in other to incorporate the
>> respective
>> changes?
>> a) recon-all -autorecon2-cp -autorecon2-noaseg
>> -autorecon3
>> -expert -parallel
>> -openmp 8
>> -bigventricles -3T -time
>>
>> or
>>
>> b) recon-all -autorecon2-cp -autorecon3 -expert
>> -parallel
>> -openmp 8
>> -bigventricles -3T -time
>>
>> Thanks.
>>
>> Best,
>> Paul
>>
>>
>>
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>>
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>> 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
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>> but does not contain patient information, please contact the
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>> properly
>> dispose of the e-mail.
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Re: [Freesurfer] control point and aseg edit

[miracle ozzoude]

Hello Bruce,

Yes, that is my end goal. I have a patient i edited the aseg to include
left-cerebral white matter and also, want to normalize the intensity using
expert option. Where should I place the "-canorm-usecps" flag ? After the
command like " recon-all -autorecon2 -autorecon3 -expert -parallel -openmp
8 -bigventricles -3T time -canorm-usecps" or before autorecon2 like "recon-all
-autorecon2 -canorm-usecps -autorecon3 -expert -parallel -openmp 8
-bigventricles -3T time. Thank you.

Best,
Paul

On Thu, Sep 14, 2017 at 3:17 PM, Bruce Fischl 
wrote:

> do you want the control points to be applied to the aseg? If so, you need
> to also specify -canorm-usecps
>
>
> cheers
> Bruce
> On Thu, 14 Sep 2017, miracle ozzoude wrote:
>
> Thanks Bruce. Yes, I want to regenerate the aseg and also use the expert
>> option for control point.
>> That's recon-all -autorecon2 -autorecon3 -expert -parallel -openmp 8
>> -bigventricles -3T time.
>> Best,
>> Paul
>>
>> On Thu, Sep 14, 2017 at 2:48 PM, Bruce Fischl 
>> wrote:
>>   do you want it to regenerate the aseg? If not, then a). If so, then
>> you would just run
>>   autorecon2 (instead of autorecon2-cp)
>>
>>   cheers
>>   Bruce
>>   On Thu, 14 Sep 2017, miracle ozzoude wrote:
>>
>> I used the expert option for control points and manually
>> edited the
>> aseg.presurf.mgz. Which is the
>> proper flag to use in other to incorporate the respective
>> changes?
>> a) recon-all -autorecon2-cp -autorecon2-noaseg -autorecon3
>> -expert -parallel
>> -openmp 8
>> -bigventricles -3T -time
>>
>> or
>>
>> b) recon-all -autorecon2-cp -autorecon3 -expert -parallel
>> -openmp 8
>> -bigventricles -3T -time
>>
>> Thanks.
>>
>> Best,
>> Paul
>>
>>
>>
>> ___
>> 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.
>>
>>
>>
>>
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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
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> but does not contain patient information, please contact the sender and
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Re: [Freesurfer] control point and aseg edit

[miracle ozzoude]

Thanks Bruce. Yes, I want to regenerate the aseg and also use the expert
option for control point. That's recon-all -autorecon2 -autorecon3 -expert
-parallel -openmp 8 -bigventricles -3T time.

Best,
Paul

On Thu, Sep 14, 2017 at 2:48 PM, Bruce Fischl 
wrote:

> do you want it to regenerate the aseg? If not, then a). If so, then you
> would just run autorecon2 (instead of autorecon2-cp)
>
> cheers
> Bruce
>
> On Thu, 14 Sep 2017, miracle ozzoude wrote:
>
> I used the expert option for control points and manually edited the
>> aseg.presurf.mgz. Which is the
>> proper flag to use in other to incorporate the respective changes?
>> a) recon-all -autorecon2-cp -autorecon2-noaseg -autorecon3 -expert
>> -parallel -openmp 8
>> -bigventricles -3T -time
>>
>> or
>>
>> b) recon-all -autorecon2-cp -autorecon3 -expert -parallel -openmp 8
>> -bigventricles -3T -time
>>
>> Thanks.
>>
>> Best,
>> Paul
>>
>>
>>
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>
>
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> 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
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[Freesurfer] control point and aseg edit

[miracle ozzoude]

I used the expert option for control points and manually edited the
aseg.presurf.mgz. Which is the proper flag to use in other to incorporate
the respective changes?

a) recon-all -autorecon2-cp -autorecon2-noaseg -autorecon3 -expert
-parallel -openmp 8 -bigventricles -3T -time

or

b) recon-all -autorecon2-cp -autorecon3 -expert -parallel -openmp 8
-bigventricles -3T -time

Thanks.

Best,
Paul
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Re: [Freesurfer] combining a stroke lesion label with aseg.presurf.mgz

[miracle ozzoude]

Thanks doug. If I run the recon-all -autorecon2-noaseg -autorecon3. Will it
incorporate the stroke? Also, does it matter if it's a cortical stroke and
i am using v6.0 and i don't see aseg.manedit.mgz.

Best,
Paul

On Thu, Sep 7, 2017 at 12:38 PM, Douglas N Greve 
wrote:

>
> try something like
>
> mergeseg --src aseg.presurf.mgz --merge stroke.mgz --o aseg.manedit.mgz
> --segid 77
>
> This will model the strokes as WM  hypointensities
>
> On 09/07/2017 11:54 AM, miracle ozzoude wrote:
> > Hello FreeSurfer expert,
> >
> > I have a binarized stroke masks of 200 stroke patients that were hand
> > traced. Since, we have a lot of patients, it will take a lot of time
> > to edit the aseg.presurf.mgz. The stroke masks were drawn in the
> > native space and I want to bring them into the freesurfer space, and
> > combine with the aseg.presurf.mgz/stamp it onto the aseg.presurf.mgz
> > and then run recon-all -autorecon2-noaseg -autorecon3.
> >
> > I have done the first part:
> > 1) mri_convert -rl /subject/mri/brainmask.mgz -rt nearest stroke.nii
> > stroke.mgz (use freeview to check the accuracy)
> >
> > I want to combine the stroke.mgz with the aseg.presurf.mgz in order to
> > create a new ROI. what command should I use to accomplish this? Thanks
> >
> > Best,
> >
> > Paul
> >
> >
> >
> >
> >
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>
> --
> 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
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> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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[Freesurfer] combining a stroke lesion label with aseg.presurf.mgz

[miracle ozzoude]

Hello FreeSurfer expert,

I have a binarized stroke masks of 200 stroke patients that were hand
traced. Since, we have a lot of patients, it will take a lot of time to
edit the aseg.presurf.mgz. The stroke masks were drawn in the native space
and I want to bring them into the freesurfer space, and combine with the
aseg.presurf.mgz/stamp it onto the aseg.presurf.mgz and then run recon-all
-autorecon2-noaseg -autorecon3.

I have done the first part:
1) mri_convert -rl /subject/mri/brainmask.mgz -rt nearest stroke.nii
stroke.mgz (use freeview to check the accuracy)

I want to combine the stroke.mgz with the aseg.presurf.mgz in order to
create a new ROI. what command should I use to accomplish this? Thanks

Best,

Paul
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