Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat

[Douglas Greve]

you would do it in fcseed-config by using -mean instead of -pca

On 7/20/18 4:06 PM, Eryilmaz, H. Hamdi wrote:


Thanks Doug!


One last question: If I wanted to regress out the average signal from 
the ventricles and the white matter (instead of using the PCA output), 
could I directly incorporate that into fcseedcor?



Best,

Hamdi



*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 


*Sent:* Friday, July 20, 2018 9:23:58 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and 
wm.dat

Hi Hamdi, sorry for the delay. Answers below.

On 6/26/18 2:50 PM, Eryilmaz, H. Hamdi wrote:

Hi Doug and Freesurfers,

I am using fcseedcor to compute the correlation between two time 
courses for each subject in my group. The command that I run is as 
follows:


fcseedcor -s $subject -fsd resting -seed seed1.dat -seed seed2.dat 
-xreg global.waveform.dat 1 -xreg vcsf.dat 5 -xreg wm.dat 5 -xreg 
mcprextreg 6 -hpf .01 -lpf .08 -nskip 4 -o cor_s1s2.dat


My first question is about the size of the vcsf.dat and wm.dat files. 
They seem to be (N+1)xN matrices, where N is the number of timepoints 
in the signal. Does this mean there are N+1 components for each time 
point (i.e., N+1 potential regressors to add)? What do they exactly 
correspond to and how do they relate to the average signal from the 
ventricles, CSF, and white matter?
Each ROI consists of a matrix of size Ntp-by-Nvoxels. A PCA is 
computed from this matrix. The the number of temporal components of 
the PCA will be either Ntp or Nvoxels, which ever is less. In this 
case, Nvoxels>Ntp, so you see the Ntp components (each Ntp long). The 
components are whatever the PCA finds. The mean is removed, so it no 
component represents the mean.


My other question is about the number of components to include for 
vcsf.dat and wm.dat. I have seen 5 recommended in examples, however, 
five components seem to explain very different amount of variance in 
different subjects and if I change this number for a given subject, I 
see substantial changes in the resulting correlation value. I would 
appreciate any suggestion on how to select an unbiased value for 
the number of components to include. Could including up to the 
component at which fixed percentage of cumulative variance is 
explained be a solution?
When I was doing experiments with this years ago, i did not find much 
of a difference with different numbers of components, but I did the 
experiments on whole brain resting state, so the ROI-wise correlation 
may be different. It seemed like 5 components explained the bulk of 
the variance within the ROI (WM or CSF). You could vary the number of 
components for each subject. Sorry, I don't have any better guidance 
on how to go about selecting the number.

doug


Many thanks for your help!

Best,
Hamdi













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[Freesurfer] Resample data for longitudinal comparisons

[James Gullickson]

External Email - Use Caution

All,

I would like to compare cortical thickness between two timepoints.

Timepoint 1 has 1mm^3 data.
Timepoint 2 has 0.8mm^3 data.

I realize that there are limitations with this change in resolution between
timepoints and that no analysis is going to be perfect, but I am trying to
come up with the best possible solution.

Would it work to resample both timepoints' raw data into 0.9mm^3 (
mri_convert --conform_size 0.9 invol outvol ), and then run the 0.9mm data
through Freesurfer 6.0 submilimeter recon? If so, are there any special
considerations I need to take into account after the initial recon, or
would longitudinal processing after this point be per normal?

Thanks,

James
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Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat

[Eryilmaz, H. Hamdi]

Thanks Doug!


One last question: If I wanted to regress out the average signal from the 
ventricles and the white matter (instead of using the PCA output), could I 
directly incorporate that into fcseedcor?


Best,

Hamdi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 

Sent: Friday, July 20, 2018 9:23:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat

Hi Hamdi, sorry for the delay. Answers below.

On 6/26/18 2:50 PM, Eryilmaz, H. Hamdi wrote:
Hi Doug and Freesurfers,

I am using fcseedcor to compute the correlation between two time courses for 
each subject in my group. The command that I run is as follows:

fcseedcor -s $subject -fsd resting -seed seed1.dat -seed seed2.dat -xreg 
global.waveform.dat 1 -xreg vcsf.dat 5 -xreg wm.dat 5 -xreg mcprextreg 6 -hpf 
.01 -lpf .08 -nskip 4 -o cor_s1s2.dat

My first question is about the size of the vcsf.dat and wm.dat files. They seem 
to be (N+1)xN matrices, where N is the number of timepoints in the signal. Does 
this mean there are N+1 components for each time point (i.e., N+1 potential 
regressors to add)? What do they exactly correspond to and how do they relate 
to the average signal from the ventricles, CSF, and white matter?
Each ROI consists of a matrix of size Ntp-by-Nvoxels. A PCA is computed from 
this matrix. The the number of temporal components of the PCA will be either 
Ntp or Nvoxels, which ever is less. In this case, Nvoxels>Ntp, so you see the 
Ntp components (each Ntp long). The components are whatever the PCA finds. The 
mean is removed, so it no component represents the mean.

My other question is about the number of components to include for vcsf.dat and 
wm.dat. I have seen 5 recommended in examples, however, five components seem to 
explain very different amount of variance in different subjects and if I change 
this number for a given subject, I see substantial changes in the resulting 
correlation value. I would appreciate any suggestion on how to select an 
unbiased value for the number of components to include. Could including up to 
the component at which fixed percentage of cumulative variance is explained be 
a solution?
When I was doing experiments with this years ago, i did not find much of a 
difference with different numbers of components, but I did the experiments on 
whole brain resting state, so the ROI-wise correlation may be different. It 
seemed like 5 components explained the bulk of the variance within the ROI (WM 
or CSF). You could vary the number of components for each subject. Sorry, I 
don't have any better guidance on how to go about selecting the number.
doug

Many thanks for your help!

Best,
Hamdi














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Re: [Freesurfer] FreeSurfer License issue

[Dianne Patterson]

External Email - Use Caution

Hi,


Here's what I've learned from my attempts (eventually successful), to run
freesurfer in docker on a mac:



There are three tricks to running the freesurfer *docker* container.

1) You must request a license.txt file from the freesurfer website:
https://surfer.nmr.mgh.harvard.edu/fswiki/License

2) You must bind mount the license file on the outside to license.txt on
the inside of the container (this is just like binding the input small_ds
and outputs directories), e.g.:


>docker run -ti --rm -v
/Volumes/Main/Working/BIDS_TESTING/license.txt:/license.txt:ro -v
/Volumes/Main/Working/BIDS_TESTING/small_ds:/bids_dataset:ro -v
/Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer
/bids_dataset /outputs participant --license_file /license.txt


3) On the mac, Docker runs in a minimal virtual machine.  By default, this
machine is allowed to access 2 GB of RAM.  recon-all requires more RAM (~4
GB or more) https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements.
See instructions here for increasing the RAM on Docker for Mac:
https://docs.docker.com/docker-for-mac/#advanced


On Fri, Jul 20, 2018 at 1:13 AM Carolina Bonivento <
boniventocarol...@gmail.com> wrote:

> External Email - Use Caution
>
> Apologize, I forgot  to attach the file with the license. Here it is.
>
> Best regards,
>
> Carolina
>
>
>
>
> Il giorno 20 lug 2018, alle ore 10:08, Carolina Bonivento <
> boniventocarol...@gmail.com> ha scritto:
>
> Dear Sir/Madame,
> I recently subscribed the FS license (attached) but when I tried to run
>  the 'recon-all’ (actually one of its steps, i.e. the MRI_ca_register) I
> received the following error message:
>
> *ERROR: Invalid FreeSurfer license key found in license file
> /root/freesurfer/license.txt*
>
> Following some instruction that I got previously, I replaced the .license
> with the license.txt in the $FREESURFER_HOME directory (in my case
> root/freesurfer) but I still get the same error message.
>
> Note that I’m running FreeSurfer through a Docker container running
> Ubuntu14 that is linked to the ‘freesurfer' folder on the' /User/home' of a
> macOS High Sierra (of course, Docker and the freesurfer folder are on the
> same machine). When I filled the license request form I’ve selected
> Linux/Intel as 'Operating System/Platform', as this is the OS of the Docker
> container. Is it possible that the issue is due to this? In that case, can
> I ask for a second license?
>
> Thank you in advance for your attention.
>
> Looking forward to hearing from you, I’m sending you my best regards,
>
> Carolina
>
>
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> e-mail
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> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>


-- 
Dianne Patterson, Ph.D.
Research Scientist
d...@email.arizona.edu 
or
dianne...@gmail.com
University of Arizona
Speech and Hearing Science 314
1131 E 2nd Street, Building #71
(Just East of Harvill)
==
If you don't hear back from me (and you expected to),
I blame the University's new SPAM filter.
Please write to my gmail account.
==
Antipiphany: That moment when you realize how little you actually know
==
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Re: [Freesurfer] mri_binarize

[Douglas Greve]

It was just an oversight on my part when I wrote the program. I've just 
updated the file in our repository and put a copy here:

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize
You can also specify all the structures you want by using the --match flag

On 7/20/18 10:00 AM, John Anderson wrote:


External Email - Use Caution

Dear Freesurfer experts,
I would like to inquire about the flag --subcort-gm in mri_binarize. 
It seems that the final product of this flag create a mask include the 
brain stem which is largely white matter. Why it was included in the 
subcortical gray matter structures?


Thanks for any clarification,
john


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Re: [Freesurfer] Exporting results from QDEC

[Douglas Greve]

which results?

On 7/20/18 9:11 AM, Avi Gharehgazlou wrote:


External Email - Use Caution

Hi experts,

I want to make plots of my results that I have from QDEC, however, I'm 
having difficulty exporting values from QDEC. I examined LGI 
differences between groups, and I want to export my results, so the 
LGI values of significant between-group differences. Will you please 
tell me how I can do this?


Thanks,

Avi


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Re: [Freesurfer] Bug in make_average_subject

[Douglas Greve]

where did you get the make_average_subject script? It is not the one 
that is released with version 6.


On 7/20/18 3:46 AM, Raffington, Laurel wrote:


External Email - Use Caution


Dear Freesurfer Developers,


My goal is to build a study-specific pediatric template brain to rerun 
the recon-all-all. I am encountering the same error while running 
make_average_subject Freesurfer version 6.0.0 on MacOS High Sierra 
10.13.6 as described here and implemented the suggested changes 
replacing mri_glmfit-sim, make_average_subject, make_average_surface, 
and mri_aparc2aseg: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054933.html 



Yet, another error persists.


Any help would be appreciated.


Thanks,


Laurel



Laurel Raffington

Postdoctoral Researcher

Center for Lifespan Psychology

Max Planck Institute for Human Development

Lentzeallee 94, 14195 Berlin, Germany

https://www.mpib-berlin.mpg.de/en/staff/laurel-raffington






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[Freesurfer] Question about Freeview, 20% threshold

[Daumail, Loic Jean]

Dear FreeSurfer experts,

I am currently using TRACULA( from freeSurfer 6.0), and on the freeview 
visualization of merged files of the probability distributions of the tracts, I 
don't understand the thing about the "20% threshold".

Indeed, on the tracula tutorial, it is written that the tracts are displayed in 
a way that they are at 20% of their maximum threshold.
However, what does this mean? Is it the 20% of the most probable paths for each 
tracts?
The adjustment bar on the side of the screen permits to vary this threshold, 
but when we reduce the level of the threshold, the size of the tracts increase, 
which seems in contradiction with the previous statements... I then suppose 
that my guess must be wrong?

Thank you for your time and consideration!

Sincerely,

Loïc
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[Freesurfer] mri_binarize

[John Anderson]

External Email - Use Caution

Dear Freesurfer experts,
I would like to inquire about the flag --subcort-gm in mri_binarize. It seems 
that the final product of this flag create a mask include the brain stem which 
is largely white matter. Why it was included in the subcortical gray matter 
structures?

Thanks for any clarification,
john___
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat

[Douglas Greve]

Hi Hamdi, sorry for the delay. Answers below.

On 6/26/18 2:50 PM, Eryilmaz, H. Hamdi wrote:

Hi Doug and Freesurfers,

I am using fcseedcor to compute the correlation between two time 
courses for each subject in my group. The command that I run is as 
follows:


fcseedcor -s $subject -fsd resting -seed seed1.dat -seed seed2.dat 
-xreg global.waveform.dat 1 -xreg vcsf.dat 5 -xreg wm.dat 5 -xreg 
mcprextreg 6 -hpf .01 -lpf .08 -nskip 4 -o cor_s1s2.dat


My first question is about the size of the vcsf.dat and wm.dat files. 
They seem to be (N+1)xN matrices, where N is the number of timepoints 
in the signal. Does this mean there are N+1 components for each time 
point (i.e., N+1 potential regressors to add)? What do they exactly 
correspond to and how do they relate to the average signal from the 
ventricles, CSF, and white matter?
Each ROI consists of a matrix of size Ntp-by-Nvoxels. A PCA is computed 
from this matrix. The the number of temporal components of the PCA will 
be either Ntp or Nvoxels, which ever is less. In this case, Nvoxels>Ntp, 
so you see the Ntp components (each Ntp long). The components are 
whatever the PCA finds. The mean is removed, so it no component 
represents the mean.


My other question is about the number of components to include for 
vcsf.dat and wm.dat. I have seen 5 recommended in examples, however, 
five components seem to explain very different amount of variance in 
different subjects and if I change this number for a given subject, I 
see substantial changes in the resulting correlation value. I would 
appreciate any suggestion on how to select an unbiased value for 
the number of components to include. Could including up to the 
component at which fixed percentage of cumulative variance is 
explained be a solution?
When I was doing experiments with this years ago, i did not find much of 
a difference with different numbers of components, but I did the 
experiments on whole brain resting state, so the ROI-wise correlation 
may be different. It seemed like 5 components explained the bulk of the 
variance within the ROI (WM or CSF). You could vary the number of 
components for each subject. Sorry, I don't have any better guidance on 
how to go about selecting the number.

doug


Many thanks for your help!

Best,
Hamdi













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[Freesurfer] Exporting results from QDEC

[Avi Gharehgazlou]

External Email - Use Caution

Hi experts,

I want to make plots of my results that I have from QDEC, however, I'm
having difficulty exporting values from QDEC. I examined LGI differences
between groups, and I want to export my results, so the LGI values of
significant between-group differences. Will you please tell me how I can do
this?

Thanks,

Avi
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Re: [Freesurfer] Label numbers for thalamic nuclei

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear KT,
They range from 8100 to 8300.
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 ?? ? 

Reply-To: Freesurfer support list 
Date: Friday, 20 July 2018 at 08:17
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Label numbers for thalamic nuclei


External Email - Use Caution

Dear Freesurfer Team,



I have been using  segmentation of thalamic nuclei from the Freesurfer dev 
version(freesurfer-linux-centos7_x86_64-dev).

I see some thalamus labels in FreeSurferColorLUT.txt(#8001-8014), but I can't 
find label numbers for 25 different nuclei. Where could I find those numbers?



Thanks in advance,

Kayeong Tak
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Re: [Freesurfer] Why I have to set the environment every time

[Carolina Bonivento]

External Email - Use Caution

Hi Ziqian,
have you tried to set the environment by writing export 
FREESURFER_HOME=/Applications/freesurfer on the .bashrc (if using a Linux 
distribution) or .bash_profile (in using macOS)?
To do so open the .bashrc (or .bash_profile) with an editor, write the command 
and save. Then write on terminal 'source .bashrc’ (or 'source .bash_profile’). 
From then on the FREESURFER_HOME should be set to correct path.

Best,

Carolina

> Il giorno 20 lug 2018, alle ore 11:41, 王子谦  ha scritto:
> 
> External Email - Use Caution
> 
> 
> Hi,
>  
> Every time I wanna use the command of freesufer I have to reset the 
> environment again, otherwise it will remind me “not found the command”.
> Only after I write “export FREESURFER_HOME=/Applications/freesurfer;
> source $FREESURFER_HOME/SetUpFreeSurfer.sh”
> Then I can use it smoothly. But after I close the terminal, I have to rewrite 
> it again.
> Any suggestion is acceptable.
> Thanks a lot
>  
>  
> Ziqian
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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] Why I have to set the environment every time

[王子谦]

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Hi,

 

Every time I wanna use the command of freesufer I have to reset the environment 
again, otherwise it will remind me “not found the command”.

Only after I write “export FREESURFER_HOME=/Applications/freesurfer;

source $FREESURFER_HOME/SetUpFreeSurfer.sh”

Then I can use it smoothly. But after I close the terminal, I have to rewrite 
it again.

Any suggestion is acceptable.

Thanks a lot

 

 

Ziqian

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Re: [Freesurfer] FreeSurfer License issue

[Carolina Bonivento]

External Email - Use CautionApologize, I forgot  to attach the file with the license. Here it is.Best regards,CarolinaCarolina Bonivento 
37084
 *Cl5ULwBr1to2
 FSr/.mH1ADRn2
Il giorno 20 lug 2018, alle ore 10:08, Carolina Bonivento  ha scritto:Dear Sir/Madame,I recently subscribed the FS license (attached) but when I tried to run  the 'recon-all’ (actually one of its steps, i.e. the MRI_ca_register) I received the following error message: ERROR: Invalid FreeSurfer license key found in license file /root/freesurfer/license.txtFollowing some instruction that I got previously, I replaced the .license with the license.txt in the $FREESURFER_HOME directory (in my case root/freesurfer) but I still get the same error message.Note that I’m running FreeSurfer through a Docker container running Ubuntu14 that is linked to the ‘freesurfer' folder on the' /User/home' of a macOS High Sierra (of course, Docker and the freesurfer folder are on the same machine). When I filled the license request form I’ve selected Linux/Intel as 'Operating System/Platform', as this is the OS of the Docker container. Is it possible that the issue is due to this? In that case, can I ask for a second license?Thank you in advance for your attention.Looking forward to hearing from you, I’m sending you my best regards,Carolina___
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[Freesurfer] FreeSurfer License issue

[Carolina Bonivento]

External Email - Use Caution

Dear Sir/Madame,
I recently subscribed the FS license (attached) but when I tried to run  the 
'recon-all’ (actually one of its steps, i.e. the MRI_ca_register) I received 
the following error message: 

ERROR: Invalid FreeSurfer license key found in license file 
/root/freesurfer/license.txt

Following some instruction that I got previously, I replaced the .license with 
the license.txt in the $FREESURFER_HOME directory (in my case root/freesurfer) 
but I still get the same error message.

Note that I’m running FreeSurfer through a Docker container running Ubuntu14 
that is linked to the ‘freesurfer' folder on the' /User/home' of a macOS High 
Sierra (of course, Docker and the freesurfer folder are on the same machine). 
When I filled the license request form I’ve selected Linux/Intel as 'Operating 
System/Platform', as this is the OS of the Docker container. Is it possible 
that the issue is due to this? In that case, can I ask for a second license?

Thank you in advance for your attention.

Looking forward to hearing from you, I’m sending you my best regards,

Carolina___
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[Freesurfer] Bug in make_average_subject

[Raffington, Laurel]

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Dear Freesurfer Developers,


My goal is to build a study-specific pediatric template brain to rerun the 
recon-all-all. I am encountering the same error while running 
make_average_subject Freesurfer version 6.0.0 on MacOS High Sierra 10.13.6 as 
described here and implemented the suggested changes replacing mri_glmfit-sim, 
make_average_subject, make_average_surface, and mri_aparc2aseg: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054933.html

Yet, another error persists.


Any help would be appreciated.


Thanks,


Laurel



Laurel Raffington

Postdoctoral Researcher

Center for Lifespan Psychology

Max Planck Institute for Human Development

Lentzeallee 94, 14195 Berlin, Germany

https://www.mpib-berlin.mpg.de/en/staff/laurel-raffington





recon-all.error
Description: recon-all.error


recon-all.log
Description: recon-all.log
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[Freesurfer] Label numbers for thalamic nuclei

[?? ?]

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Dear Freesurfer Team,


I have been using  segmentation of thalamic nuclei from the Freesurfer dev 
version(freesurfer-linux-centos7_x86_64-dev).

I see some thalamus labels in FreeSurferColorLUT.txt(#8001-8014), but I can't 
find label numbers for 25 different nuclei. Where could I find those numbers?


Thanks in advance,

Kayeong Tak
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