Re: [Freesurfer] Extract specific LGI and Volume values

2020-01-16 Thread Tien Pham 
External Email - Use Caution

Thank you for your help.
I cannot load the label on surface, this is the error:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% qdec



Reading /applications/freesurfer/tktools/tkUtils.tcl



Using /applications/freesurfer/lib/tcl/fsgdfPlot.tcl

qdec.bin(41334,0xa15971a8) malloc: *** mach_vm_map(size=114944) failed
(error code=3)

*** error: can't allocate region

*** set a breakpoint in malloc_error_break to debug

MRISalloc(15124178, 76): could not allocate faces

Cannot allocate memory


What do you mean how many point? How do I find it?

On Fri, Jan 17, 2020 at 1:17 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Is the label valid? Can you load it on a surface? How many points are in
> it?
>
> On 1/16/2020 9:51 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Thank you for your e-mail.
> It seems I got another error. This is what it showed in terminal:
>
> [toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats
> --i lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum
> sum.dat
>
>
>
> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
>
> cwd
>
> cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh
> lh.frontoinsula.label --id 1 --sum sum.dat
>
> sysname  Darwin
>
> hostname toyama-no-iMac.local
>
> machine  x86_64
>
> user toyama
>
> UseRobust  0
>
> Constructing seg from label
>
> Segmentation fault
>
>
> Could you help me please?
>
> On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Sorry, it should have been --sum instead of --o
>> the subject name is subject_id
>> --id 1 just means to take the vertices in the label (--id 0 would mean to
>> take the background)
>>
>> On 1/16/2020 7:07 PM, Tien Pham wrote:
>>
>> External Email - Use Caution
>> Thank you very much for your e-mail.
>> I tried, but this '' --o '' is unknown showing in terminal and the ''
>> --id '' flag is subject name?
>> Could you please help me?
>> For example, I found the change in frontoinsula region between 2 groups
>> in my dataset and I want to extract the values of this region.
>>
>> On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> It might be easier to use mri_segstats, eg,
>>>
>>> mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label
>>> --id 1 --o sum.dat
>>>
>>> The mean value will be in the "Mean" column of the sum.dat
>>>
>>>
>>> On 1/14/2020 7:08 PM, Tien Pham wrote:
>>>
>>> External Email - Use Caution
>>> Dear FreeSurfer Experts,
>>>
>>> I am Tien Pham, I am stucked at this situation. I calculated
>>> longitudinal LGI changes in my data set with two time points using
>>> longitudinal pipeline. Now I would like to extract the regional LGI and
>>> gray matter volume in my longitudinal results using QDEC to draw the ROIs
>>> which is showed significant differences, label it and map to all subjects.
>>> Then I get the LGI value of the ROI I saved before using the command below:
>>>
>>> cd $SUBJECTS_DIR
>>> mris_anatomical_stats -l lh.untitled.label \
>>>  -t lh.pial_lgi \
>>>  -b \
>>>  -f subject_id/stats/lh.untitled.stats subject_id lh
>>>
>>> And this is the result:
>>>
>>> [toyama-no-iMac:/applications/freesurfer/subjects] toyama%
>>> mris_anatomical_stats -l lh.frontoinsula.label \
>>>
>>> ? -t lh.pial_lgi \
>>>
>>> ? -b \
>>>
>>> ? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
>>>
>>> limiting computations to label lh.frontoinsula.label.
>>>
>>> using thickness file lh.pial_lgi.
>>>
>>> reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
>>>
>>> reading input surface
>>> /applications/freesurfer/subjects/VC019_1/surf/lh.white...
>>>
>>> reading input pial surface
>>> /applications/freesurfer/subjects/VC019_1/surf/lh.pial...
>>>
>>> reading input white surface
>>> /applications/freesurfer/subjects/VC019_1/surf/lh.white...
>>>
>>>
>>>
>>> table columns are:
>>>
>>> number of vertices
>>>
>>> total surface area (mm^2)
>>>
>>> total gray matter volume (mm^3)
>>>
>>> average cortical thickness +- standard deviation (mm)
>>>
>>> integrated rectified mean curvature
>>>
>>> integrated rectified Gaussian curvature
>>>
>>> folding index
>>>
>>> intrinsic curvature index
>>>
>>> structure name
>>>
>>>
>>>
>>>  6595   4368  15935  3.311 0.895 0.158 0.077  13519.7
>>> lh.frontoinsula.label
>>>
>>>
>>> As I saw there was no columns showing the LGI value, I did similar with
>>> gray matter volume, the result displayed the different in some values of
>>> the columns.
>>> Could you please help me to explain about this?
>>>
>>> Thank you very much.
>>>
>>>
>>> Best regards,
>>>
>>> Tien Pham
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>

Re: [Freesurfer] Extract specific LGI and Volume values

2020-01-16 Thread Greve, Douglas N.,Ph.D. 
Is the label valid? Can you load it on a surface? How many points are in it?

On 1/16/2020 9:51 PM, Tien Pham wrote:

External Email - Use Caution

Thank you for your e-mail.
It seems I got another error. This is what it showed in terminal:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats --i 
lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum sum.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label 
--id 1 --sum sum.dat
sysname  Darwin
hostname toyama-no-iMac.local
machine  x86_64
user toyama
UseRobust  0
Constructing seg from label
Segmentation fault

Could you help me please?

On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Sorry, it should have been --sum instead of --o
the subject name is subject_id
--id 1 just means to take the vertices in the label (--id 0 would mean to take 
the background)

On 1/16/2020 7:07 PM, Tien Pham wrote:

External Email - Use Caution

Thank you very much for your e-mail.
I tried, but this '' --o '' is unknown showing in terminal and the '' --id '' 
flag is subject name?
Could you please help me?
For example, I found the change in frontoinsula region between 2 groups in my 
dataset and I want to extract the values of this region.

On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
It might be easier to use mri_segstats, eg,

mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1 
--o sum.dat

The mean value will be in the "Mean" column of the sum.dat


On 1/14/2020 7:08 PM, Tien Pham wrote:

External Email - Use Caution

Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI 
changes in my data set with two time points using longitudinal pipeline. Now I 
would like to extract the regional LGI and gray matter volume in my 
longitudinal results using QDEC to draw the ROIs which is showed significant 
differences, label it and map to all subjects. Then I get the LGI value of the 
ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \
 -f subject_id/stats/lh.untitled.stats subject_id lh

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% 
mris_anatomical_stats -l lh.frontoinsula.label \
? -t lh.pial_lgi \
? -b \
? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
limiting computations to label lh.frontoinsula.label.
using thickness file lh.pial_lgi.
reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white...
reading input pial surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.pial...
reading input white surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.white...

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

 6595   4368  15935  3.311 0.895 0.158 0.077  13519.7  
lh.frontoinsula.label

As I saw there was no columns showing the LGI value, I did similar with gray 
matter volume, the result displayed the different in some values of the columns.
Could you please help me to explain about this?
Thank you very much.

Best regards,
Tien Pham



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Re: [Freesurfer] Extract specific LGI and Volume values

2020-01-16 Thread Tien Pham 
External Email - Use Caution

Thank you for your e-mail.
It seems I got another error. This is what it showed in terminal:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats --i
lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum sum.dat



$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $

cwd

cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh
lh.frontoinsula.label --id 1 --sum sum.dat

sysname  Darwin

hostname toyama-no-iMac.local

machine  x86_64

user toyama

UseRobust  0

Constructing seg from label

Segmentation fault


Could you help me please?

On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Sorry, it should have been --sum instead of --o
> the subject name is subject_id
> --id 1 just means to take the vertices in the label (--id 0 would mean to
> take the background)
>
> On 1/16/2020 7:07 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Thank you very much for your e-mail.
> I tried, but this '' --o '' is unknown showing in terminal and the '' --id
> '' flag is subject name?
> Could you please help me?
> For example, I found the change in frontoinsula region between 2 groups in
> my dataset and I want to extract the values of this region.
>
> On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> It might be easier to use mri_segstats, eg,
>>
>> mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label
>> --id 1 --o sum.dat
>>
>> The mean value will be in the "Mean" column of the sum.dat
>>
>>
>> On 1/14/2020 7:08 PM, Tien Pham wrote:
>>
>> External Email - Use Caution
>> Dear FreeSurfer Experts,
>>
>> I am Tien Pham, I am stucked at this situation. I calculated longitudinal
>> LGI changes in my data set with two time points using longitudinal
>> pipeline. Now I would like to extract the regional LGI and gray matter
>> volume in my longitudinal results using QDEC to draw the ROIs which is
>> showed significant differences, label it and map to all subjects. Then I
>> get the LGI value of the ROI I saved before using the command below:
>>
>> cd $SUBJECTS_DIR
>> mris_anatomical_stats -l lh.untitled.label \
>>  -t lh.pial_lgi \
>>  -b \
>>  -f subject_id/stats/lh.untitled.stats subject_id lh
>>
>> And this is the result:
>>
>> [toyama-no-iMac:/applications/freesurfer/subjects] toyama%
>> mris_anatomical_stats -l lh.frontoinsula.label \
>>
>> ? -t lh.pial_lgi \
>>
>> ? -b \
>>
>> ? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
>>
>> limiting computations to label lh.frontoinsula.label.
>>
>> using thickness file lh.pial_lgi.
>>
>> reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
>>
>> reading input surface
>> /applications/freesurfer/subjects/VC019_1/surf/lh.white...
>>
>> reading input pial surface
>> /applications/freesurfer/subjects/VC019_1/surf/lh.pial...
>>
>> reading input white surface
>> /applications/freesurfer/subjects/VC019_1/surf/lh.white...
>>
>>
>>
>> table columns are:
>>
>> number of vertices
>>
>> total surface area (mm^2)
>>
>> total gray matter volume (mm^3)
>>
>> average cortical thickness +- standard deviation (mm)
>>
>> integrated rectified mean curvature
>>
>> integrated rectified Gaussian curvature
>>
>> folding index
>>
>> intrinsic curvature index
>>
>> structure name
>>
>>
>>
>>  6595   4368  15935  3.311 0.895 0.158 0.077  13519.7
>> lh.frontoinsula.label
>>
>>
>> As I saw there was no columns showing the LGI value, I did similar with
>> gray matter volume, the result displayed the different in some values of
>> the columns.
>> Could you please help me to explain about this?
>>
>> Thank you very much.
>>
>>
>> Best regards,
>>
>> Tien Pham
>>
>> ___
>> 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
>
>
> ___
> 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
___
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Re: [Freesurfer] Extract specific LGI and Volume values

2020-01-16 Thread Greve, Douglas N.,Ph.D. 
Sorry, it should have been --sum instead of --o
the subject name is subject_id
--id 1 just means to take the vertices in the label (--id 0 would mean to take 
the background)

On 1/16/2020 7:07 PM, Tien Pham wrote:

External Email - Use Caution

Thank you very much for your e-mail.
I tried, but this '' --o '' is unknown showing in terminal and the '' --id '' 
flag is subject name?
Could you please help me?
For example, I found the change in frontoinsula region between 2 groups in my 
dataset and I want to extract the values of this region.

On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
It might be easier to use mri_segstats, eg,

mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1 
--o sum.dat

The mean value will be in the "Mean" column of the sum.dat


On 1/14/2020 7:08 PM, Tien Pham wrote:

External Email - Use Caution

Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI 
changes in my data set with two time points using longitudinal pipeline. Now I 
would like to extract the regional LGI and gray matter volume in my 
longitudinal results using QDEC to draw the ROIs which is showed significant 
differences, label it and map to all subjects. Then I get the LGI value of the 
ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \
 -f subject_id/stats/lh.untitled.stats subject_id lh

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% 
mris_anatomical_stats -l lh.frontoinsula.label \
? -t lh.pial_lgi \
? -b \
? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
limiting computations to label lh.frontoinsula.label.
using thickness file lh.pial_lgi.
reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white...
reading input pial surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.pial...
reading input white surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.white...

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

 6595   4368  15935  3.311 0.895 0.158 0.077  13519.7  
lh.frontoinsula.label

As I saw there was no columns showing the LGI value, I did similar with gray 
matter volume, the result displayed the different in some values of the columns.
Could you please help me to explain about this?
Thank you very much.

Best regards,
Tien Pham



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Re: [Freesurfer] Extract specific LGI and Volume values

2020-01-16 Thread Tien Pham 
External Email - Use Caution

Thank you very much for your e-mail.
I tried, but this '' --o '' is unknown showing in terminal and the '' --id
'' flag is subject name?
Could you please help me?
For example, I found the change in frontoinsula region between 2 groups in
my dataset and I want to extract the values of this region.

On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> It might be easier to use mri_segstats, eg,
>
> mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id
> 1 --o sum.dat
>
> The mean value will be in the "Mean" column of the sum.dat
>
>
> On 1/14/2020 7:08 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Dear FreeSurfer Experts,
>
> I am Tien Pham, I am stucked at this situation. I calculated longitudinal
> LGI changes in my data set with two time points using longitudinal
> pipeline. Now I would like to extract the regional LGI and gray matter
> volume in my longitudinal results using QDEC to draw the ROIs which is
> showed significant differences, label it and map to all subjects. Then I
> get the LGI value of the ROI I saved before using the command below:
>
> cd $SUBJECTS_DIR
> mris_anatomical_stats -l lh.untitled.label \
>  -t lh.pial_lgi \
>  -b \
>  -f subject_id/stats/lh.untitled.stats subject_id lh
>
> And this is the result:
>
> [toyama-no-iMac:/applications/freesurfer/subjects] toyama%
> mris_anatomical_stats -l lh.frontoinsula.label \
>
> ? -t lh.pial_lgi \
>
> ? -b \
>
> ? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
>
> limiting computations to label lh.frontoinsula.label.
>
> using thickness file lh.pial_lgi.
>
> reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
>
> reading input surface
> /applications/freesurfer/subjects/VC019_1/surf/lh.white...
>
> reading input pial surface
> /applications/freesurfer/subjects/VC019_1/surf/lh.pial...
>
> reading input white surface
> /applications/freesurfer/subjects/VC019_1/surf/lh.white...
>
>
>
> table columns are:
>
> number of vertices
>
> total surface area (mm^2)
>
> total gray matter volume (mm^3)
>
> average cortical thickness +- standard deviation (mm)
>
> integrated rectified mean curvature
>
> integrated rectified Gaussian curvature
>
> folding index
>
> intrinsic curvature index
>
> structure name
>
>
>
>  6595   4368  15935  3.311 0.895 0.158 0.077  13519.7
> lh.frontoinsula.label
>
>
> As I saw there was no columns showing the LGI value, I did similar with
> gray matter volume, the result displayed the different in some values of
> the columns.
> Could you please help me to explain about this?
>
> Thank you very much.
>
>
> Best regards,
>
> Tien Pham
>
> ___
> 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
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Re: [Freesurfer] `GLIBCXX_3.4.19' not found error

2020-01-16 Thread fsbuild 
External Email - Use Caution

Hello Pascale,
Yes, that kind of symbol error has been posted before, and it can from the 
version of the standard C++ (or C) libraries being too different on the machine 
the binaries are running on - compared to the machine they were built on. 
Generally speaking, newer versions of the OS try to be backwards 
compatible, e.g., such that binaries built on CentOS 6 could run on CentOS7. 
However, forward compatibility may not to work, e.g., CentOS 7 binaries 
may not run on CentOS 5 or 6.

You could let us know something more about the binaries you are using and the 
version of the OS you are running on in order to match them up, but using 
different version of the standard C libraries to run only some binaries is not 
recommended.
- R.

On Jan 16, 2020, at 12:33, Pascale Patenaude 
pascalepatena...@hotmail.com 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,

I'm attempting to produce an automated segmentation of the hippocampal 
substructures and the nuclei of the amygdala (see hippocampal module 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).
 When I try to run the segmentHA_T1.sh bert [SUBJECTS_DIR] command with 
the dev version of freesurfer, I keep getting this error: 
/freesurfer-dev/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.19' 
not found /freesurfer-dev/MCRv84//sys/os/glnxa64/libstdc++.so.6: version 
`GLIBCXX_3.4.19' not found It was suggested in the archives that this is a 
library problem but does anyone have any suggestions on how this can be fixed? 
Thank you in advance,Pascale 
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Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

2020-01-16 Thread Swati Rane 
External Email - Use Caution

It is the file computed longitudinal processing that represents the rate with 
respect to the thickness at the first time point computed by long_mris_slopes.

Swati





Swati Rane Levendovszky, PhD
Interim Director, Diagnostic Imaging Sciences Center
Assistant Professor, Integrated Brain Imaging Center
Radiology
University of Washington
Box 357115 | AA035 HSB | Seattle, WA 98195
srle...@uw.edu | Ph: 206 543 6159
Web: https://sites.google.com/site/uwswatirane/



From:  on behalf of "Greve, Douglas 
N.,Ph.D." 
Reply-To: Freesurfer support list 
Date: Thursday, January 16, 2020 at 3:26 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

Sorry, what is "pc1"?
On 1/14/2020 9:44 AM, Swati Rane wrote:

External Email - Use Caution
Hello,

I was wondering if someone could answer my question below

Can I use mri_glmfit-sim after mri_glmfit on the longitudinal pc1 files.

Are there any set of parameters that should be set differently when using pc1 
instead of thickness files?


Thanks!
Swati




Swati Rane Levendovszky, PhD
Interim Director,Diagnostic Imaging Sciences Center
Assistant Professor,Integrated Brain Imaging Center
Radiology
University of Washington
Box 357115 | AA035 HSB | Seattle, WA 98195
srle...@uw.edu | Ph: 206 543 6159
Web: https://sites.google.com/site/uwswatirane/



From: 

 on behalf of Swati Rane 
Reply-To: Freesurfer support list 

Date: Friday, January 10, 2020 at 10:06 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: [Freesurfer] mri_glmfit-sim for longitudinal pipelines


External Email - Use Caution
Hello FreeSurfer Developers,

I'm attempting to compare longitudinal cortical thinning rates (pc1) between 3 
groups using mri_glmfit using FreeSurfer 6.0. The tutorial suggests that you 
could use the multiple comparisons corrections that come with it but does not 
comment on using the mri_glmfit-sim option.

I just want to confirm whether there is anything prohibiting me from using 
mri_glmfit-sim. Are there any set of parameters that should be set differently 
when using pc-1 instead of thickness files?

Also, would you do a stricter correction and stick to the longitudinal model or 
prefer the linear mixed effects model and do a FDR? How do you decide between 
the two?

Thanks!
Swati





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Re: [Freesurfer] Edit surface in Freeview

2020-01-16 Thread Greve, Douglas N.,Ph.D. 
No, sorry, I don't have a simple fix.

On 1/11/2020 5:05 PM, Davide Momi wrote:

External Email - Use Caution

Thanks Doug,

I followed your tips and try to run mris_remove_intersection. However  the 
result looks like the same than before. Maybe I am doing something wrong. Could 
you please provide me more details?

Do you have any other suggestions?

Thanks again for your help

Dave

Il giorno sab 11 gen 2020 alle ore 15:56 Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> ha scritto:
YOu can try running mris_remove_intersection (or something like that)

On 1/11/2020 12:48 PM, Davide Momi wrote:

External Email - Use Caution

Dear Freesurfer expert,

I am working with bem model and I have created the outer and the inner skull. 
Unfortunately, for few subjects the two surfaces intersect each other (see 
attached). I've tried to edit it manually but I had hard time in figuring it 
out. Could you please help me with this?

thanks

Dave



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Re: [Freesurfer] Segmentation Fault during recon-all using FLAIR Image

2020-01-16 Thread Greve, Douglas N.,Ph.D. 
It is seg faulting at the defect correction stage which is before the FLAIR 
would be used. At this point it should be identical to the T1-only analysis. 
Check your commands to make sure they are the same except for the FLAIR part

On 1/16/2020 9:55 AM, Swanson,Clayton wrote:

External Email - Use Caution

Hello FreeSurfer Developers,
I am attempting to perform a recon-all using a T2-FLAIR image.  I have already 
run this particular participant through recon-all with their T1 image without 
error.  While running the recon-all using the T2 the process exited with error 
stating a segmentation fault.

Is there any way to run fix this problem on my end or better understand why 
this would be occurring?

I have uploaded the recon-all.log for your convenience.

Thank you,
Clayton



Clayton Swanson MS
Graduate Research Assistant & PhD Student
Sensorimotor Neuroimaging Laboratory
Colorado State University
Office: (970) 491-6160
clayton.swan...@colostate.edu




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Re: [Freesurfer] FreeSurfer analyses in MatLab

2020-01-16 Thread Greve, Douglas N.,Ph.D. 


On 1/15/2020 3:08 PM, Graduate Imaging wrote:

External Email - Use Caution

Hello,

I recently ran a vertex wise analysis on two different projects the first had 
three groups with three co-variates that looked at if group membership was 
associated with brain volume. The second project had two groups with three 
co-variates looking at psychiatric x BMI interaction effect on brain volume. 
I'm interested in running ROI analyses in matlab to ensure the same matrices 
were used.

To run the ROI analyses I'm going to important the design matrix from the 
vertex wise analysis and use the fast_glmfit and fast_fratio commands as shown 
below:
X = load('Xg.dat');
C = load('C.dat');
y = load('ROI.dat'); text file containing participant ROI values from the DKT 
atlas.
[beta rvar] = fast_glmfit(y,X);
[F pvalues] = fast_fratio(beta,X,rvar,C

My first question is the beta values that are calculated from fast_glmfit are 
unstandardized is there anyway way to have it compute standardized values?
I think this is how you would compute that
betastddev = sqrt(rvar*diag(inv(X'*X)));
betastandard = beta./betastddev;

My second question is when I ran the ROI analyses looking at the diagnosis x 
BMI interaction effect it outputs an array of beta values for each regressor. 
In addition to each groups beta value (for BMI) I'm interested in the beta 
value of the interaction (ie diagnosis x BMI). I was wondering how do i go 
about obtaining this? Would I have to create a new matrix with the interaction 
term included in it?

If so would the analysis essentially be one group with the diagnosis x BMI 
interaction term plus the three co-variates?
If you are using an FSGD file and have used DODS, then you can create an 
interaction contrast. Send me your fsgd file if you want further help



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Re: [Freesurfer] Flag for recon-all to output aparc2005 labels (freesurfer 6.0)

2020-01-16 Thread Greve, Douglas N.,Ph.D. 
I don't think so, but you can run mris_ca_label by hand. Look in the 
recon-all.log file for the command, then use the 2005 tif instead of the 2009 
tif. I think it should work.

On 1/16/2020 3:31 PM, Grodin, Erica wrote:

External Email - Use Caution

Hello,

I am running recon-all on my data using freesurfer 6.0 which is working 
correctly. However, I need to create some VOIs which labels are only outputted 
from the aparc2005 set and do not appear in  the aparc2009 set; specifically:


9001, 9501   ctx-lh-primary-motor, ctx-rh-primary-motor

9005, 9505   ctx-lh-prim-sec-somatosensory, ctx-rh- 
prim-sec-somatosensory

9002, 9502   ctx-lh-premotor, ctx-rh-premotor

9004, 9504   ctx-lh-posterior-parietal, ctx-rh-posterior-parietal


Is there a flag or some other option to output the 2005 set in addition to the 
2009?


Thank you for your help,


Erica Grodin


--
Erica Grodin, Ph.D.
Postdoctoral Fellow
University of California, Dept. of Psychology and Psychiatry



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Re: [Freesurfer] Qdec and TkSurfer input boxes

2020-01-16 Thread Greve, Douglas N.,Ph.D. 
Sorry, qdec and tksurfer are becoming (have become?) obsolete. I think you can 
load an fsgd file in freeview

On 1/15/2020 11:02 AM, Marcos Martins da Silva wrote:

External Email - Use Caution

Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with 
input/entry/edit boxes in Qdec and TkSurfer. I can see box content, click 
inside the box and even select the content but it seems read only: I can't 
change it. So it is impossible to see the scatter plot from a specific vertex 
inputing its number. Any clue about what happened and how to fix it? Thank you 
for your attention.



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Re: [Freesurfer] Oval shape in average subject inflated

2020-01-16 Thread Greve, Douglas N.,Ph.D. 

Nothing wrong per se, it is just that the inflation was done assuming a certain 
number of vertices. You can try changing the number of iterations in the 
inflation with,eg,
cd $SUBJECTS/fsaverage/surf
mris_inflate -dist .01 -f .001 -no-save-sulc 5 lh.smoothwm lh.inflated
In this case I set it to 5, but you can play with it.

If you don't need the inflated for this, then you can just ignore

On 1/15/2020 6:24 AM, Marina Fernández wrote:

External Email - Use Caution

Is there something wrong?

> Dear Freesurfer team,
>
> I created the FS average subject of the same dataset with 5th and 6th order 
> icosahedron tesselation using the following commands:
> make_average_subject --fsgd fsgd.txt --ico 5 --out avg_subject_ico5
> make_average_subject --fsgd fsgd.txt --ico 6 --out avg_subject_ico6
>
> When I load the inflated surface of the avg_subject_ico5 with tksurfer , it 
> has a oval shape while > when I load the avg_subject_ico6 it seems to be a 
> normal shape.
> Please, see attached image.
>
> Thank you in advance.
 >
> Best wishes,
> Marina.






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Re: [Freesurfer] Extract specific LGI and Volume values

2020-01-16 Thread Greve, Douglas N.,Ph.D. 
It might be easier to use mri_segstats, eg,

mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1 
--o sum.dat

The mean value will be in the "Mean" column of the sum.dat


On 1/14/2020 7:08 PM, Tien Pham wrote:

External Email - Use Caution

Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI 
changes in my data set with two time points using longitudinal pipeline. Now I 
would like to extract the regional LGI and gray matter volume in my 
longitudinal results using QDEC to draw the ROIs which is showed significant 
differences, label it and map to all subjects. Then I get the LGI value of the 
ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \
 -f subject_id/stats/lh.untitled.stats subject_id lh

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% 
mris_anatomical_stats -l lh.frontoinsula.label \
? -t lh.pial_lgi \
? -b \
? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
limiting computations to label lh.frontoinsula.label.
using thickness file lh.pial_lgi.
reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white...
reading input pial surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.pial...
reading input white surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.white...

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

 6595   4368  15935  3.311 0.895 0.158 0.077  13519.7  
lh.frontoinsula.label

As I saw there was no columns showing the LGI value, I did similar with gray 
matter volume, the result displayed the different in some values of the columns.
Could you please help me to explain about this?
Thank you very much.

Best regards,
Tien Pham



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Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

2020-01-16 Thread Greve, Douglas N.,Ph.D. 
Sorry, what is "pc1"?

On 1/14/2020 9:44 AM, Swati Rane wrote:

External Email - Use Caution
Hello,

I was wondering if someone could answer my question below

Can I use mri_glmfit-sim after mri_glmfit on the longitudinal pc1 files.

Are there any set of parameters that should be set differently when using pc1 
instead of thickness files?


Thanks!
Swati




Swati Rane Levendovszky, PhD
Interim Director,Diagnostic Imaging Sciences Center
Assistant Professor,Integrated Brain Imaging Center
Radiology
University of Washington
Box 357115 | AA035 HSB | Seattle, WA 98195
srle...@uw.edu | Ph: 206 543 6159
Web: https://sites.google.com/site/uwswatirane/



From: 

 on behalf of Swati Rane 
Reply-To: Freesurfer support list 

Date: Friday, January 10, 2020 at 10:06 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: [Freesurfer] mri_glmfit-sim for longitudinal pipelines


External Email - Use Caution
Hello FreeSurfer Developers,

I'm attempting to compare longitudinal cortical thinning rates (pc1) between 3 
groups using mri_glmfit using FreeSurfer 6.0. The tutorial suggests that you 
could use the multiple comparisons corrections that come with it but does not 
comment on using the mri_glmfit-sim option.

I just want to confirm whether there is anything prohibiting me from using 
mri_glmfit-sim. Are there any set of parameters that should be set differently 
when using pc-1 instead of thickness files?

Also, would you do a stricter correction and stick to the longitudinal model or 
prefer the linear mixed effects model and do a FDR? How do you decide between 
the two?

Thanks!
Swati





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Re: [Freesurfer] Change the subject ID after recon-all?

2020-01-16 Thread Greve, Douglas N.,Ph.D. 
Hi Tim, can you send a list of files that have the identifier. For 
volumes and surfaces, it might be as easy as running 
mri_convert/mris_convert using the same file as input and output.

On 1/13/2020 5:54 AM, Tim Schäfer wrote:
>  External Email - Use Caution
>
> Dear FreeSurfer experts,
>
>
> I have two questions on subject IDs in FreeSurfer output.
>
> 1) is it possible to change to subject identifier in the FreeSurfer output 
> after recon-all has been run?
>
> Background: I would like to upload data pre-processed with FreeSurfer to a 
> consortium server. The subject ID is a random identifier, but the upload 
> guidelines say this identifier must only occur in certain file types (Excel 
> files, .log files, and some more, but not in any other files).
>
> I noticed that a lot of the output files produced by FreeSurfer contain the 
> subject identifier somewhere, including various binary files, so I guess 
> there is no easy way to change it. But maybe there is? Like rerunning a part 
> of recon-all?
>
>
>
> 2) If not, I could rename the source NIFTI files (e.g., from the identifiers 
> to something like 'subject001', 'subject002', ...) and re-process everything. 
> This would take some computational time for the > 500 subjects, but it would 
> be okay I guess.
>
> But a large number of the subjects have manual edits applied already. Is 
> there a way to keep the manual edits? E.g., I thought maybe I could rename 
> the individual directories of the edited subjects, leave the edited files in 
> there, and run recon-all again. But what would happen? Will the new output 
> files have the renamed ID from the directory name (and thus the recon-all 
> command line), or will they still use the old ID (from the header of the 
> existing files)? Or will the existing, edited files which contain a different 
> ID be ignored during the new run because the IDs do not match, and thus the 
> existing edits would have no effect?
>
>
> All the best,
>
> Tim
>
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and 
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>
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Re: [Freesurfer] (no subject)

2020-01-16 Thread Greve, Douglas N.,Ph.D. 
I'm guessing that the fragments might cause problems later either in gtmseg as 
a hard failure or in gtmpvc as an ill-conditioned matrix. But you can try it 
out:)

On 1/11/2020 6:04 PM, Boris Rauchmann wrote:

External Email - Use Caution

Thanks, that solution seems to work finally. I just ignored the remaining 
voxels labeled according to the standard aseg scheme and proceeded with the the 
PET analysis and the combined LUT.
I will ignore the remaining fragment labels from the original aseg and only use 
the output from the BN labels (starting with 211), these are the only results 
im really interested in. Is that ok?

Here an example stats file I got:

  12 Left-Cerebral-White-Matter  wm 41550 13909.534
0.989   0.0935
  27 Left-Cerebellum-White-Matterwm  2276 1037.525
0.854   0.0811
  38 Left-Cerebellum-Cortex  cortex 10936 6010.637
1.015   0.1339
  4   10 Left-Thalamus-Propersubcort_gm 30.024   
-0.815   0.2251
  5   11 Left-Caudatesubcort_gm 30.035   
21.480   0.1746
  6   12 Left-Putamensubcort_gm250.459
3.161   0.0615
  7   13 Left-Pallidum   subcort_gm491.497
1.474   0.0667
  8   16 Brain-Stem  subcort_gm  4599 2714.856
0.929   0.1000
  9   17 Left-Hippocampussubcort_gm 20.023   
-3.152   0.1702
 10   18 Left-Amygdala   subcort_gm 10.005   
-7.082   0.1060
 11   24 CSF csf 7468 2623.527
0.251   0.2568
 12   26 Left-Accumbens-area subcort_gm 00.004
0.879  nan
 13   28 Left-VentralDC  subcort_gm   714  205.288
1.358   0.1427
 14   31 Left-choroid-plexus csf  220   18.333
5.945   0.6080
 15   41 Right-Cerebral-White-Matter wm 40645 13911.597
0.987   0.0841
 16   46 Right-Cerebellum-White-Matter   wm  2146  990.941
0.862   0.0826
 17   47 Right-Cerebellum-Cortex cortex 11029 6187.241
0.985   0.1317
 18   49 Right-Thalamus-Proper   subcort_gm110.140
0.032   0.2024
 19   50 Right-Caudate   subcort_gm 10.009   
-2.162   0.0258
 20   51 Right-Putamen   subcort_gm442.020
3.727   0.1893
 21   52 Right-Pallidum  subcort_gm240.316
5.739   0.1814
 22   53 Right-Hippocampus   subcort_gm 30.026   
16.575   0.2951
 23   54 Right-Amygdala  subcort_gm 70.081
4.637   0.0897
 24   58 Right-Accumbens-areasubcort_gm 00.000   
-4.474  nan
 25   60 Right-VentralDC subcort_gm   728  198.051
1.430   0.2142
 26   63 Right-choroid-plexuscsf  136   10.088
6.633   0.5924
 27  211 mAmyg_L subcort_gm   264   48.960
1.126   0.1262
 28  212 mAmyg_R subcort_gm   268   46.429
1.292   0.1920
 29  213 lAmyg_L subcort_gm   1316.503
1.889   0.1003
 30  214 lAmyg_R subcort_gm   181   13.490
1.382   0.1237
 31  215 rHipp_L subcort_gm  1020  260.090
1.166   0.1828
 32  216 rHipp_R subcort_gm   833  241.777
1.149   0.2291
 33  217 cHipp_L subcort_gm   911  288.346
1.578   0.3201
 34  218 cHipp_R subcort_gm  1050  330.445
1.273   0.2312
 35  219 vCa_L   subcort_gm   626  170.254
1.205   0.0829
 36  220 vCa_R   subcort_gm   477   84.269
1.491   0.0933
 37  221 GP_Lsubcort_gm   597  133.161
1.369   0.0977
 38  222 GP_Rsubcort_gm   514   93.978
1.491   0.0811
 39  223 NAC_L   subcort_gm   412   67.647
1.348   0.1591
 40  224 NAC_R   subcort_gm   503   87.917
1.240   0.1258
 41  225 vmPu_L  subcort_gm   465  128.509
1.740   0.0783
 42  226 vmPu_R  subcort_gm   367   83.411
1.588   0.0699
 43  227 dCa_L   subcort_gm   997  255.259
0.821   0.1448
 44  228 dCa_R   subcort_gm  1271  405.156
1.017   0.1380
 45  229

[Freesurfer] Flag for recon-all to output aparc2005 labels (freesurfer 6.0)

2020-01-16 Thread Grodin, Erica 
External Email - Use Caution

Hello,

I am running recon-all on my data using freesurfer 6.0 which is working 
correctly. However, I need to create some VOIs which labels are only outputted 
from the aparc2005 set and do not appear in  the aparc2009 set; specifically:


9001, 9501   ctx-lh-primary-motor, ctx-rh-primary-motor

9005, 9505   ctx-lh-prim-sec-somatosensory, ctx-rh- 
prim-sec-somatosensory

9002, 9502   ctx-lh-premotor, ctx-rh-premotor

9004, 9504   ctx-lh-posterior-parietal, ctx-rh-posterior-parietal


Is there a flag or some other option to output the 2005 set in addition to the 
2009?


Thank you for your help,


Erica Grodin


--
Erica Grodin, Ph.D.
Postdoctoral Fellow
University of California, Dept. of Psychology and Psychiatry
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[Freesurfer] `GLIBCXX_3.4.19' not found error

2020-01-16 Thread Pascale Patenaude 
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Hello FreeSurfer Developers,

I'm attempting to produce an automated segmentation of the hippocampal 
substructures and the nuclei of the amygdala (see hippocampal module 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).
 When I try to run the segmentHA_T1.sh bert  [SUBJECTS_DIR] command with the 
dev version of freesurfer, I keep getting this error:

/freesurfer-dev/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.19' 
not found
/freesurfer-dev/MCRv84//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.19' 
not found

It was suggested in the archives that this is a library problem but does anyone 
have any suggestions on how this can be fixed?

Thank you in advance,

Pascale

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Re: [Freesurfer] Segfault in mris_topo_fixer

2020-01-16 Thread Hoopes, Andrew 
Hi Christian, if you send me that surface, I can take a look at what's going 
wrong.

best
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Christian O'Reilly, Dr 

Sent: Thursday, January 16, 2020 9:57 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Segfault in mris_topo_fixer

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Hi,

I got the following error running mris_topo_fixer:

~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh
INFO: assuming .mgz format
verbose mode on (medium mode): printing warnings
reading input surface 
/usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig...
Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1)
Surface Diagnostics:
   eno=0 (nv=43656, nf=87312, ne=130968)
   # of border vertices [ #v ~ #f ] 0
   # of edges with single face  0
   # of edges with more than 2 faces0
   # of corner configurations   0
   The original surface is a valid manifold
   Counting the number of connected components
   The original surface has one component
   The original surface does not self-intersect

The surface has 1 loops (X=0)

Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
identify defects...
marking ambiguous vertices...
1527 ambiguous faces found in tessellation
segmenting defects...
analyzing defects for overlaps...
reading brain volume from brain...
reading wm segmentation from wm...
Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ]
ASSERTION FAILED: 
/local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002
 vt->nsizeMax > 0
ASSERTION FAILED: 
/local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002
 vt->nsizeMax > 0
Segmentation fault (core dumped)

Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be 
triggered? Any idea how to go around it?

Thank you,

Christian

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[Freesurfer] Segfault in mris_topo_fixer

2020-01-16 Thread Christian O'Reilly, Dr 
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Hi,

I got the following error running mris_topo_fixer:

~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh
INFO: assuming .mgz format
verbose mode on (medium mode): printing warnings
reading input surface 
/usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig...
Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1)
Surface Diagnostics:
   eno=0 (nv=43656, nf=87312, ne=130968)
   # of border vertices [ #v ~ #f ] 0
   # of edges with single face  0
   # of edges with more than 2 faces0
   # of corner configurations   0
   The original surface is a valid manifold
   Counting the number of connected components
   The original surface has one component
   The original surface does not self-intersect

The surface has 1 loops (X=0)

Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
identify defects...
marking ambiguous vertices...
1527 ambiguous faces found in tessellation
segmenting defects...
analyzing defects for overlaps...
reading brain volume from brain...
reading wm segmentation from wm...
Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ]
ASSERTION FAILED: 
/local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002
 vt->nsizeMax > 0
ASSERTION FAILED: 
/local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002
 vt->nsizeMax > 0
Segmentation fault (core dumped)

Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be 
triggered? Any idea how to go around it?

Thank you,

Christian
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Re: [Freesurfer] Oval shape in average subject inflated

2020-01-16 Thread Marina Fernández 
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It works! Thank you very much Bruce!
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