subject:"\[Freesurfer\] fsfast"

[Freesurfer] FSFAST Download

2023-06-15 Thread Emily Iannazzi

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Hello,

I’m attempting to download FSFAST on my non-MGH computer using the instructions 
here 
(http://secure-web.cisco.com/1n4qrYftNmBzlQYL-31wPAegOcrSfYRBH8975kyPjOBIYuySQDIjSDekUmoCNLDawG9fcYCUhpK8MIhnMGNe1MYO0o7Jw4QxJNDS6OXNKAy6UwLLNHfdx8heUQlvlp6k08bTiIdnXulyI7hEmgGSQjM_S17vGBHDohVFN5I4VSsAu5nR1QqT1NVMCod66yn-7Jdx_tsSX4F_7BP4DZQ6grvTRa-g6IbknVeh6cKedJk5XZHveMMUlKojKlvE0cgd6CUL8f5Gvar3RTOU1H2JQPnHS1QQQJRdmndy2ZH8JhnKeOKhas_Y1fdrgJ7VNJ5ClxkkmhKzAl061pEb6HYX3BA/http%3A%2F%2Fftp.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Ftutorial_packages%2FOSX%2Ffreesurfer%2Ffsfast%2Fdocs%2FINSTALL.pdf),
 however I’m not able to follow the following step:

ftp> cd pub/flat/fmri-analysis
due to the directory “flat” not appearing. When I ls into the “pub” directory I 
can only see the following contents:

articles
data
dist
docs
lost+found
misc
optseq
projects
security

Could you let me know if the directory “flat” still exists, and if so how to 
access it? If not, could you please verify the location of “fmri-analysis”?

Thank you!
Emily
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Re: [Freesurfer] fsfast percent signal change

2023-05-25 Thread Douglas N. Greve

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Use the cespct.nii.mgz file

On 5/24/2023 10:18 AM, Maria Czarnecka wrote:


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Dear experts,

I struggle with the functional analysis in Freesurfer. How can I 
calculate the percent signal change in a specific contrast in an ROI?


I will be grateful for your suggestions (especially if you point 
toward a specific function).


Kind regards,
Maria Czarnecka

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[Freesurfer] fsfast percent signal change

2023-05-24 Thread Maria Czarnecka

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Dear experts,

I struggle with the functional analysis in Freesurfer. How can I calculate
the percent signal change in a specific contrast in an ROI?

I will be grateful for your suggestions (especially if you point toward a
specific function).

Kind regards,
Maria Czarnecka
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Re: [Freesurfer] FSFAST: wrong brain mask in preproc

2023-04-27 Thread Elmira Hassanzadeh

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Thank you for clarifying.

Elmira

On Wed, Apr 26, 2023 at 6:44 PM Douglas N. Greve 
wrote:

> External Email - Use Caution
>
> Yes, this is the expected behavior, ie, it should cover only subcortical
> GM regions. It is expected that cortical regions will be handled with the
> surface based analysis. You can recombine the results at the end with
> vlrmerge.
>
> On 4/26/2023 12:22 PM, Elmira Hassanzadeh wrote:
>
> External Email - Use Caution
> Hi everyone,
>
> We preprocessed resting-state data with preproc-sess. In the output, I
> noticed although *fmcpr.nii* covers the whole brain,*
> fmcpr.sm6.mni305.2mm.nii* is only covering brain stem+cerebellum
> (screenshots attached).
>
> Any clue what went wrong? This is an example of the command we ran for one
> of our subjects(R19):
>
> *preproc-sess -surface R19 lhrh -s R19 -fwhm 6 -fsd rest -mni305 -per-run*
>
> Thanks,
> Elmira
>
>
>
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Re: [Freesurfer] FSFAST: multiple resting state runs

2023-04-26 Thread Douglas N. Greve

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if you set up the data in the fsfast format, eg, subject/rest/001 
subject/rest/002 etc, then it will handle it automatically


On 4/26/2023 12:30 PM, Elmira Hassanzadeh wrote:


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Hi,

How do we analyze multiple resting state runs for a subject at once?

- do we need certain folder structure/naming?
- do we do concatenation?

Thanks,
Elmira

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Re: [Freesurfer] FSFAST: multiple resting state runs

2023-04-26 Thread Douglas N. Greve

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it will also handle the concatenation

On 4/26/2023 12:30 PM, Elmira Hassanzadeh wrote:


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Hi,

How do we analyze multiple resting state runs for a subject at once?

- do we need certain folder structure/naming?
- do we do concatenation?

Thanks,
Elmira

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Re: [Freesurfer] FSFAST: wrong brain mask in preproc

2023-04-26 Thread Douglas N. Greve

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Yes, this is the expected behavior, ie, it should cover only subcortical
GM regions. It is expected that cortical regions will be handled with
the surface based analysis. You can recombine the results at the end
with vlrmerge.

On 4/26/2023 12:22 PM, Elmira Hassanzadeh wrote:

External Email - Use Caution

Hi everyone,

We preprocessed resting-state data with preproc-sess. In the output, I
noticed although *fmcpr.nii* covers the whole
brain,*fmcpr.sm6.mni305.2mm.nii* is only covering brain
stem+cerebellum (screenshots attached).

Any clue what went wrong? This is an example of the command we ran for
one of our subjects(R19):

*preproc-sess -surface R19 lhrh -s R19 -fwhm 6 -fsd rest -mni305 -per-run*

Thanks,
Elmira

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[Freesurfer] FSFAST: multiple resting state runs

2023-04-26 Thread Elmira Hassanzadeh

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Hi,

How do we analyze multiple resting state runs for a subject at once?

- do we need certain folder structure/naming?
- do we do concatenation?

Thanks,
Elmira
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[Freesurfer] FsFast retinotopy and its flags

2023-04-17 Thread IOANNUCCI Stefano

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Dear Freesurfer experts,


I am attempting to run an old-fashioned polar angle retinotopy analysis through 
FsFast.

Unsurprisingly, the tutorials I've found on the topic are somewhat outdated 
(>10 years ago) and seem to suggest employing flags that are no longer valid in 
mkanalysis-sess.


For instance, it seems that -ncycles is no longer a valid flag, instead giving 
-retinotopy with the period of a cycle seems to be sufficient. Yet, from my 
understanding, this implies giving a -tpef flag pointing to a file that has the 
timepoints to exclude (i.e. before and and after the wedge stimulus has been 
displayed, in my case both 'off' periods last 12 seconds).


My functional images have gone through fmriprep, so are already preprocessed 
and have the motion parameters estimated. Accordingly, I have put these in a 
file to give through the flag -extreg to mkanalysis-sess. However, I get the 
"flag unrecognized" error if I attempt to include it in my call. Is there some 
other way to do this?


Moreover, the wiki page on mkanalysis-sess mentions that retinotopy runs must 
be analyzed through sfa-sess command, yet a tutorial I've found employs 
selxavg3-sess, I assume this is wrong? Telling the difference between the two 
based on their pages in the wiki is challenging.


Many thanks in advance for any help you may provide.


Best,

Stefano Ioannucci
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Re: [Freesurfer] FSFAST first level covariates

2022-08-31 Thread Angela Fang

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Sorry if I was unclear. The analysis we have set up will allow me to test for 
the difference between self and non self valence slope, but I’m also interested 
in testing for the slope of valence alone (identifying the brain regions 
associated with increasing valence ratings). Can I add another condition for 
valence, and if so, how do we make the weights different from the self*valence 
condition (because self is always coded 1 so the weights for self*valence and 
valence only will be identical)?


On Aug 31, 2022, at 8:08 PM, Douglas N. Greve  wrote:

 sorry, you lost me there ...

On 8/31/2022 12:39 PM, Angela Fang wrote:

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That makes sense! And if we wanted to identify brain regions associated with 
valence (across self/non-self) that is unique from condition 2, can we add a 
5th condition? Maybe we can code self as 2 and non-self as 1 so that condition 
2 (self*valence) would be different from condition 5 (valence ratings only)?

Incredibly helpful, Doug- thank you so much!

From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, August 30, 2022 at 7:38 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST first level covariates

Oh, I think I see now. In realty, each trial is either self or not self and 
then you have a separate valence measure, so your coding should be
1. Self-offset
2. SelfValence
3. NoSelf-offset
4. NoSelfValence

Where 1+2 are used for a self event and 3+4 are used for a noself event. If you 
want to test for the difference between self and noself valence slope, then you 
would just use -a 2 -c 4

On 8/29/2022 12:08 PM, Angela Fang wrote:

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Great, thanks so much Doug- this setup makes sense to me. However, isn’t it a 
problem that the brain regions associated with the contrast for -a 3 and the 
contrast for -a 4 would be the same for trials that subjects rate as 1 
(self-relevant) vs 0 (not self-relevant)? Could we code it as 2 (self-relevant) 
and 1 (not self-relevant)?

Many thanks!!

From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, August 28, 2022 at 1:07 PM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST first level covariates

I was under the impression that Self and Valence were ratings from the same 
event (in that mail archive, they were different events and so needed different 
offsets). If Self and Valence are from the same event, then you would have 
something like
1. Offset
2. Self
3. Valence
4. Self*Valence
I've never tried the interaction (self*valence). You might have to demean 
before computing the product
On 8/14/2022 4:58 PM, Angela Fang wrote:

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The two coding schemes are different because the second one does include the 
self*valence variable you’re talking about, whereas the first one doesn’t. I 
only included the 2nd offset because you suggested to someone else to include 
it (see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1ibJu9DNCEQ80IS8XnYQe64G3qUwBk_mJpSfJiHpiFjdObD9fykxEUJll6wFW1-iyN02rfgtRiXTnU4tJAcadUeslBYPf-5CRhCzFKS5taH5e0tcr9yHQucLQZtMPwSNjLSKr-EMGQl4s3bOljQ7SzM7l6ZQZBC6x74q-pCqkQlgW50Mo8uKIDwwDfPnF04ok_kWyqNSL0h4dA3bGXpjQGWY4qb8REA8F3zJTfPieNKjhTBe92G4KDFXX89v_EwUnQw-1GiIs15MK4BUf5eS1LmzTtShQ99QPfHfFSABruvyX4IXN1a1oyCVeBCtRlgya/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html
 
[secure-web.cisco.com]<https://secure-web.cisco.com/1n9NaxxOQGYBn2vf8MJ5Y3HsNwtbaKNPmxR056SHywqcZ1M5Pr3EmrcpD5GO7Bz4VWqz0_QYUglcetQzxo3XfZo52OzpC1h-OFx-iNmhdpBsBWhahZ6gq3wTQ-7drXxoKE3PW6bJvfRmwtp6ttZtwroM5e7FgTaNR0-rYAe7OULwrxMTvFRHcwUT9ZBRYZA_hbtEv0-G0ytcUWEDBddCevIKtYVhpgVwLLS0Exk_XdFbnAvvT1GZTg2WfFucz-ljQluQXurRZBZ6pXaLlq0MOQtFA2RGTM46p_WEB8ZrlOwRc4pLoR-O7EzXnBEQFv2P0/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1UvSz7SvjZnlE1QfkdS-VBc1GzXeZMYqUcsOqE3dGoo43anjoKIpvfs4NnozgTlCx23dB10wC_oFWTi8Zyazh1v1oufO7QQBf9hJanKAiwbu0cr4NfMvGMSOSaaOt5nSATHi-J-55MTqcCUhjz8_rRM1YuYWhtxzDVrlNJ5mD3QlEmdQlhRlYoneii_5mWjAZB1gcbpR_0Zl1nUaCy9BfmpcQRNLpIdfE1NMjg7OnqHOX5jAdPz1gGqxVTKgstTqx8RhxmTkDYOQPLc6hC3by-Atu2VfBnloD3GbZOzG04LjV1Of0uYaB6pk6oSsZFULTsifcwPSiwh1m9gKSg5lD7Q%2Fhttps*3A*2F*2Fwww.mail-archive.com*2Ffreesurfer*40nmr.mgh.harvard.edu*2Fmsg19957.html__;JSUlJSUl!!K-Hz7

Re: [Freesurfer] FSFAST first level covariates

2022-08-31 Thread Douglas N. Greve

sorry, you lost me there ...

On 8/31/2022 12:39 PM, Angela Fang wrote:

External Email - Use Caution

That makes sense! And if we wanted to identify brain regions
associated with valence (across self/non-self) that is unique from
condition 2, can we add a 5^th condition? Maybe we can code self as 2
and non-self as 1 so that condition 2 (self*valence) would be
different from condition 5 (valence ratings only)?

Incredibly helpful, Doug- thank you so much!

*From: * on behalf of "Douglas
N. Greve"

*Reply-To: *Freesurfer support list
*Date: *Tuesday, August 30, 2022 at 7:38 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] FSFAST first level covariates

Oh, I think I see now. In realty, each trial is either self or not
self and then you have a separate valence measure, so your coding
should be

1. Self-offset
2. SelfValence
3. NoSelf-offset
4. NoSelfValence

Where 1+2 are used for a self event and 3+4 are used for a noself
event. If you want to test for the difference between self and noself
valence slope, then you would just use -a 2 -c 4

On 8/29/2022 12:08 PM, Angela Fang wrote:

*External Email - Use Caution *

Great, thanks so much Doug- this setup makes sense to me. However,
isn’t it a problem that the brain regions associated with the
contrast for -a 3 and the contrast for -a 4 would be the same for
trials that subjects rate as 1 (self-relevant) vs 0 (not
self-relevant)? Could we code it as 2 (self-relevant) and 1 (not
self-relevant)?

Many thanks!!

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve"
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Sunday, August 28, 2022 at 1:07 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] FSFAST first level covariates

I was under the impression that Self and Valence were ratings from
the same event (in that mail archive, they were different events
and so needed different offsets). If Self and Valence are from the
same event, then you would have something like
1. Offset
2. Self
3. Valence
4. Self*Valence
I've never tried the interaction (self*valence). You might have to
demean before computing the product

On 8/14/2022 4:58 PM, Angela Fang wrote:

*External Email - Use Caution *

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19957.html

<https://secure-web.cisco.com/1UvSz7SvjZnlE1QfkdS-VBc1GzXeZMYqUcsOqE3dGoo43anjoKIpvfs4NnozgTlCx23dB10wC_oFWTi8Zyazh1v1oufO7QQBf9hJanKAiwbu0cr4NfMvGMSOSaaOt5nSATHi-J-55MTqcCUhjz8_rRM1YuYWhtxzDVrlNJ5mD3QlEmdQlhRlYoneii_5mWjAZB1gcbpR_0Zl1nUaCy9BfmpcQRNLpIdfE1NMjg7OnqHOX5jAdPz1gGqxVTKgstTqx8RhxmTkDYOQPLc6hC3by-Atu2VfBnloD3GbZOzG04LjV1Of0uYaB6pk6oSsZFULTsifcwPSiwh1m9gKSg5lD7Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>).
If we don’t need it, would it just be 2 conditions, as follows?

1. SelfOffset
2. Self*ValenceSlope

But then I’m not clear how to get the main effect of valence
(brain regions that scale with increasing emotion valence,
while holding self-relevance constant)?

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve"
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Sunday, August 14, 2022 at 1:37 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] FSFAST first level covariates

Those look like they are the same coding scheme. What is
different? You can only have one offset. The Self vs Valence
-a 2 -a 4 is not testing for an interaction. If you want an
interaction you have to create a new variable which is
SelfRating*ValenceRating.

On 8/10/2022 2:38 PM, Angela Fang wrote:

*External Email - Use Caution *

Hello,

Just re-sending my question below. If I have a variable
with 2 levels

Re: [Freesurfer] FSFAST first level covariates

2022-08-31 Thread Angela Fang

External Email - Use Caution

That makes sense! And if we wanted to identify brain regions associated with 
valence (across self/non-self) that is unique from condition 2, can we add a 
5th condition? Maybe we can code self as 2 and non-self as 1 so that condition 
2 (self*valence) would be different from condition 5 (valence ratings only)?

Incredibly helpful, Doug- thank you so much!

From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Tuesday, August 30, 2022 at 7:38 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FSFAST first level covariates

Oh, I think I see now. In realty, each trial is either self or not self and 
then you have a separate valence measure, so your coding should be
1. Self-offset
2. SelfValence
3. NoSelf-offset
4. NoSelfValence

Where 1+2 are used for a self event and 3+4 are used for a noself event. If you 
want to test for the difference between self and noself valence slope, then you 
would just use -a 2 -c 4

On 8/29/2022 12:08 PM, Angela Fang wrote:

External Email - Use Caution
Great, thanks so much Doug- this setup makes sense to me. However, isn’t it a 
problem that the brain regions associated with the contrast for -a 3 and the 
contrast for -a 4 would be the same for trials that subjects rate as 1 
(self-relevant) vs 0 (not self-relevant)? Could we code it as 2 (self-relevant) 
and 1 (not self-relevant)?

Many thanks!!

From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, August 28, 2022 at 1:07 PM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST first level covariates

I was under the impression that Self and Valence were ratings from the same 
event (in that mail archive, they were different events and so needed different 
offsets). If Self and Valence are from the same event, then you would have 
something like
1. Offset
2. Self
3. Valence
4. Self*Valence
I've never tried the interaction (self*valence). You might have to demean 
before computing the product
On 8/14/2022 4:58 PM, Angela Fang wrote:

External Email - Use Caution
The two coding schemes are different because the second one does include the 
self*valence variable you’re talking about, whereas the first one doesn’t. I 
only included the 2nd offset because you suggested to someone else to include 
it (see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1axFb8Uk3EidN7RU3PxCMFcOtbS8C3cmNULxUDXhNgudqc2v-5LUyAYUUUC6m-FcwrPwdVKy2Y7n8DAVcyRmfV5k4NWvno0aemc07RzaIinRQ8-6_FFiXeiHdOzhbARiwJyY4xdCGKBBbKJGuolxWhUQ5ZaDv2NtX0TJ7BmyhFTGOFw4S9sp6o7il_xApboosWIOBOJb1zh7hBwMks3eFrd04OkImYWLahgGjjS7Zs4BjsQy1dYPiBCXK_vv2cHadYnHraA451p-pjerGjuvaFs9cp4jm03dcia0ilLlFFYK5n74UApp-Da_ShPd4EN_o7az4F96Vwm7OtA1A2eemJw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html<https://secure-web.cisco.com/1UvSz7SvjZnlE1QfkdS-VBc1GzXeZMYqUcsOqE3dGoo43anjoKIpvfs4NnozgTlCx23dB10wC_oFWTi8Zyazh1v1oufO7QQBf9hJanKAiwbu0cr4NfMvGMSOSaaOt5nSATHi-J-55MTqcCUhjz8_rRM1YuYWhtxzDVrlNJ5mD3QlEmdQlhRlYoneii_5mWjAZB1gcbpR_0Zl1nUaCy9BfmpcQRNLpIdfE1NMjg7OnqHOX5jAdPz1gGqxVTKgstTqx8RhxmTkDYOQPLc6hC3by-Atu2VfBnloD3GbZOzG04LjV1Of0uYaB6pk6oSsZFULTsifcwPSiwh1m9gKSg5lD7Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>).
 If we don’t need it, would it just be 2 conditions, as follows?


  1.  SelfOffset
  2.  Self*ValenceSlope

But then I’m not clear how to get the main effect of valence (brain regions 
that scale with increasing emotion valence, while holding self-relevance 
constant)?

From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, August 14, 2022 at 1:37 PM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST first level covariates

Those look like they are the same coding scheme. What is different? You can 
only have one offset. The Self vs Valence -a 2 -a 4 is not testing for an 
interaction. If you want an interaction you have to create a new variable which 
is SelfRating*ValenceRating.

On 8/10/2022 2:38 PM, Angela Fang wrote:

External Email - Use Caution
Hello,

Just re-sending my question below. If I have a variable with 2 levels (yes/no) 
and another variable that is continuous, based on this post (MailScanner has 
detected a possible fraud attemp

Re: [Freesurfer] FSFAST first level covariates

2022-08-30 Thread Douglas N. Greve

Oh, I think I see now. In realty, each trial is either self or not self
and then you have a separate valence measure, so your coding should be

1. Self-offset
2. SelfValence
3. NoSelf-offset
4. NoSelfValence

Where 1+2 are used for a self event and 3+4 are used for a noself event.
If you want to test for the difference between self and noself valence
slope, then you would just use -a 2 -c 4

On 8/29/2022 12:08 PM, Angela Fang wrote:

External Email - Use Caution

Great, thanks so much Doug- this setup makes sense to me. However,
isn’t it a problem that the brain regions associated with the contrast
for -a 3 and the contrast for -a 4 would be the same for trials that
subjects rate as 1 (self-relevant) vs 0 (not self-relevant)? Could we
code it as 2 (self-relevant) and 1 (not self-relevant)?

Many thanks!!

*From: * on behalf of "Douglas
N. Greve"

*Reply-To: *Freesurfer support list
*Date: *Sunday, August 28, 2022 at 1:07 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] FSFAST first level covariates

1. Offset
2. Self
3. Valence
4. Self*Valence
I've never tried the interaction (self*valence). You might have to
demean before computing the product

On 8/14/2022 4:58 PM, Angela Fang wrote:

*External Email - Use Caution *

1. SelfOffset
2. Self*ValenceSlope

But then I’m not clear how to get the main effect of valence
(brain regions that scale with increasing emotion valence, while
holding self-relevance constant)?

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve"
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Sunday, August 14, 2022 at 1:37 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] FSFAST first level covariates

Those look like they are the same coding scheme. What is
different? You can only have one offset. The Self vs Valence -a 2
-a 4 is not testing for an interaction. If you want an interaction
you have to create a new variable which is SelfRating*ValenceRating.

On 8/10/2022 2:38 PM, Angela Fang wrote:

*External Email - Use Caution *

Hello,

Just re-sending my question below. If I have a variable with 2
levels (yes/no) and another variable that is continuous, based
on this post (*MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to be*

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19957.html

<https://secure-web.cisco.com/1S2s08xk6_r2FFsEB5S1KdOcfq6G8ToJwyZuNFONdwgOYd87JJkB-uznJW2pelg24KQwX3lweVOmFs99TCKitjbJOqKWgEH_UW7wir5JQ113csODerDntanBrEibOdt6Mxs2QeQ5D7n69Ds6NaOSOJIbLFeMjuoaTXCkNccNydn7jvjmVd0zW2YhEXG9JtLxMNVIYt8q48ZK0sJUt8sjTP6xuCzA1pzB19MUHA078Zgygtns0YVgn1n5Sg41ZbVZ3jWciX5ZF34AejW5nWj1Z4mWO1Xyd_7RwNbKkVMPeDwG6K9W59gzBf_t0G-AzmUhxGC8zfKM0bxA9hhZv4GR2BQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>),
it sounds like I should code as follows:

1. SelfOffset
2. Self-ValenceSlope (would the weight in the 4^th column
reflect the value of self multiplied by the value of
valence for this participant?)
3. NonSelfOffset
4. NonSelf-ValenceSlope

If the other way of modifying the paradigm file is also
acceptable to test the interaction (as I describe below), that
would also

Re: [Freesurfer] FSFAST first level covariates

2022-08-29 Thread Angela Fang

External Email - Use Caution

Great, thanks so much Doug- this setup makes sense to me. However, isn’t it a 
problem that the brain regions associated with the contrast for -a 3 and the 
contrast for -a 4 would be the same for trials that subjects rate as 1 
(self-relevant) vs 0 (not self-relevant)? Could we code it as 2 (self-relevant) 
and 1 (not self-relevant)?

Many thanks!!

From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Sunday, August 28, 2022 at 1:07 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FSFAST first level covariates

I was under the impression that Self and Valence were ratings from the same 
event (in that mail archive, they were different events and so needed different 
offsets). If Self and Valence are from the same event, then you would have 
something like
1. Offset
2. Self
3. Valence
4. Self*Valence
I've never tried the interaction (self*valence). You might have to demean 
before computing the product
On 8/14/2022 4:58 PM, Angela Fang wrote:

External Email - Use Caution
The two coding schemes are different because the second one does include the 
self*valence variable you’re talking about, whereas the first one doesn’t. I 
only included the 2nd offset because you suggested to someone else to include 
it (see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1sZZR9kggc35UyK7lSAda3dE6il9II_AD7YGowE7cmcitllK2WkMkXZrYMKNHWVfSSVhSBTpzhl3tRvJs-7MjxeemfsGXeS63jstCurLf6ur3TzjDLZaSY3nEp6mFhrKVYKnRkv7Wdxkn-BI3_cR0HvigETBgmiDZpQpzNHRDgc-7DYuwysbhd26aCuwOQ6YPKSgA5EhF0RwgNj-Y5XAyBeBe3b0QJ7Xgsxvk-wejbxLU2hQx3CIxif6YZC-0J5u3IdWQ1xP3WxhoSZ_z3MEylWxOEDyLyIWLX2dGKMd6-xvTML2huIRERSgZF-zI8ZNUPUzt2Klohmq9IfNQbdNZVw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html<https://secure-web.cisco.com/1UvSz7SvjZnlE1QfkdS-VBc1GzXeZMYqUcsOqE3dGoo43anjoKIpvfs4NnozgTlCx23dB10wC_oFWTi8Zyazh1v1oufO7QQBf9hJanKAiwbu0cr4NfMvGMSOSaaOt5nSATHi-J-55MTqcCUhjz8_rRM1YuYWhtxzDVrlNJ5mD3QlEmdQlhRlYoneii_5mWjAZB1gcbpR_0Zl1nUaCy9BfmpcQRNLpIdfE1NMjg7OnqHOX5jAdPz1gGqxVTKgstTqx8RhxmTkDYOQPLc6hC3by-Atu2VfBnloD3GbZOzG04LjV1Of0uYaB6pk6oSsZFULTsifcwPSiwh1m9gKSg5lD7Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>).
 If we don’t need it, would it just be 2 conditions, as follows?


  1.  SelfOffset
  2.  Self*ValenceSlope

But then I’m not clear how to get the main effect of valence (brain regions 
that scale with increasing emotion valence, while holding self-relevance 
constant)?

From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, August 14, 2022 at 1:37 PM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST first level covariates

Those look like they are the same coding scheme. What is different? You can 
only have one offset. The Self vs Valence -a 2 -a 4 is not testing for an 
interaction. If you want an interaction you have to create a new variable which 
is SelfRating*ValenceRating.

On 8/10/2022 2:38 PM, Angela Fang wrote:

External Email - Use Caution
Hello,

Just re-sending my question below. If I have a variable with 2 levels (yes/no) 
and another variable that is continuous, based on this post (MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1sZZR9kggc35UyK7lSAda3dE6il9II_AD7YGowE7cmcitllK2WkMkXZrYMKNHWVfSSVhSBTpzhl3tRvJs-7MjxeemfsGXeS63jstCurLf6ur3TzjDLZaSY3nEp6mFhrKVYKnRkv7Wdxkn-BI3_cR0HvigETBgmiDZpQpzNHRDgc-7DYuwysbhd26aCuwOQ6YPKSgA5EhF0RwgNj-Y5XAyBeBe3b0QJ7Xgsxvk-wejbxLU2hQx3CIxif6YZC-0J5u3IdWQ1xP3WxhoSZ_z3MEylWxOEDyLyIWLX2dGKMd6-xvTML2huIRERSgZF-zI8ZNUPUzt2Klohmq9IfNQbdNZVw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html<https://secure-web.cisco.com/1S2s08xk6_r2FFsEB5S1KdOcfq6G8ToJwyZuNFONdwgOYd87JJkB-uznJW2pelg24KQwX3lweVOmFs99TCKitjbJOqKWgEH_UW7wir5JQ113csODerDntanBrEibOdt6Mxs2QeQ5D7n69Ds6NaOSOJIbLFeMjuoaTXCkNccNydn7jvjmVd0zW2YhEXG9JtLxMNVIYt8q48ZK0sJUt8sjTP6xuCzA1pzB19MUHA078Zgygtns0YVgn1n5Sg41ZbVZ3jWciX5ZF34AejW5nWj1Z4mWO1Xyd_7RwNbKkVMPeDwG6K9W59gzBf_t0G-AzmUhxGC8zfKM0bxA9hhZv4GR2BQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>),
 it sounds like I should code as follows:


  1.  SelfOffset
  2.  Self-ValenceSlope (would the weight in the 4th column reflect the value 
of self multiplied by the value of valence for this participant?)
  3.  NonSelfOffset
  4.  NonSelf-ValenceSlope

If the other way of modifying the paradigm file is also acceptable to test the 
interaction (as

Re: [Freesurfer] FSFAST first level covariates

2022-08-28 Thread Douglas N. Greve

1. Offset
2. Self
3. Valence
4. Self*Valence
I've never tried the interaction (self*valence). You might have to
demean before computing the product

On 8/14/2022 4:58 PM, Angela Fang wrote:

External Email - Use Caution

The two coding schemes are different because the second one does
include the self*valence variable you’re talking about, whereas the
first one doesn’t. I only included the 2^nd offset because you
suggested to someone else to include it (see *MailScanner has detected
a possible fraud attempt from "secure-web.cisco.com" claiming to be*
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19957.html
<https://secure-web.cisco.com/1UvSz7SvjZnlE1QfkdS-VBc1GzXeZMYqUcsOqE3dGoo43anjoKIpvfs4NnozgTlCx23dB10wC_oFWTi8Zyazh1v1oufO7QQBf9hJanKAiwbu0cr4NfMvGMSOSaaOt5nSATHi-J-55MTqcCUhjz8_rRM1YuYWhtxzDVrlNJ5mD3QlEmdQlhRlYoneii_5mWjAZB1gcbpR_0Zl1nUaCy9BfmpcQRNLpIdfE1NMjg7OnqHOX5jAdPz1gGqxVTKgstTqx8RhxmTkDYOQPLc6hC3by-Atu2VfBnloD3GbZOzG04LjV1Of0uYaB6pk6oSsZFULTsifcwPSiwh1m9gKSg5lD7Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>).
If we don’t need it, would it just be 2 conditions, as follows?

1. SelfOffset
2. Self*ValenceSlope

But then I’m not clear how to get the main effect of valence (brain
regions that scale with increasing emotion valence, while holding
self-relevance constant)?

*From: * on behalf of "Douglas
N. Greve"

*Reply-To: *Freesurfer support list
*Date: *Sunday, August 14, 2022 at 1:37 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] FSFAST first level covariates

Those look like they are the same coding scheme. What is different?
You can only have one offset. The Self vs Valence -a 2 -a 4 is not
testing for an interaction. If you want an interaction you have to
create a new variable which is SelfRating*ValenceRating.

On 8/10/2022 2:38 PM, Angela Fang wrote:

*External Email - Use Caution *

Hello,

Just re-sending my question below. If I have a variable with 2
levels (yes/no) and another variable that is continuous, based on
this post (*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19957.html

1. SelfOffset
2. Self-ValenceSlope (would the weight in the 4^th column reflect
the value of self multiplied by the value of valence for this
participant?)
3. NonSelfOffset
4. NonSelf-ValenceSlope

If the other way of modifying the paradigm file is also acceptable
to test the interaction (as I describe below), that would also be
helpful to know.

Thanks!

Angela

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Angela Fang <mailto:angf...@uw.edu>
*Reply-To: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, August 1, 2022 at 4:35 PM
*To: *Freesurfer support list
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] FSFAST first level covariates

*External Email - Use Caution *

Hi Doug,

Nevermind to my first question! I read this post (*MailScanner has
detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be*
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32235.html

<https://secure-web.cisco.com/1646ymi0_yM9ab72e81bZdCKw_zNbXr9RihxDaiDVPq0_Qd4EXYgDmO56zQdi9l_AyV3uyyiURXHoYWQmiu56CbMuIGdZz8EH0gbsnVrAz9KwunZAwLzh0kh-jzVwHtlbEdd1ExEJYHT7o7JtUWg2GM484JTyL0VZJymRuGRyD0ag1nQ_0BPPjQHxPCqNHEU4Y_seBsq9XsUROgyR-bX-tHVXxhshVUHgneudw6tEB2lIVYfYrL3srRbjy1QN9Bq_e3_WaNCDhkXdixnae24i41HHYwJfn3KwsmNoZ2RxLoh3SMkXXwVntAewl8PeldBY0s3UxoEPiFbDdXXuJLUjlw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg32235.html>)
and realized that we always include a subject-specific par file in
each run for first-level analyses.

However, I’m still confused about how to modify my paradigm file.
I also need to model the trials of non-interest, so would it be as
f

Re: [Freesurfer] FSFAST first level covariates

2022-08-14 Thread Angela Fang

External Email - Use Caution

The two coding schemes are different because the second one does include the 
self*valence variable you’re talking about, whereas the first one doesn’t. I 
only included the 2nd offset because you suggested to someone else to include 
it (see 
https://secure-web.cisco.com/1UvSz7SvjZnlE1QfkdS-VBc1GzXeZMYqUcsOqE3dGoo43anjoKIpvfs4NnozgTlCx23dB10wC_oFWTi8Zyazh1v1oufO7QQBf9hJanKAiwbu0cr4NfMvGMSOSaaOt5nSATHi-J-55MTqcCUhjz8_rRM1YuYWhtxzDVrlNJ5mD3QlEmdQlhRlYoneii_5mWjAZB1gcbpR_0Zl1nUaCy9BfmpcQRNLpIdfE1NMjg7OnqHOX5jAdPz1gGqxVTKgstTqx8RhxmTkDYOQPLc6hC3by-Atu2VfBnloD3GbZOzG04LjV1Of0uYaB6pk6oSsZFULTsifcwPSiwh1m9gKSg5lD7Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html).
 If we don’t need it, would it just be 2 conditions, as follows?


  1.  SelfOffset
  2.  Self*ValenceSlope

But then I’m not clear how to get the main effect of valence (brain regions 
that scale with increasing emotion valence, while holding self-relevance 
constant)?

From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Sunday, August 14, 2022 at 1:37 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FSFAST first level covariates

Those look like they are the same coding scheme. What is different? You can 
only have one offset. The Self vs Valence -a 2 -a 4 is not testing for an 
interaction. If you want an interaction you have to create a new variable which 
is SelfRating*ValenceRating.

On 8/10/2022 2:38 PM, Angela Fang wrote:

External Email - Use Caution
Hello,

Just re-sending my question below. If I have a variable with 2 levels (yes/no) 
and another variable that is continuous, based on this post (MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1UvSz7SvjZnlE1QfkdS-VBc1GzXeZMYqUcsOqE3dGoo43anjoKIpvfs4NnozgTlCx23dB10wC_oFWTi8Zyazh1v1oufO7QQBf9hJanKAiwbu0cr4NfMvGMSOSaaOt5nSATHi-J-55MTqcCUhjz8_rRM1YuYWhtxzDVrlNJ5mD3QlEmdQlhRlYoneii_5mWjAZB1gcbpR_0Zl1nUaCy9BfmpcQRNLpIdfE1NMjg7OnqHOX5jAdPz1gGqxVTKgstTqx8RhxmTkDYOQPLc6hC3by-Atu2VfBnloD3GbZOzG04LjV1Of0uYaB6pk6oSsZFULTsifcwPSiwh1m9gKSg5lD7Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html<https://secure-web.cisco.com/1S2s08xk6_r2FFsEB5S1KdOcfq6G8ToJwyZuNFONdwgOYd87JJkB-uznJW2pelg24KQwX3lweVOmFs99TCKitjbJOqKWgEH_UW7wir5JQ113csODerDntanBrEibOdt6Mxs2QeQ5D7n69Ds6NaOSOJIbLFeMjuoaTXCkNccNydn7jvjmVd0zW2YhEXG9JtLxMNVIYt8q48ZK0sJUt8sjTP6xuCzA1pzB19MUHA078Zgygtns0YVgn1n5Sg41ZbVZ3jWciX5ZF34AejW5nWj1Z4mWO1Xyd_7RwNbKkVMPeDwG6K9W59gzBf_t0G-AzmUhxGC8zfKM0bxA9hhZv4GR2BQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>),
 it sounds like I should code as follows:


  1.  SelfOffset
  2.  Self-ValenceSlope (would the weight in the 4th column reflect the value 
of self multiplied by the value of valence for this participant?)
  3.  NonSelfOffset
  4.  NonSelf-ValenceSlope

If the other way of modifying the paradigm file is also acceptable to test the 
interaction (as I describe below), that would also be helpful to know.

Thanks!
Angela

From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Angela Fang <mailto:angf...@uw.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Monday, August 1, 2022 at 4:35 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST first level covariates


External Email - Use Caution
Hi Doug,

Nevermind to my first question! I read this post (MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1HVMVTjRAiW9L4gY48Veh_kfiv1-IcKlH19YGnZA4uiivgCNnRBDiv1ha5bxC1DRvtBdo4S9DEUaBOOp996Bdoi48IxhMuUmcx4E11Q99LMPWXjV0ecDedB5lM7q-j6FaDPW_yfxmKxeLQI69yz9F7iGzCVSPjYO7_j48Y_0GQwwlNxpi1PogvndydGw96sgQmHDfsqftIDgpdKoQR5mq560WyTAUgVDQNiSRTqxYnUgrm6S315JtmMFs8DczARMB5Y3Dj19BwS9yGVTRpaOJSQTsTswFIgqA2CnTKjgtiUWGy8TCI2QjTXdaWfOdW83XCXkMMOwu1kghjraT1mnSqw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg32235.html<https://secure-web.cisco.com/1646ymi0_yM9ab72e81bZdCKw_zNbXr9RihxDaiDVPq0_Qd4EXYgDmO56zQdi9l_AyV3uyyiURXHoYWQmiu56CbMuIGdZz8EH0gbsnVrAz9KwunZAwLzh0kh-jzVwHtlbEdd1ExEJYHT7o7JtUWg2GM484JTyL0VZJymRuGRyD0ag1nQ_0BPPjQHxPCqNHEU4Y_seBsq9XsUROgyR-bX-tHVXxhshVUHgneudw6tEB2lIVYfYrL3srRbjy1QN9Bq_e3_WaNCDhkXdixnae24i41HHYwJfn3KwsmNoZ2RxLoh3SMkXXwVntAewl8PeldBY0s3UxoEPiFbDdXXuJLUjlw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg32235.html>)
 and realized that we always include a subject-specific par file in each run 
for first-level analyses.

However, I’m still confused about how to modify my paradigm file. I also need 
to model the trials of non-interest, so would it be as follows?

0 1  2.5

Re: [Freesurfer] FSFAST first level covariates

2022-08-14 Thread Douglas N. Greve

Those look like they are the same coding scheme. What is different? You 
can only have one offset. The Self vs Valence -a 2 -a 4 is not testing 
for an interaction. If you want an interaction you have to create a new 
variable which is SelfRating*ValenceRating.



On 8/10/2022 2:38 PM, Angela Fang wrote:


External Email - Use Caution

Hello,

Just re-sending my question below. If I have a variable with 2 levels 
(yes/no) and another variable that is continuous, based on this post 
(*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19957.html 
<https://secure-web.cisco.com/1S2s08xk6_r2FFsEB5S1KdOcfq6G8ToJwyZuNFONdwgOYd87JJkB-uznJW2pelg24KQwX3lweVOmFs99TCKitjbJOqKWgEH_UW7wir5JQ113csODerDntanBrEibOdt6Mxs2QeQ5D7n69Ds6NaOSOJIbLFeMjuoaTXCkNccNydn7jvjmVd0zW2YhEXG9JtLxMNVIYt8q48ZK0sJUt8sjTP6xuCzA1pzB19MUHA078Zgygtns0YVgn1n5Sg41ZbVZ3jWciX5ZF34AejW5nWj1Z4mWO1Xyd_7RwNbKkVMPeDwG6K9W59gzBf_t0G-AzmUhxGC8zfKM0bxA9hhZv4GR2BQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html>), 
it sounds like I should code as follows:


 1. SelfOffset
 2. Self-ValenceSlope (would the weight in the 4^th column reflect the
value of self multiplied by the value of valence for this
participant?)
 3. NonSelfOffset
 4. NonSelf-ValenceSlope

If the other way of modifying the paradigm file is also acceptable to 
test the interaction (as I describe below), that would also be helpful 
to know.


Thanks!

Angela

*From: * on behalf of Angela 
Fang 

*Reply-To: *Freesurfer support list 
*Date: *Monday, August 1, 2022 at 4:35 PM
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] FSFAST first level covariates

*External Email - Use Caution *

Hi Doug,

Nevermind to my first question! I read this post (*MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming 
to be* 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32235.html 
<https://secure-web.cisco.com/1646ymi0_yM9ab72e81bZdCKw_zNbXr9RihxDaiDVPq0_Qd4EXYgDmO56zQdi9l_AyV3uyyiURXHoYWQmiu56CbMuIGdZz8EH0gbsnVrAz9KwunZAwLzh0kh-jzVwHtlbEdd1ExEJYHT7o7JtUWg2GM484JTyL0VZJymRuGRyD0ag1nQ_0BPPjQHxPCqNHEU4Y_seBsq9XsUROgyR-bX-tHVXxhshVUHgneudw6tEB2lIVYfYrL3srRbjy1QN9Bq_e3_WaNCDhkXdixnae24i41HHYwJfn3KwsmNoZ2RxLoh3SMkXXwVntAewl8PeldBY0s3UxoEPiFbDdXXuJLUjlw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg32235.html>) 
and realized that we always include a subject-specific par file in 
each run for first-level analyses.


However, I’m still confused about how to modify my paradigm file. I 
also need to model the trials of non-interest, so would it be as follows?


0 1  2.5  1.0  SelfOffset

0 2  2.5  1.0  SelfSlope (equal to 
subject’s rating of self-relevance)


0 3  2.5  1.0  ValenceOffset

0 4  2.5  3.0  ValenceSlope (equal to 
subject’s rating of valence)


2.5 0  2.5  1.0  FIXATION

5.0 1  2.5  1.0  SelfOffset

5.0 2  2.5  0  SelfSlope (equal to 
subject’s rating of self-relevance, in this case subject responded 0, 
or non-relevant)


5.0 3  2.5  1.0  ValenceOffset

5.0 4  2.5  2.0  ValenceSlope (equal to 
subject’s rating of valence)


7.5 5  2.5  1.0  OTHER

Do these contrasts look correct to you?

Self vs Fixation -a 1 -c 0 (main effect of self)

Valence vs Fixation -a 3 -c 0 (main effect of valence)

Self vs Valence -a 2 -a 4 (interaction between self x valence)

Thank you so much for your help!

Angela

*From: * on behalf of Angela 
Fang 

*Reply-To: *Freesurfer support list 
*Date: *Thursday, July 28, 2022 at 1:02 PM
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] FSFAST first level covariates

Thanks Doug. This wiki page is extremely helpful. However, my question 
is about individual subject responses. I could see how you could 
include a summary (e.g., average) value of the parametric variable 
across subjects in your “weight” column but it’s not clear to me how 
you could integrate individual subject responses to each word in the 
parametric modulation paradigm file? I’m imagining something like the 
FSGD file where a value is given for each subject, but for first-level 
analysis.


We have a similar design as someone else who posted a similar question 
(*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19957.html 
<https://secure-web.cisco.com/11nFbIrJYBqRI1W_4wY-HvfdEF3GG6xLL8So8t0i9yKbcElVyl_nJoDI6XedAGY2kKd_eP-dnsWeccOw2qajd375GRCeiUjqaXv3C7vOkrGEOiSiqfcPQ9y73ROdtl0jJIGemdoYQDd3GcX-dKx6qDwBcPE_qNlqxB0Z

Re: [Freesurfer] FSFAST first level covariates

2022-08-10 Thread Angela Fang

External Email - Use Caution

Hello,

Just re-sending my question below. If I have a variable with 2 levels (yes/no) 
and another variable that is continuous, based on this post 
(https://secure-web.cisco.com/1S2s08xk6_r2FFsEB5S1KdOcfq6G8ToJwyZuNFONdwgOYd87JJkB-uznJW2pelg24KQwX3lweVOmFs99TCKitjbJOqKWgEH_UW7wir5JQ113csODerDntanBrEibOdt6Mxs2QeQ5D7n69Ds6NaOSOJIbLFeMjuoaTXCkNccNydn7jvjmVd0zW2YhEXG9JtLxMNVIYt8q48ZK0sJUt8sjTP6xuCzA1pzB19MUHA078Zgygtns0YVgn1n5Sg41ZbVZ3jWciX5ZF34AejW5nWj1Z4mWO1Xyd_7RwNbKkVMPeDwG6K9W59gzBf_t0G-AzmUhxGC8zfKM0bxA9hhZv4GR2BQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html),
 it sounds like I should code as follows:


  1.  SelfOffset
  2.  Self-ValenceSlope (would the weight in the 4th column reflect the value 
of self multiplied by the value of valence for this participant?)
  3.  NonSelfOffset
  4.  NonSelf-ValenceSlope

If the other way of modifying the paradigm file is also acceptable to test the 
interaction (as I describe below), that would also be helpful to know.

Thanks!
Angela

From:  on behalf of Angela Fang 

Reply-To: Freesurfer support list 
Date: Monday, August 1, 2022 at 4:35 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] FSFAST first level covariates


External Email - Use Caution
Hi Doug,

Nevermind to my first question! I read this post (MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1CMVIrMV5SzmWczLBYJ8wrbs4I4fTd5TDfoZl4aAcMRL9BIQ-Qtf_TNzQRr7zOVT5cTiOFV8Ra3a94S103KieE3Tx520Wc4b13Figq023v6mGeLMvO4ta3onkEAhJTj2BPvgC68B6vwZKYOcU5mDuxxjAtn326ZOpm1upylv6_uFul29AAJsOxJDurtJ2p-3ktjc51QB3JOLJ_DxxHV8RQayh1MZMEkZETrsXsAYS8AzD9VTXBGYU8dxrvNBiJNcqZj1E5qRoV6I70Z6gjddHCEkR-mmClpRrGkHTBUq-0_Zgg10-XRZQFiw2xc9V9h595go0ZToz7UxuSDBebc9JAA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg32235.html<https://secure-web.cisco.com/1646ymi0_yM9ab72e81bZdCKw_zNbXr9RihxDaiDVPq0_Qd4EXYgDmO56zQdi9l_AyV3uyyiURXHoYWQmiu56CbMuIGdZz8EH0gbsnVrAz9KwunZAwLzh0kh-jzVwHtlbEdd1ExEJYHT7o7JtUWg2GM484JTyL0VZJymRuGRyD0ag1nQ_0BPPjQHxPCqNHEU4Y_seBsq9XsUROgyR-bX-tHVXxhshVUHgneudw6tEB2lIVYfYrL3srRbjy1QN9Bq_e3_WaNCDhkXdixnae24i41HHYwJfn3KwsmNoZ2RxLoh3SMkXXwVntAewl8PeldBY0s3UxoEPiFbDdXXuJLUjlw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg32235.html>)
 and realized that we always include a subject-specific par file in each run 
for first-level analyses.

However, I’m still confused about how to modify my paradigm file. I also need 
to model the trials of non-interest, so would it be as follows?

0 1  2.5  1.0  SelfOffset
0  2  2.5  1.0  SelfSlope (equal to 
subject’s rating of self-relevance)
0  3  2.5  1.0  ValenceOffset
0  4  2.5  3.0  ValenceSlope (equal to 
subject’s rating of valence)

2.5  0  2.5  1.0  FIXATION

5.0  1  2.5  1.0  SelfOffset
5.0  2  2.5  0  SelfSlope (equal to 
subject’s rating of self-relevance, in this case subject responded 0, or 
non-relevant)
5.0  3  2.5  1.0  ValenceOffset
5.0  4  2.5  2.0  ValenceSlope (equal to 
subject’s rating of valence)

7.5  5  2.5  1.0  OTHER

Do these contrasts look correct to you?
Self vs Fixation -a 1 -c 0 (main effect of self)
Valence vs Fixation -a 3 -c 0 (main effect of valence)
Self vs Valence -a 2 -a 4 (interaction between self x valence)

Thank you so much for your help!
Angela

From:  on behalf of Angela Fang 

Reply-To: Freesurfer support list 
Date: Thursday, July 28, 2022 at 1:02 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] FSFAST first level covariates

Thanks Doug. This wiki page is extremely helpful. However, my question is about 
individual subject responses. I could see how you could include a summary 
(e.g., average) value of the parametric variable across subjects in your 
“weight” column but it’s not clear to me how you could integrate individual 
subject responses to each word in the parametric modulation paradigm file? I’m 
imagining something like the FSGD file where a value is given for each subject, 
but for first-level analysis.

We have a similar design as someone else who posted a similar question 
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1S2s08xk6_r2FFsEB5S1KdOcfq6G8ToJwyZuNFONdwgOYd87JJkB-uznJW2pelg24KQwX3lweVOmFs99TCKitjbJOqKWgEH_UW7wir5JQ113csODerDntanBrEibOdt6Mxs2QeQ5D7n69Ds6NaOSOJIbLFeMjuoaTXCkNccNydn7jvjmVd0zW2YhEXG9JtLxMNVIYt8q48ZK0sJUt8sjTP6xuCzA1pzB19MUHA078Zgygtns0YVgn1n5Sg41ZbVZ3jWciX5ZF34AejW5nWj1Z4mWO1Xyd_7R

Re: [Freesurfer] FSFAST first level covariates

2022-08-01 Thread Angela Fang

External Email - Use Caution

Hi Doug,

Nevermind to my first question! I read this post 
(https://secure-web.cisco.com/1646ymi0_yM9ab72e81bZdCKw_zNbXr9RihxDaiDVPq0_Qd4EXYgDmO56zQdi9l_AyV3uyyiURXHoYWQmiu56CbMuIGdZz8EH0gbsnVrAz9KwunZAwLzh0kh-jzVwHtlbEdd1ExEJYHT7o7JtUWg2GM484JTyL0VZJymRuGRyD0ag1nQ_0BPPjQHxPCqNHEU4Y_seBsq9XsUROgyR-bX-tHVXxhshVUHgneudw6tEB2lIVYfYrL3srRbjy1QN9Bq_e3_WaNCDhkXdixnae24i41HHYwJfn3KwsmNoZ2RxLoh3SMkXXwVntAewl8PeldBY0s3UxoEPiFbDdXXuJLUjlw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg32235.html)
 and realized that we always include a subject-specific par file in each run 
for first-level analyses.

However, I’m still confused about how to modify my paradigm file. I also need 
to model the trials of non-interest, so would it be as follows?

0 1  2.5  1.0  SelfOffset
0  2  2.5  1.0  SelfSlope (equal to 
subject’s rating of self-relevance)
0  3  2.5  1.0  ValenceOffset
0  4  2.5  3.0  ValenceSlope (equal to 
subject’s rating of valence)

2.5  0  2.5  1.0  FIXATION

5.0  1  2.5  1.0  SelfOffset
5.0  2  2.5  0  SelfSlope (equal to 
subject’s rating of self-relevance, in this case subject responded 0, or 
non-relevant)
5.0  3  2.5  1.0  ValenceOffset
5.0  4  2.5  2.0  ValenceSlope (equal to 
subject’s rating of valence)

7.5  5  2.5  1.0  OTHER

Do these contrasts look correct to you?
Self vs Fixation -a 1 -c 0 (main effect of self)
Valence vs Fixation -a 3 -c 0 (main effect of valence)
Self vs Valence -a 2 -a 4 (interaction between self x valence)

Thank you so much for your help!
Angela

From:  on behalf of Angela Fang 

Reply-To: Freesurfer support list 
Date: Thursday, July 28, 2022 at 1:02 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] FSFAST first level covariates

Thanks Doug. This wiki page is extremely helpful. However, my question is about 
individual subject responses. I could see how you could include a summary 
(e.g., average) value of the parametric variable across subjects in your 
“weight” column but it’s not clear to me how you could integrate individual 
subject responses to each word in the parametric modulation paradigm file? I’m 
imagining something like the FSGD file where a value is given for each subject, 
but for first-level analysis.

We have a similar design as someone else who posted a similar question 
(https://secure-web.cisco.com/11nFbIrJYBqRI1W_4wY-HvfdEF3GG6xLL8So8t0i9yKbcElVyl_nJoDI6XedAGY2kKd_eP-dnsWeccOw2qajd375GRCeiUjqaXv3C7vOkrGEOiSiqfcPQ9y73ROdtl0jJIGemdoYQDd3GcX-dKx6qDwBcPE_qNlqxB0ZTcsDfTwK88OkoVtftMo1zKBWSiZBV9p0GO2erUcSoXtVI-AITDr9jULRDzVL_IzxtPdtuSBrYXMASRi7ex2oKftjJjyG_HMgygf_ULhSYIsHviihCwfx4uO5_zrvh8H84AxAsv33zsFjOaYeZ826JkD3E99hxrAKW3jYr3PjfN-zNZjQLJA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg19957.html).
 We have an event-related experiment presenting trait adjectives in terms of 
whether they describe themselves (SELF condition) or someone else (OTHER 
condition). We are interested in testing a 2x2 ANOVA to examine an interaction 
between self-relevance x emotional valence. Assuming you can’t integrate 
individual subject responses to each word in the paradigm file, would we set it 
up as follows?

“Usual” paradigm file:
0  1  2.5  1.0  SELF
2.5  0  2.5  1.0  FIXATION
5.0  1  2.5  1.0  SELF
7.5  2  2.5  1.0  OTHER

Parametric modulation paradigm file:
0  1  2.5  1.0  SELFoffset
0  2  2.5  0.8  SELFslope
0  3  2.5  1.0  VALENCEoffset
0  4  2.5  2.0  VALENCEslope

(where 0.8 reflects the percentage of time the word was endorsed as 
self-relevant and 2.0 is the average valence rating given for that word)

And then create a contrast of 2 vs 4 to test the interaction? Would testing 
contrast 1 vs 0 be a test of the main effect of self-relevance and contrast 3 
vs 0 the main effect of valence?

Thanks so much for your help!
Angela

From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Thursday, July 28, 2022 at 10:25 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FSFAST first level covariates

Yes, see 
https://secure-web.cisco.com/1vlnv3wLgT6AWyuomHXVnJCfD3bAT8O6KYN-6kv4DVE_Kbs9JwI6WLDqHM7UN7cfJ1TP0eQKgCtR-KXf01ehJnqsV2jW5XmAXQr0QnOlGk4--dT54zncT2aoK1njMKmN9ayqCJ_tFar2vbW-JGXSkTcg6gdUPh_mngiG7m

Re: [Freesurfer] FSFAST first level covariates

2022-07-28 Thread Angela Fang

Thanks Doug. This wiki page is extremely helpful. However, my question is about 
individual subject responses. I could see how you could include a summary 
(e.g., average) value of the parametric variable across subjects in your 
“weight” column but it’s not clear to me how you could integrate individual 
subject responses to each word in the parametric modulation paradigm file? I’m 
imagining something like the FSGD file where a value is given for each subject, 
but for first-level analysis.

We have a similar design as someone else who posted a similar question 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19957.html). We 
have an event-related experiment presenting trait adjectives in terms of 
whether they describe themselves (SELF condition) or someone else (OTHER 
condition). We are interested in testing a 2x2 ANOVA to examine an interaction 
between self-relevance x emotional valence. Assuming you can’t integrate 
individual subject responses to each word in the paradigm file, would we set it 
up as follows?

“Usual” paradigm file:
0  1  2.5  1.0  SELF
2.5  0  2.5  1.0  FIXATION
5.0  1  2.5  1.0  SELF
7.5  2  2.5  1.0  OTHER

Parametric modulation paradigm file:
0  1  2.5  1.0  SELFoffset
0  2  2.5  0.8  SELFslope
0  3  2.5  1.0  VALENCEoffset
0  4  2.5  2.0  VALENCEslope

(where 0.8 reflects the percentage of time the word was endorsed as 
self-relevant and 2.0 is the average valence rating given for that word)

And then create a contrast of 2 vs 4 to test the interaction? Would testing 
contrast 1 vs 0 be a test of the main effect of self-relevance and contrast 3 
vs 0 the main effect of valence?

Thanks so much for your help!
Angela

From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Thursday, July 28, 2022 at 10:25 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FSFAST first level covariates

Yes, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation

On 7/25/2022 6:56 PM, Angela Fang wrote:

External Email - Use Caution
Hi Freesurfer community,
I have run participants through an event-related fMRI task in which subjects 
rate whether trait adjectives are descriptive of themselves or not, and 
afterwards asked them to rate each trait word on emotional valence. Is it 
possible to include these individual level subjective ratings of emotional 
valence as covariates in the first level contrast in FSFAST? If so, how?
Thanks,
Angela

---
Angela Fang, Ph.D.
Assistant Professor
Department of Psychology
University of Washington
Lab website: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
www.uwconnectlab.com<http://secure-web.cisco.com/1EJiZPvng9zcCEb0OA91-g6prvoE6x8E2RuCN3eRqnJvVyWnOZIhlVqHUDwmp2WEJbpju-V9f5K_n7JLkG1IXMgF6ntSJr6Aa91zEsfied2HyjVTkJZCXxMUYkbVQwHF0Z6PuuEgJy0xZF4iWLQMnW1WHJWnTXmRF8Gn92JXWkNX3veeq3YElwnE8vUuXUBgXGmmFtbKV7dJKfvdquLkJq0ApBJuwyNBrhKCoiBCQx4GIbuAfZ0iAsH5aL5xid2f1julAWTaA4EyB2BlTn9hUZcuoJNQPs89B-fNI4SA4inRY7YD67lmo-MehxlSgl0xO/http%3A%2F%2Fwww.uwconnectlab.com>
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Re: [Freesurfer] FSFAST first level covariates

2022-07-28 Thread Douglas N. Greve

Yes, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation



On 7/25/2022 6:56 PM, Angela Fang wrote:


External Email - Use Caution

Hi Freesurfer community,

I have run participants through an event-related fMRI task in which 
subjects rate whether trait adjectives are descriptive of themselves 
or not, and afterwards asked them to rate each trait word on emotional 
valence. Is it possible to include these individual level subjective 
ratings of emotional valence as covariates in the first level contrast 
in FSFAST? If so, how?


Thanks,

Angela

---

Angela Fang, Ph.D.

Assistant Professor
Department of Psychology

University of Washington

Lab website: *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* www.uwconnectlab.com 



Pronouns: she, her, hers


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[Freesurfer] FSFAST first level covariates

2022-07-25 Thread Angela Fang

External Email - Use Caution

Hi Freesurfer community,
I have run participants through an event-related fMRI task in which subjects 
rate whether trait adjectives are descriptive of themselves or not, and 
afterwards asked them to rate each trait word on emotional valence. Is it 
possible to include these individual level subjective ratings of emotional 
valence as covariates in the first level contrast in FSFAST? If so, how?
Thanks,
Angela

---
Angela Fang, Ph.D.
Assistant Professor
Department of Psychology
University of Washington
Lab website: 
http://secure-web.cisco.com/1EJiZPvng9zcCEb0OA91-g6prvoE6x8E2RuCN3eRqnJvVyWnOZIhlVqHUDwmp2WEJbpju-V9f5K_n7JLkG1IXMgF6ntSJr6Aa91zEsfied2HyjVTkJZCXxMUYkbVQwHF0Z6PuuEgJy0xZF4iWLQMnW1WHJWnTXmRF8Gn92JXWkNX3veeq3YElwnE8vUuXUBgXGmmFtbKV7dJKfvdquLkJq0ApBJuwyNBrhKCoiBCQx4GIbuAfZ0iAsH5aL5xid2f1julAWTaA4EyB2BlTn9hUZcuoJNQPs89B-fNI4SA4inRY7YD67lmo-MehxlSgl0xO/http%3A%2F%2Fwww.uwconnectlab.com
Pronouns: she, her, hers

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Re: [Freesurfer] FSFAST (mkcontrast-sess) with Octave

2021-08-17 Thread Douglas N. Greve

Hi Lauri, I was able to run this successfully here on 7.2. What version 
of FS are you using? Can you send

/tmp/mkcontrast2.28236.m

(if still there)?
doug

On 8/17/2021 3:10 PM, Lauri Tuominen wrote:
>  External Email - Use Caution
>
> Dear Surfers,
> I am trying to run fsfast mkcontrast-sess with octave. I used the following 
> command:
>
> "mkcontrast-sess -analysis ../mkanalysis/ftap.sm05.lh  -contrast ftap -a 1 
> -octave"
>
> I get the output below. I wonder if you could help me out? Am I missing a 
> file or a path?
>
> Thank you so much
> Lauri Tuominen
>
>
> INFO: Found 2 Non-Null Conditions
> INFO: Found 1 Delays
> Condition Weights: 1. 0
> mkcontrast2 -config ../mkanalysis/ftap.sm05.lh/ftap.config -anadir 
> ../mkanalysis/ftap.sm05.lh -wcond 1. 0 -sumconds -o 
> ../mkanalysis/ftap.sm05.lh/ftap.mat -prestim 0 -wdelay 1 -octave
>mkcontrast2 7.1.1
> cmtxfile  ../mkanalysis/ftap.sm05.lh/ftap.mat
> nconds2,  wcond  1. 0
> ndelays   1, wdelay 1
> ndelays   1, wpsa
> sumconds  1
> sumdelays 0
> nircorr   0
> TER   0.05
> rdelta
> rtau
>cmtxfile  ../mkanalysis/ftap.sm05.lh/ftap.mat
>monly  0
>NCond   2
>WCond   1. 0
>NDelay  1
>WDelay  1
>TER 0.05
>sumconds   1
>sumdelays  0
>nircorr  0
>TPreStim  0
>RmPreStim  0
>rdelta 0 0
>rtau   0 0
>ndelays1
>CNorm  1
>setwdelay  0
>setwcond   0
> Matlab file is /tmp/mkcontrast2.28236.m
> --- octave output 
> error: 'mkcontrast2m' undefined near line 1, column 1
>
> Tue 17 Aug 2021 15:04:43 EDT
>
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[Freesurfer] FSFAST (mkcontrast-sess) with Octave

2021-08-17 Thread Lauri Tuominen

External Email - Use Caution

Dear Surfers,
I am trying to run fsfast mkcontrast-sess with octave. I used the following 
command: 

"mkcontrast-sess -analysis ../mkanalysis/ftap.sm05.lh  -contrast ftap -a 1 
-octave"

I get the output below. I wonder if you could help me out? Am I missing a file 
or a path? 

Thank you so much
Lauri Tuominen


INFO: Found 2 Non-Null Conditions
INFO: Found 1 Delays
Condition Weights: 1. 0
mkcontrast2 -config ../mkanalysis/ftap.sm05.lh/ftap.config -anadir 
../mkanalysis/ftap.sm05.lh -wcond 1. 0 -sumconds -o 
../mkanalysis/ftap.sm05.lh/ftap.mat -prestim 0 -wdelay 1 -octave
  mkcontrast2 7.1.1
cmtxfile  ../mkanalysis/ftap.sm05.lh/ftap.mat
nconds2,  wcond  1. 0
ndelays   1, wdelay 1
ndelays   1, wpsa   
sumconds  1
sumdelays 0
nircorr   0
TER   0.05
rdelta
rtau  
  cmtxfile  ../mkanalysis/ftap.sm05.lh/ftap.mat
  monly  0
  NCond   2
  WCond   1. 0
  NDelay  1
  WDelay  1
  TER 0.05
  sumconds   1
  sumdelays  0
  nircorr  0
  TPreStim  0
  RmPreStim  0
  rdelta 0 0
  rtau   0 0
  ndelays1
  CNorm  1
  setwdelay  0
  setwcond   0
Matlab file is /tmp/mkcontrast2.28236.m
--- octave output 
error: 'mkcontrast2m' undefined near line 1, column 1

Tue 17 Aug 2021 15:04:43 EDT

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Re: [Freesurfer] FsFast Question

2020-01-08 Thread Greve, Douglas N.,Ph.D.

Not directly as an external regressor. You would have to extract the 
info and create a waveform, one value for each TR in the external 
regressor file. You might also want to convolve it with a hemodynamic 
response function

On 1/8/20 11:15 AM, Swetara Joshi wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am new to fmri processing/FsFast and I had a question on creating 
> nuisance variables. Is it possible to set a block-design task fMRI 
> paradigm file as a nuisance variable, so that it can be inputted at a 
> .dat file for themkanalysis-sess command?
>
> Thank you!
>
> Best,
> Sweta
>
>
> *Sweta Joshi *
>
> *Research Assistant*
>
> Department of Neurology
>
> -
>
> GW Medical Faculty Associates
>
> George Washington University Hospital
>
> 2150 Pennsylvania Ave, NW, 9th Floor, Washington, DC 20037
>
> Office: 202.655.5888
>
> Email: sjo...@mfa.gwu.edu
>
>
>
> Confidentiality Note: This e-mail is intended only for the person or 
> entity to which it is addressed and may contain information that is 
> privileged, confidential or otherwise protected from disclosure. 
> Dissemination, distribution or copying of this e-mail or the 
> information herein by anyone other than the intended recipient, or an 
> employee or agent responsible for delivering the message to the 
> intended recipient, is prohibited. If you have received this e-mail in 
> error, please call (202) 741-3636 and destroy the original message and 
> all copies.
>
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[Freesurfer] FsFast Question

2020-01-08 Thread Swetara Joshi

External Email - Use Caution

Hello,

I am new to fmri processing/FsFast and I had a question on creating nuisance 
variables. Is it possible to set a block-design task fMRI paradigm file as a 
nuisance variable, so that it can be inputted at a .dat file for the  
mkanalysis-sess command?

Thank you!

Best,
Sweta



Sweta Joshi

Research Assistant

Department of Neurology

-

GW Medical Faculty Associates

George Washington University Hospital

2150 Pennsylvania Ave, NW, 9th Floor, Washington, DC 20037

Office: 202.655.5888

Email: sjo...@mfa.gwu.edu



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Re: [Freesurfer] FSFAST registration

2020-01-02 Thread Greve, Douglas N.,Ph.D.

On 12/30/2019 7:55 PM, Star Xi wrote:

External Email - Use Caution

Dear FS experts,

I’m processing the task-related fMRI using FS-FAST. I check the quality
assurance and modified some subjects’ registration file(named new one as
“register_manual.lta”). Then I do the first level analysis and group analysis.

My first question is:

should I apply the new registration file into the following first level
analysis and group analysis?

You should keep the registration filenames the same, then just re-run
selxavg3-sess. it will determine that the registration file changed and then
update everything afterwards.

I found a tutorial may be answer my question , but I’m not sure about it.

http://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0/FMRIGroupAnalysis#GroupROIfMRIAnalysis

Assemble the data using new registration file by the command:

mris_preproc --target fsaverage --hemi lh \

--iv fbirn-101/ces.nii fbirn-101/register.lta \

--iv fbirn-103/ces.nii fbirn-103/register.lta \

--iv fbirn-104/ces.nii fbirn-104/register.lta \

--projfrac 0.5 \

--out lh.ces.mgh

Then use “mri_surf2surf”, “mri_glmfit” to do the group analysis.

My second question is: does the following two procedures both feasible for fMRI
group analysis ?

1. Isxconcat-sess —> mri_glmfit —> mri-glnfit-sim
2. mris_preproc —> mri_surf2surf —> mri_glmfit —> mri-glmfit-sim

Both are feasible, but isxconcat-sess will be easier

Thank you!

Regards,

Star

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[Freesurfer] FSFAST registration

2019-12-30 Thread Star Xi



External Email - Use Caution




Dear FS experts,
I’m processing the task-related fMRI using FS-FAST. I check the quality assurance and modified some subjects’ registration file(named new one as “register_manual.lta”). Then I do the first level analysis and group analysis.
My first question is: 
should I apply the new registration file into the following first level analysis and group analysis?

I found a tutorial may be answer my question , but I’m not sure about it.
http://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0/FMRIGroupAnalysis#GroupROIfMRIAnalysis
Assemble the data using new registration file by the command:
    mris_preproc --target fsaverage --hemi lh \
       --iv  fbirn-101/ces.nii fbirn-101/register.lta \
       --iv  fbirn-103/ces.nii fbirn-103/register.lta \
       --iv  fbirn-104/ces.nii fbirn-104/register.lta \
       --projfrac 0.5 \
      --out lh.ces.mgh
Then use “mri_surf2surf”, “mri_glmfit” to do the group analysis.

My second question is: does the following two procedures both feasible for fMRI group analysis ?

Isxconcat-sess —>  mri_glmfit  —> mri-glnfit-sim
 mris_preproc —> mri_surf2surf —> mri_glmfit  —> mri-glmfit-sim
Thank you! 
Regards,
Star




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Re: [Freesurfer] fsfast no run directories

2019-12-02 Thread Greve, Douglas N.,Ph.D.

In the bold directory, it looks like you have one run directory called "1". 
Change this to "001"

On 11/29/2019 1:48 AM, Renew Andrade wrote:

External Email - Use Caution

Dear FreeSurfer experts:
I have some issues with "preproc-sess" because I cannot seem to get the setup 
of the directory structure or files to connect different things(the T1 subjects 
with functional bold or rest files). I have this output.


root@andraderenew:/home/andraderenew/Downloads/barrios/project# preproc-sess -s 
sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
--
preproc-sess logfile is log/preproc-sess.sess1.log
--
$Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $
root
setenv FREESURFER_HOME /usr/local/freesurfer
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
Linux andraderenew 5.0.0-36-generic #39~18.04.1-Ubuntu SMP Tue Nov 12 11:09:50 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
/home/andraderenew/Downloads/barrios/project
/usr/local/freesurfer/fsfast/bin/preproc-sess
-s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
vie nov 29 07:33:28 CET 2019
instem   f
mc   1 f fmcpr
stc  1fmcpr fmcpr.up
sm   0
mask 1   brain
sess1 Template -
mktemplate-sess -s sess1 -d /home/andraderenew/Downloads/barrios/project -fsd 
bold -update

Session: /home/andraderenew/Downloads/barrios/project/sess1 
vie nov 29 07:33:28 CET 2019
ERROR: no run directories found



my working directory is

root@andraderenew:/home/andraderenew/Downloads/barrios/project# pwd
/home/andraderenew/Downloads/barrios/project

and

root@andraderenew:/home/andraderenew/Downloads/barrios/project# ls
copy.sh  sess1   sess2  sess4  sess6  sess8  sessidlist
log  sess10  sess3  sess5  sess7  sess9  sessidlist~


root@andraderenew:/home/andraderenew/Downloads/barrios/project# cd sess1
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1# ls
bold  rest  subjectname


root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1#  cd bold
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# ls
1
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# cd 1
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold/1# ls
sub-0030689_task-resthypnotic_bold.nii.gz



And that is all. If I try with tutorial data there is no problem. One of the 
obvious differences is SUBJECTS_DIR is pointing not to subjects in freesurfer 
but to another folder where also is fsaverage. I don't know if this is required 
or I am missing another linking file.

There you can see the files I have searched with terminal.

Sincerely,
Andrade.



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[Freesurfer] fsfast no run directories

2019-11-28 Thread Renew Andrade

External Email - Use Caution

Dear FreeSurfer experts:I have some issues with "preproc-sess" because I cannot 
seem to get the setup of the directory structure or files to connect different 
things(the T1 subjects with functional bold or rest files). I have this output. 
 


root@andraderenew:/home/andraderenew/Downloads/barrios/project# preproc-sess -s 
sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
--
preproc-sess logfile is log/preproc-sess.sess1.log
--
$Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $
root
setenv FREESURFER_HOME /usr/local/freesurfer
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
Linux andraderenew 5.0.0-36-generic #39~18.04.1-Ubuntu SMP Tue Nov 12 11:09:50 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
/home/andraderenew/Downloads/barrios/project
/usr/local/freesurfer/fsfast/bin/preproc-sess
-s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
vie nov 29 07:33:28 CET 2019
instem   f 
mc   1 f fmcpr 
stc  1    fmcpr fmcpr.up
sm   0   
mask 1   brain
sess1 Template -
mktemplate-sess -s sess1 -d /home/andraderenew/Downloads/barrios/project -fsd 
bold -update
 
Session: /home/andraderenew/Downloads/barrios/project/sess1 
vie nov 29 07:33:28 CET 2019
ERROR: no run directories found



my working directory is 

root@andraderenew:/home/andraderenew/Downloads/barrios/project# pwd
/home/andraderenew/Downloads/barrios/project

and 

root@andraderenew:/home/andraderenew/Downloads/barrios/project# ls
copy.sh  sess1   sess2  sess4  sess6  sess8  sessidlist
log  sess10  sess3  sess5  sess7  sess9  sessidlist~


root@andraderenew:/home/andraderenew/Downloads/barrios/project# cd sess1
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1# ls
bold  rest  subjectname


root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1#  cd bold
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# ls
1
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# cd 1
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold/1# ls
sub-0030689_task-resthypnotic_bold.nii.gz



And that is all. If I try with tutorial data there is no problem. One of the 
obvious differences is SUBJECTS_DIR is pointing not to subjects in freesurfer 
but to another folder where also is fsaverage. I don't know if this is required 
or I am missing another linking file. 

There you can see the files I have searched with terminal. 

Sincerely, 
Andrade. 


sessidlist
Description: Binary data


subjectname
Description: Binary data
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Re: [Freesurfer] FSFAST group analysis problem: dimension mismatch between y and X

2019-04-08 Thread Greve, Douglas N.,Ph.D.

Can you check the modification time of 
~/audio/all/audio.lh/tones/ces.nii.gz ? Try deleting it and rerunning 
isxconcat-sess. The only other thing that I can think of is that some of 
the individual ces files have multiple frames. You can check that with 
mri_info --nframes */bold/audio.lh/tones/ces.nii.gz
If the problem persists, send the terminal output of isxconcat-sess

On 4/5/19 8:05 AM, Keri Woods wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer experts
>
> I'm having a problem running an FSFAST group analysis. When I try to 
> run the second level GLM, I get the following error:
>
> keri@buddha:~/audio_108_no_stc_tau1,5$ mri_glmfit --y 
> ~/audio/all/audio.lh/tones/ces.nii.gz   --wls 
> ~/audio/all/audio.lh/tones/cesvar.nii.gz   --fsgd 2groups.fsgd  --C 
> groupdiff.mtx   --surface fsaverage lh   --glmdir 
> all_tones_left_glm.wls   --nii.gz
> gdfRead(): reading 2groups.fsgd
> INFO: gd2mtx_method is dods
> Reading source surface 
> /home/keri/recon_all/subjects/fsaverage/surf/lh.white
> Number of vertices 163842
> Number of faces    327680
> Total area 65416.984375
> AvgVtxArea   0.399269
> AvgVtxDist   0.721953
> StdVtxDist   0.195470
>
> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
> cwd /home/keri/audio_108_no_stc_tau1,5
> cmdline mri_glmfit.bin --y 
> /home/keri/audio/all/audio.lh/tones/ces.nii.gz --wls 
> /home/keri/audio/all/audio.lh/tones/cesvar.nii.gz --fsgd 2groups.fsgd 
> --C groupdiff.mtx --surface fsaverage lh --glmdir 
> all_tones_left_glm.wls --nii.gz
> sysname  Linux
> hostname buddha
> machine  x86_64
> user keri
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y    /home/keri/audio/all/audio.lh/tones/ces.nii.gz
> logyflag 0
> usedti  0
> FSGD 2groups.fsgd
> labelmask /home/keri/recon_all/subjects/fsaverage/label/lh.cortex.label
> maskinv 0
> glmdir all_tones_left_glm.wls
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> wFile /home/keri/audio/all/audio.lh/tones/cesvar.nii.gz
> weightinv  1
> weightsqrt 1
> Creating output directory all_tones_left_glm.wls
> Loading y from /home/keri/audio/all/audio.lh/tones/ces.nii.gz
>    ... done reading.
> INFO: gd2mtx_method is dods
> Saving design matrix to all_tones_left_glm.wls/Xg.dat
> Computing normalized matrix
> Normalized matrix condition is 1
> Matrix condition is 1.34783
> Found 149955 points in label.
> Pruning voxels by thr: 1.175494e-38
> Found 66097 voxels in mask
> Saving mask to all_tones_left_glm.wls/mask.nii.gz
> Reshaping mriglm->mask...
> search space = 31233.070725
> ERROR: dimension mismatch between y and X.
>   y has 116 inputs, X has 108 rows.
>
>
> 108 is the number of subjects that I have. I can see that the y file 
> with 116 inputs is /home/keri/audio/all/audio.lh/tones/ces.nii.gz , 
> and checking the dimension of it, it confirms that it is a 4D matrix 
> with the 4th dimension of 116. It seems as if this file is created 
> during isxoconcat-sess, and I have checked and the session ID file 
> being used here has only 108 entries. It appears that 108 subjects are 
> being used in this step, as part of the output is:
>
> ninputs = 108
> Checking inputs
> nframestot = 108
> Allocing output
> Done allocing
> nframes = 108
>
>
> I think that a source of the error could be the fact that at one time 
> I did have 116 subjects. I've created a new folder, copying in the 
> unpacked files for each subject, and repeating from the preprocessing 
> step, but this doesn't make any difference. Is there are chance that 
> there's a file outside the functional directory that has stored this 116?
>
> Any help is greatly appreciated.
>
> Best wishes,
> Keri
>
>
>
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[Freesurfer] FSFAST group analysis problem: dimension mismatch between y and X

2019-04-05 Thread Keri Woods

External Email - Use Caution

Hi Freesurfer experts

I'm having a problem running an FSFAST group analysis. When I try to run
the second level GLM, I get the following error:

keri@buddha:~/audio_108_no_stc_tau1,5$ mri_glmfit --y
~/audio/all/audio.lh/tones/ces.nii.gz   --wls
~/audio/all/audio.lh/tones/cesvar.nii.gz   --fsgd 2groups.fsgd  --C
groupdiff.mtx   --surface fsaverage lh   --glmdir all_tones_left_glm.wls
--nii.gz
gdfRead(): reading 2groups.fsgd
INFO: gd2mtx_method is dods
Reading source surface /home/keri/recon_all/subjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.984375
AvgVtxArea   0.399269
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /home/keri/audio_108_no_stc_tau1,5
cmdline mri_glmfit.bin --y /home/keri/audio/all/audio.lh/tones/ces.nii.gz
--wls /home/keri/audio/all/audio.lh/tones/cesvar.nii.gz --fsgd 2groups.fsgd
--C groupdiff.mtx --surface fsaverage lh --glmdir all_tones_left_glm.wls
--nii.gz
sysname  Linux
hostname buddha
machine  x86_64
user keri
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/home/keri/audio/all/audio.lh/tones/ces.nii.gz
logyflag 0
usedti  0
FSGD 2groups.fsgd
labelmask  /home/keri/recon_all/subjects/fsaverage/label/lh.cortex.label
maskinv 0
glmdir all_tones_left_glm.wls
IllCondOK 0
ReScaleX 1
DoFFx 0
wFile /home/keri/audio/all/audio.lh/tones/cesvar.nii.gz
weightinv  1
weightsqrt 1
Creating output directory all_tones_left_glm.wls
Loading y from /home/keri/audio/all/audio.lh/tones/ces.nii.gz
   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to all_tones_left_glm.wls/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1
Matrix condition is 1.34783
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 66097 voxels in mask
Saving mask to all_tones_left_glm.wls/mask.nii.gz
Reshaping mriglm->mask...
search space = 31233.070725
ERROR: dimension mismatch between y and X.
  y has 116 inputs, X has 108 rows.


108 is the number of subjects that I have. I can see that the y file with
116 inputs is /home/keri/audio/all/audio.lh/tones/ces.nii.gz , and checking
the dimension of it, it confirms that it is a 4D matrix with the 4th
dimension of 116. It seems as if this file is created during
isxoconcat-sess, and I have checked and the session ID file being used here
has only 108 entries. It appears that 108 subjects are being used in this
step, as part of the output is:

ninputs = 108
Checking inputs
nframestot = 108
Allocing output
Done allocing
nframes = 108


I think that a source of the error could be the fact that at one time I did
have 116 subjects. I've created a new folder, copying in the unpacked files
for each subject, and repeating from the preprocessing step, but this
doesn't make any difference. Is there are chance that there's a file
outside the functional directory that has stored this 116?

Any help is greatly appreciated.

Best wishes,
Keri
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Re: [Freesurfer] FSFAST poor registration

2019-01-25 Thread Keri Woods

External Email - Use Caution

Good thing it's not the software :) Also makes it easier for me to fix. In
my script there was one tiny mistake - the anatomical image for one subject
was repeated each time instead of using the files for different subjects. I
ran recon-all 100+ times on the same subject!! Checking the registration
was definitely worthwhile. Thanks again for the help, it made me look at
the problem in a different.

On Fri, Jan 25, 2019 at 6:34 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Yes, that file is the only thing linking the functional to the anatomical.
> It's too bad you messed up the files, but I'm relieved it was not my
> software:).
>
> On 1/25/19 5:09 AM, Keri Woods wrote:
>
> External Email - Use Caution
> Hi Douglas
>
> Thanks very much for getting back to me. I created new separate
> directories and re-processed one of the problem subjects individually, and
> the registration worked well. So the problem is that the anatomical and
> functional images come from different subjects. But I've checked and the
> subjectname files are correct. That's the only thing linking the anatomical
> and functional images? Thanks very much, you've helped me a lot. Now I just
> have to go and see where I mixed up the files!
>
> Thanks again,
> Keri
>
> On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Can you tar up the anatomical and functional analyses and send them to
>> me through our filedrop?
>>
>> https://gate.nmr.mgh.harvard.edu/filedrop2/
>>
>> when it asks for an email of the recipient, use gr...@nmr.mgh.harvard.edu
>>
>>
>> On 1/23/19 5:57 AM, Keri Woods wrote:
>> >
>> > External Email - Use Caution
>> >
>> > I meant some are nearly perfect.
>> >
>> > On Wed, Jan 23, 2019 at 11:49 AM Keri Woods > > > wrote:
>> >
>> > Hi Douglas
>> >
>> > Thanks for the response.
>> >
>> > No, some of the registrations are fine. Some are close, but not
>> > perfect, while others are very bad.
>> >
>> > I've checked the subjectname file for some subjects with poor
>> > registration (eg 20_101), and they are correct.
>> >
>> > Thanks,
>> > Keri
>> >
>> > On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>> >
>> > Are you saying that all of them have bad registrations? Some
>> > of them
>> > (eg, 20_1, 20_10) look like they should be good. Others (eg,
>> > 20_101)
>> > look like they could be bad. For the bad ones, are you totally
>> > sure that
>> > the subjetname file has the correct name of the subject?
>> >
>> > On 1/21/19 3:19 AM, Keri Woods wrote:
>> > >
>> > > External Email - Use Caution
>> > >
>> > > Hi Douglas
>> > >
>> > > Thank you for your reply.
>> > >
>> > > I'm using
>> > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
>> > >
>> > > I am using whole brain data. The functional and structural
>> > images were
>> > > acquired in different sessions on the same day, I don't know
>> > if that
>> > > complicated things? Each subject has 2 runs of the same task.
>> > >
>> > > This is what I get after running the command in the format of
>> > > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold
>> > -per-run -bbr-sum
>> > >
>> > > 20_1   013 0.5155
>> > > 20_1   014 0.5090
>> > > 20_10  013 0.5247
>> > > 20_10  014 0.5229
>> > > 20_100 038 0.8420
>> > > 20_100 040 0.8443
>> > > 20_101 008 0.9052
>> > > 20_101 010 0.9289
>> > > 20_102 058 0.6924
>> > > 20_102 059 0.6902
>> > > 20_103 045 0.9778
>> > > 20_103 046 0.9931
>> > > 20_104 010 0.9324
>> > > 20_104 012 0.9413
>> > > 20_105 013 0.8754
>> > > 20_105 014 0.8937
>> > > 20_106 047 0.4433
>> > > 20_106 048 0.4377
>> > > 20_107 008 0.9178
>> > > 20_107 010 0.9238
>> > > 20_11  013 0.7631
>> > > 20_11  014 0.7615
>> > > 20_110 048 0.7687
>> > > 20_110 049 0.7549
>> > > 20_112 013 0.8821
>> > > 20_112 014 0.9161
>> > > 20_113 052 0.7689
>> > > 20_113 053 0.7757
>> > > 20_116 046 1.0072
>> > > 20_116 047 1.0256
>> > > 20_117 008 0.7742
>> > > 20_117 010 0.7826
>> > > 20_119 013 0.7929
>> > > 20_119 014 0.7854
>> > > 20_120 048 0.5090
>> > > 20_120 049 0.4973
>> > > 20_126 047 0.8285
>> > > 20_126 048 0.8281
>> > > 20_128 046 0.9580
>> >

Re: [Freesurfer] FSFAST poor registration

2019-01-25 Thread Greve, Douglas N.,Ph.D.

Yes, that file is the only thing linking the functional to the anatomical. It's 
too bad you messed up the files, but I'm relieved it was not my software:).

On 1/25/19 5:09 AM, Keri Woods wrote:

External Email - Use Caution

Hi Douglas

Thanks very much for getting back to me. I created new separate directories and 
re-processed one of the problem subjects individually, and the registration 
worked well. So the problem is that the anatomical and functional images come 
from different subjects. But I've checked and the subjectname files are 
correct. That's the only thing linking the anatomical and functional images? 
Thanks very much, you've helped me a lot. Now I just have to go and see where I 
mixed up the files!

Thanks again,
Keri

On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Can you tar up the anatomical and functional analyses and send them to
me through our filedrop?

https://gate.nmr.mgh.harvard.edu/filedrop2/

when it asks for an email of the recipient, use 
gr...@nmr.mgh.harvard.edu


On 1/23/19 5:57 AM, Keri Woods wrote:
>
> External Email - Use Caution
>
> I meant some are nearly perfect.
>
> On Wed, Jan 23, 2019 at 11:49 AM Keri Woods 
> mailto:keri.wo...@gmail.com>
> >> wrote:
>
> Hi Douglas
>
> Thanks for the response.
>
> No, some of the registrations are fine. Some are close, but not
> perfect, while others are very bad.
>
> I've checked the subjectname file for some subjects with poor
> registration (eg 20_101), and they are correct.
>
> Thanks,
> Keri
>
> On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu> 
> >> wrote:
>
> Are you saying that all of them have bad registrations? Some
> of them
> (eg, 20_1, 20_10) look like they should be good. Others (eg,
> 20_101)
> look like they could be bad. For the bad ones, are you totally
> sure that
> the subjetname file has the correct name of the subject?
>
> On 1/21/19 3:19 AM, Keri Woods wrote:
> >
> > External Email - Use Caution
> >
> > Hi Douglas
> >
> > Thank you for your reply.
> >
> > I'm using
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
> >
> > I am using whole brain data. The functional and structural
> images were
> > acquired in different sessions on the same day, I don't know
> if that
> > complicated things? Each subject has 2 runs of the same task.
> >
> > This is what I get after running the command in the format of
> > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold
> -per-run -bbr-sum
> >
> > 20_1   013 0.5155
> > 20_1   014 0.5090
> > 20_10  013 0.5247
> > 20_10  014 0.5229
> > 20_100 038 0.8420
> > 20_100 040 0.8443
> > 20_101 008 0.9052
> > 20_101 010 0.9289
> > 20_102 058 0.6924
> > 20_102 059 0.6902
> > 20_103 045 0.9778
> > 20_103 046 0.9931
> > 20_104 010 0.9324
> > 20_104 012 0.9413
> > 20_105 013 0.8754
> > 20_105 014 0.8937
> > 20_106 047 0.4433
> > 20_106 048 0.4377
> > 20_107 008 0.9178
> > 20_107 010 0.9238
> > 20_11  013 0.7631
> > 20_11  014 0.7615
> > 20_110 048 0.7687
> > 20_110 049 0.7549
> > 20_112 013 0.8821
> > 20_112 014 0.9161
> > 20_113 052 0.7689
> > 20_113 053 0.7757
> > 20_116 046 1.0072
> > 20_116 047 1.0256
> > 20_117 008 0.7742
> > 20_117 010 0.7826
> > 20_119 013 0.7929
> > 20_119 014 0.7854
> > 20_120 048 0.5090
> > 20_120 049 0.4973
> > 20_126 047 0.8285
> > 20_126 048 0.8281
> > 20_128 046 0.9580
> > 20_128 047 0.9314
> > 20_130 047 0.9439
> > 20_130 048 0.9425
> > 20_132 047 0.8550
> > 20_132 048 0.8558
> > 20_134_1   013 0.5716
> > 20_134_1   015 0.5744
> > 20_135 011 0.8357
> > 20_135 012 0.8401
> > 20_136 044 0.9995
> > 20_136 045 0.9604
> > 20_137 047 0.7922
> > 20_137 048 0.7990
> > 20_142 047 0.5282
> > 20_142 048 0.5278
> > 20_144 013 0.8755
> > 20_144 014 0.8838
> > 20_146 047 0.7997
> > 20_146 048 0.7895
> > 20_149 049 0.9251
> > 20_149 050

Re: [Freesurfer] FSFAST poor registration

2019-01-25 Thread Keri Woods

External Email - Use Caution

Hi Douglas

Thanks very much for getting back to me. I created new separate directories
and re-processed one of the problem subjects individually, and the
registration worked well. So the problem is that the anatomical and
functional images come from different subjects. But I've checked and the
subjectname files are correct. That's the only thing linking the anatomical
and functional images? Thanks very much, you've helped me a lot. Now I just
have to go and see where I mixed up the files!

Thanks again,
Keri

On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Can you tar up the anatomical and functional analyses and send them to
> me through our filedrop?
>
> https://gate.nmr.mgh.harvard.edu/filedrop2/
>
> when it asks for an email of the recipient, use gr...@nmr.mgh.harvard.edu
>
>
> On 1/23/19 5:57 AM, Keri Woods wrote:
> >
> > External Email - Use Caution
> >
> > I meant some are nearly perfect.
> >
> > On Wed, Jan 23, 2019 at 11:49 AM Keri Woods  > > wrote:
> >
> > Hi Douglas
> >
> > Thanks for the response.
> >
> > No, some of the registrations are fine. Some are close, but not
> > perfect, while others are very bad.
> >
> > I've checked the subjectname file for some subjects with poor
> > registration (eg 20_101), and they are correct.
> >
> > Thanks,
> > Keri
> >
> > On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Are you saying that all of them have bad registrations? Some
> > of them
> > (eg, 20_1, 20_10) look like they should be good. Others (eg,
> > 20_101)
> > look like they could be bad. For the bad ones, are you totally
> > sure that
> > the subjetname file has the correct name of the subject?
> >
> > On 1/21/19 3:19 AM, Keri Woods wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hi Douglas
> > >
> > > Thank you for your reply.
> > >
> > > I'm using
> > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
> > >
> > > I am using whole brain data. The functional and structural
> > images were
> > > acquired in different sessions on the same day, I don't know
> > if that
> > > complicated things? Each subject has 2 runs of the same task.
> > >
> > > This is what I get after running the command in the format of
> > > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold
> > -per-run -bbr-sum
> > >
> > > 20_1   013 0.5155
> > > 20_1   014 0.5090
> > > 20_10  013 0.5247
> > > 20_10  014 0.5229
> > > 20_100 038 0.8420
> > > 20_100 040 0.8443
> > > 20_101 008 0.9052
> > > 20_101 010 0.9289
> > > 20_102 058 0.6924
> > > 20_102 059 0.6902
> > > 20_103 045 0.9778
> > > 20_103 046 0.9931
> > > 20_104 010 0.9324
> > > 20_104 012 0.9413
> > > 20_105 013 0.8754
> > > 20_105 014 0.8937
> > > 20_106 047 0.4433
> > > 20_106 048 0.4377
> > > 20_107 008 0.9178
> > > 20_107 010 0.9238
> > > 20_11  013 0.7631
> > > 20_11  014 0.7615
> > > 20_110 048 0.7687
> > > 20_110 049 0.7549
> > > 20_112 013 0.8821
> > > 20_112 014 0.9161
> > > 20_113 052 0.7689
> > > 20_113 053 0.7757
> > > 20_116 046 1.0072
> > > 20_116 047 1.0256
> > > 20_117 008 0.7742
> > > 20_117 010 0.7826
> > > 20_119 013 0.7929
> > > 20_119 014 0.7854
> > > 20_120 048 0.5090
> > > 20_120 049 0.4973
> > > 20_126 047 0.8285
> > > 20_126 048 0.8281
> > > 20_128 046 0.9580
> > > 20_128 047 0.9314
> > > 20_130 047 0.9439
> > > 20_130 048 0.9425
> > > 20_132 047 0.8550
> > > 20_132 048 0.8558
> > > 20_134_1   013 0.5716
> > > 20_134_1   015 0.5744
> > > 20_135 011 0.8357
> > > 20_135 012 0.8401
> > > 20_136 044 0.9995
> > > 20_136 045 0.9604
> > > 20_137 047 0.7922
> > > 20_137 048 0.7990
> > > 20_142 047 0.5282
> > > 20_142 048 0.5278
> > > 20_144 013 0.8755
> > > 20_144 014 0.8838
> > > 20_146 047 0.7997
> > > 20_146 048 0.7895
> > > 20_149 049 0.9251
> > > 20_149 050 0.9408
> > > 20_151 048 0.5905
> > > 20_151 049 0.5519
> > > 20_152 048 0.9024
> >

Re: [Freesurfer] FSFAST poor registration

2019-01-24 Thread Greve, Douglas N.,Ph.D.

Can you tar up the anatomical and functional analyses and send them to 
me through our filedrop?

https://gate.nmr.mgh.harvard.edu/filedrop2/

when it asks for an email of the recipient, use gr...@nmr.mgh.harvard.edu


On 1/23/19 5:57 AM, Keri Woods wrote:
>
> External Email - Use Caution
>
> I meant some are nearly perfect.
>
> On Wed, Jan 23, 2019 at 11:49 AM Keri Woods  > wrote:
>
> Hi Douglas
>
> Thanks for the response.
>
> No, some of the registrations are fine. Some are close, but not
> perfect, while others are very bad.
>
> I've checked the subjectname file for some subjects with poor
> registration (eg 20_101), and they are correct.
>
> Thanks,
> Keri
>
> On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Are you saying that all of them have bad registrations? Some
> of them
> (eg, 20_1, 20_10) look like they should be good. Others (eg,
> 20_101)
> look like they could be bad. For the bad ones, are you totally
> sure that
> the subjetname file has the correct name of the subject?
>
> On 1/21/19 3:19 AM, Keri Woods wrote:
> >
> > External Email - Use Caution
> >
> > Hi Douglas
> >
> > Thank you for your reply.
> >
> > I'm using
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
> >
> > I am using whole brain data. The functional and structural
> images were
> > acquired in different sessions on the same day, I don't know
> if that
> > complicated things? Each subject has 2 runs of the same task.
> >
> > This is what I get after running the command in the format of
> > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold
> -per-run -bbr-sum
> >
> > 20_1   013 0.5155
> > 20_1   014 0.5090
> > 20_10  013 0.5247
> > 20_10  014 0.5229
> > 20_100 038 0.8420
> > 20_100 040 0.8443
> > 20_101 008 0.9052
> > 20_101 010 0.9289
> > 20_102 058 0.6924
> > 20_102 059 0.6902
> > 20_103 045 0.9778
> > 20_103 046 0.9931
> > 20_104 010 0.9324
> > 20_104 012 0.9413
> > 20_105 013 0.8754
> > 20_105 014 0.8937
> > 20_106 047 0.4433
> > 20_106 048 0.4377
> > 20_107 008 0.9178
> > 20_107 010 0.9238
> > 20_11  013 0.7631
> > 20_11  014 0.7615
> > 20_110 048 0.7687
> > 20_110 049 0.7549
> > 20_112 013 0.8821
> > 20_112 014 0.9161
> > 20_113 052 0.7689
> > 20_113 053 0.7757
> > 20_116 046 1.0072
> > 20_116 047 1.0256
> > 20_117 008 0.7742
> > 20_117 010 0.7826
> > 20_119 013 0.7929
> > 20_119 014 0.7854
> > 20_120 048 0.5090
> > 20_120 049 0.4973
> > 20_126 047 0.8285
> > 20_126 048 0.8281
> > 20_128 046 0.9580
> > 20_128 047 0.9314
> > 20_130 047 0.9439
> > 20_130 048 0.9425
> > 20_132 047 0.8550
> > 20_132 048 0.8558
> > 20_134_1   013 0.5716
> > 20_134_1   015 0.5744
> > 20_135 011 0.8357
> > 20_135 012 0.8401
> > 20_136 044 0.9995
> > 20_136 045 0.9604
> > 20_137 047 0.7922
> > 20_137 048 0.7990
> > 20_142 047 0.5282
> > 20_142 048 0.5278
> > 20_144 013 0.8755
> > 20_144 014 0.8838
> > 20_146 047 0.7997
> > 20_146 048 0.7895
> > 20_149 049 0.9251
> > 20_149 050 0.9408
> > 20_151 048 0.5905
> > 20_151 049 0.5519
> > 20_152 048 0.9024
> > 20_152 049 0.9021
> > 20_155 048 0.5285
> > 20_155 049 0.5324
> > 20_156 048 0.8883
> > 20_156 049 0.9267
> > 20_158 048 0.5404
> > 20_158 049 0.5297
> > 20_159 048 0.8021
> > 20_160 013 0.5002
> > 20_160 014 0.4942
> > 20_162 047 0.5401
> > 20_162 048 0.5401
> > 20_164 047 0.8944
> > 20_164 048 0.8940
> > 20_165 047 0.9163
> > 20_165 048 0.9077
> > 20_166 045 0.8787
> > 20_166 046 0.8848
> > 20_167 050 0.8428
> > 20_167 051 0.8442
> > 20_169 049 0.9407
> > 20_169 050 0.9462
> > 20_170 047 0.8921
> > 20_170 048 0.9113
> > 20_171 013 0.9060
> > 20_171 014 0.9060
> > 20_173

Re: [Freesurfer] FSFAST poor registration

2019-01-23 Thread Keri Woods

External Email - Use Caution

I meant some are nearly perfect.

On Wed, Jan 23, 2019 at 11:49 AM Keri Woods  wrote:

> Hi Douglas
>
> Thanks for the response.
>
> No, some of the registrations are fine. Some are close, but not perfect,
> while others are very bad.
>
> I've checked the subjectname file for some subjects with poor registration
> (eg 20_101), and they are correct.
>
> Thanks,
> Keri
>
> On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Are you saying that all of them have bad registrations? Some of them
>> (eg, 20_1, 20_10) look like they should be good. Others (eg, 20_101)
>> look like they could be bad. For the bad ones, are you totally sure that
>> the subjetname file has the correct name of the subject?
>>
>> On 1/21/19 3:19 AM, Keri Woods wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hi Douglas
>> >
>> > Thank you for your reply.
>> >
>> > I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
>> >
>> > I am using whole brain data. The functional and structural images were
>> > acquired in different sessions on the same day, I don't know if that
>> > complicated things? Each subject has 2 runs of the same task.
>> >
>> > This is what I get after running the command in the format of
>> > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run
>> -bbr-sum
>> >
>> > 20_1   013 0.5155
>> > 20_1   014 0.5090
>> > 20_10  013 0.5247
>> > 20_10  014 0.5229
>> > 20_100 038 0.8420
>> > 20_100 040 0.8443
>> > 20_101 008 0.9052
>> > 20_101 010 0.9289
>> > 20_102 058 0.6924
>> > 20_102 059 0.6902
>> > 20_103 045 0.9778
>> > 20_103 046 0.9931
>> > 20_104 010 0.9324
>> > 20_104 012 0.9413
>> > 20_105 013 0.8754
>> > 20_105 014 0.8937
>> > 20_106 047 0.4433
>> > 20_106 048 0.4377
>> > 20_107 008 0.9178
>> > 20_107 010 0.9238
>> > 20_11  013 0.7631
>> > 20_11  014 0.7615
>> > 20_110 048 0.7687
>> > 20_110 049 0.7549
>> > 20_112 013 0.8821
>> > 20_112 014 0.9161
>> > 20_113 052 0.7689
>> > 20_113 053 0.7757
>> > 20_116 046 1.0072
>> > 20_116 047 1.0256
>> > 20_117 008 0.7742
>> > 20_117 010 0.7826
>> > 20_119 013 0.7929
>> > 20_119 014 0.7854
>> > 20_120 048 0.5090
>> > 20_120 049 0.4973
>> > 20_126 047 0.8285
>> > 20_126 048 0.8281
>> > 20_128 046 0.9580
>> > 20_128 047 0.9314
>> > 20_130 047 0.9439
>> > 20_130 048 0.9425
>> > 20_132 047 0.8550
>> > 20_132 048 0.8558
>> > 20_134_1   013 0.5716
>> > 20_134_1   015 0.5744
>> > 20_135 011 0.8357
>> > 20_135 012 0.8401
>> > 20_136 044 0.9995
>> > 20_136 045 0.9604
>> > 20_137 047 0.7922
>> > 20_137 048 0.7990
>> > 20_142 047 0.5282
>> > 20_142 048 0.5278
>> > 20_144 013 0.8755
>> > 20_144 014 0.8838
>> > 20_146 047 0.7997
>> > 20_146 048 0.7895
>> > 20_149 049 0.9251
>> > 20_149 050 0.9408
>> > 20_151 048 0.5905
>> > 20_151 049 0.5519
>> > 20_152 048 0.9024
>> > 20_152 049 0.9021
>> > 20_155 048 0.5285
>> > 20_155 049 0.5324
>> > 20_156 048 0.8883
>> > 20_156 049 0.9267
>> > 20_158 048 0.5404
>> > 20_158 049 0.5297
>> > 20_159 048 0.8021
>> > 20_160 013 0.5002
>> > 20_160 014 0.4942
>> > 20_162 047 0.5401
>> > 20_162 048 0.5401
>> > 20_164 047 0.8944
>> > 20_164 048 0.8940
>> > 20_165 047 0.9163
>> > 20_165 048 0.9077
>> > 20_166 045 0.8787
>> > 20_166 046 0.8848
>> > 20_167 050 0.8428
>> > 20_167 051 0.8442
>> > 20_169 049 0.9407
>> > 20_169 050 0.9462
>> > 20_170 047 0.8921
>> > 20_170 048 0.9113
>> > 20_171 013 0.9060
>> > 20_171 014 0.9060
>> > 20_173 048 0.9193
>> > 20_173 049 0.9141
>> > 20_177 048 0.8695
>> > 20_177 049 0.8600
>> > 20_178 048 1.0327
>> > 20_178 049 0.8979
>> > 20_180 045 0.7999
>> > 20_180 046 0.8002
>> > 20_182 047 0.9135
>> > 20_182 048 0.9130
>> > 20_184 048 0.9842
>> > 20_184 049 0.9960
>> > 20_185 046 0.9640
>> > 20_185 047 0.9514
>> > 20_187 048 0.8134
>> > 20_187 049 0.8082
>> > 20_189 047 1.0063
>> > 20_189 048 0.9701
>> > 20_19  013 0.8485
>> > 20_19  014 0.8534
>> > 20_190 047 0.9279
>> > 20_190 048 0.9169
>> > 20_191 046 0.9586
>> > 20_191 047 0.9751
>> > 20_192 049 0.8544
>> > 20_193 013 0.9084
>> > 20_193 014 0.9110
>> > 20_194 047 0.9220
>> > 20_194 048 0.9166
>> > 20_195 048 0.9552
>> > 20_195 049 0.9508
>> > 20_196 047 0.9098
>> > 20_196 048 0.9011
>> > 20_199 048 0.8569
>> > 20_199 049 0.8567
>> > 20_20  013 0.8750
>> > 20_20  014 0.8749
>> > 20_201 048 0.8864
>> > 20_201 049 1.0040
>> > 20_202 048 0.8542
>> > 20_202 049 0.8516
>> > 20_203 048 1.0267
>> > 20_203 049 1.0060
>> > 20_204 048 0.8513
>> >

Re: [Freesurfer] FSFAST poor registration

2019-01-23 Thread Keri Woods

External Email - Use Caution

Hi Douglas

Thanks for the response.

No, some of the registrations are fine. Some are close, but not perfect,
while others are very bad.

I've checked the subjectname file for some subjects with poor registration
(eg 20_101), and they are correct.

Thanks,
Keri

On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Are you saying that all of them have bad registrations? Some of them
> (eg, 20_1, 20_10) look like they should be good. Others (eg, 20_101)
> look like they could be bad. For the bad ones, are you totally sure that
> the subjetname file has the correct name of the subject?
>
> On 1/21/19 3:19 AM, Keri Woods wrote:
> >
> > External Email - Use Caution
> >
> > Hi Douglas
> >
> > Thank you for your reply.
> >
> > I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
> >
> > I am using whole brain data. The functional and structural images were
> > acquired in different sessions on the same day, I don't know if that
> > complicated things? Each subject has 2 runs of the same task.
> >
> > This is what I get after running the command in the format of
> > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum
> >
> > 20_1   013 0.5155
> > 20_1   014 0.5090
> > 20_10  013 0.5247
> > 20_10  014 0.5229
> > 20_100 038 0.8420
> > 20_100 040 0.8443
> > 20_101 008 0.9052
> > 20_101 010 0.9289
> > 20_102 058 0.6924
> > 20_102 059 0.6902
> > 20_103 045 0.9778
> > 20_103 046 0.9931
> > 20_104 010 0.9324
> > 20_104 012 0.9413
> > 20_105 013 0.8754
> > 20_105 014 0.8937
> > 20_106 047 0.4433
> > 20_106 048 0.4377
> > 20_107 008 0.9178
> > 20_107 010 0.9238
> > 20_11  013 0.7631
> > 20_11  014 0.7615
> > 20_110 048 0.7687
> > 20_110 049 0.7549
> > 20_112 013 0.8821
> > 20_112 014 0.9161
> > 20_113 052 0.7689
> > 20_113 053 0.7757
> > 20_116 046 1.0072
> > 20_116 047 1.0256
> > 20_117 008 0.7742
> > 20_117 010 0.7826
> > 20_119 013 0.7929
> > 20_119 014 0.7854
> > 20_120 048 0.5090
> > 20_120 049 0.4973
> > 20_126 047 0.8285
> > 20_126 048 0.8281
> > 20_128 046 0.9580
> > 20_128 047 0.9314
> > 20_130 047 0.9439
> > 20_130 048 0.9425
> > 20_132 047 0.8550
> > 20_132 048 0.8558
> > 20_134_1   013 0.5716
> > 20_134_1   015 0.5744
> > 20_135 011 0.8357
> > 20_135 012 0.8401
> > 20_136 044 0.9995
> > 20_136 045 0.9604
> > 20_137 047 0.7922
> > 20_137 048 0.7990
> > 20_142 047 0.5282
> > 20_142 048 0.5278
> > 20_144 013 0.8755
> > 20_144 014 0.8838
> > 20_146 047 0.7997
> > 20_146 048 0.7895
> > 20_149 049 0.9251
> > 20_149 050 0.9408
> > 20_151 048 0.5905
> > 20_151 049 0.5519
> > 20_152 048 0.9024
> > 20_152 049 0.9021
> > 20_155 048 0.5285
> > 20_155 049 0.5324
> > 20_156 048 0.8883
> > 20_156 049 0.9267
> > 20_158 048 0.5404
> > 20_158 049 0.5297
> > 20_159 048 0.8021
> > 20_160 013 0.5002
> > 20_160 014 0.4942
> > 20_162 047 0.5401
> > 20_162 048 0.5401
> > 20_164 047 0.8944
> > 20_164 048 0.8940
> > 20_165 047 0.9163
> > 20_165 048 0.9077
> > 20_166 045 0.8787
> > 20_166 046 0.8848
> > 20_167 050 0.8428
> > 20_167 051 0.8442
> > 20_169 049 0.9407
> > 20_169 050 0.9462
> > 20_170 047 0.8921
> > 20_170 048 0.9113
> > 20_171 013 0.9060
> > 20_171 014 0.9060
> > 20_173 048 0.9193
> > 20_173 049 0.9141
> > 20_177 048 0.8695
> > 20_177 049 0.8600
> > 20_178 048 1.0327
> > 20_178 049 0.8979
> > 20_180 045 0.7999
> > 20_180 046 0.8002
> > 20_182 047 0.9135
> > 20_182 048 0.9130
> > 20_184 048 0.9842
> > 20_184 049 0.9960
> > 20_185 046 0.9640
> > 20_185 047 0.9514
> > 20_187 048 0.8134
> > 20_187 049 0.8082
> > 20_189 047 1.0063
> > 20_189 048 0.9701
> > 20_19  013 0.8485
> > 20_19  014 0.8534
> > 20_190 047 0.9279
> > 20_190 048 0.9169
> > 20_191 046 0.9586
> > 20_191 047 0.9751
> > 20_192 049 0.8544
> > 20_193 013 0.9084
> > 20_193 014 0.9110
> > 20_194 047 0.9220
> > 20_194 048 0.9166
> > 20_195 048 0.9552
> > 20_195 049 0.9508
> > 20_196 047 0.9098
> > 20_196 048 0.9011
> > 20_199 048 0.8569
> > 20_199 049 0.8567
> > 20_20  013 0.8750
> > 20_20  014 0.8749
> > 20_201 048 0.8864
> > 20_201 049 1.0040
> > 20_202 048 0.8542
> > 20_202 049 0.8516
> > 20_203 048 1.0267
> > 20_203 049 1.0060
> > 20_204 048 0.8513
> > 20_204 049 0.8588
> > 20_208 014 0.9130
> > 20_208 015 0.9329
> > 20_209 047 1.0020
> > 20_209 048 1.0120
> > 20_21  027 0.9747
> > 20_21  028 1.0081
> > 20_210 048 0.8607
> > 20_210 049 0.8564
> > 20_220 047 0.
> > 20_220 048

Re: [Freesurfer] FSFAST poor registration

2019-01-22 Thread Greve, Douglas N.,Ph.D.

Are you saying that all of them have bad registrations? Some of them 
(eg, 20_1, 20_10) look like they should be good. Others (eg, 20_101) 
look like they could be bad. For the bad ones, are you totally sure that 
the subjetname file has the correct name of the subject?

On 1/21/19 3:19 AM, Keri Woods wrote:
>
> External Email - Use Caution
>
> Hi Douglas
>
> Thank you for your reply.
>
> I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
>
> I am using whole brain data. The functional and structural images were 
> acquired in different sessions on the same day, I don't know if that 
> complicated things? Each subject has 2 runs of the same task.
>
> This is what I get after running the command in the format of
> tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum
>
> 20_1   013 0.5155
> 20_1   014 0.5090
> 20_10  013 0.5247
> 20_10  014 0.5229
> 20_100 038 0.8420
> 20_100 040 0.8443
> 20_101 008 0.9052
> 20_101 010 0.9289
> 20_102 058 0.6924
> 20_102 059 0.6902
> 20_103 045 0.9778
> 20_103 046 0.9931
> 20_104 010 0.9324
> 20_104 012 0.9413
> 20_105 013 0.8754
> 20_105 014 0.8937
> 20_106 047 0.4433
> 20_106 048 0.4377
> 20_107 008 0.9178
> 20_107 010 0.9238
> 20_11  013 0.7631
> 20_11  014 0.7615
> 20_110 048 0.7687
> 20_110 049 0.7549
> 20_112 013 0.8821
> 20_112 014 0.9161
> 20_113 052 0.7689
> 20_113 053 0.7757
> 20_116 046 1.0072
> 20_116 047 1.0256
> 20_117 008 0.7742
> 20_117 010 0.7826
> 20_119 013 0.7929
> 20_119 014 0.7854
> 20_120 048 0.5090
> 20_120 049 0.4973
> 20_126 047 0.8285
> 20_126 048 0.8281
> 20_128 046 0.9580
> 20_128 047 0.9314
> 20_130 047 0.9439
> 20_130 048 0.9425
> 20_132 047 0.8550
> 20_132 048 0.8558
> 20_134_1   013 0.5716
> 20_134_1   015 0.5744
> 20_135 011 0.8357
> 20_135 012 0.8401
> 20_136 044 0.9995
> 20_136 045 0.9604
> 20_137 047 0.7922
> 20_137 048 0.7990
> 20_142 047 0.5282
> 20_142 048 0.5278
> 20_144 013 0.8755
> 20_144 014 0.8838
> 20_146 047 0.7997
> 20_146 048 0.7895
> 20_149 049 0.9251
> 20_149 050 0.9408
> 20_151 048 0.5905
> 20_151 049 0.5519
> 20_152 048 0.9024
> 20_152 049 0.9021
> 20_155 048 0.5285
> 20_155 049 0.5324
> 20_156 048 0.8883
> 20_156 049 0.9267
> 20_158 048 0.5404
> 20_158 049 0.5297
> 20_159 048 0.8021
> 20_160 013 0.5002
> 20_160 014 0.4942
> 20_162 047 0.5401
> 20_162 048 0.5401
> 20_164 047 0.8944
> 20_164 048 0.8940
> 20_165 047 0.9163
> 20_165 048 0.9077
> 20_166 045 0.8787
> 20_166 046 0.8848
> 20_167 050 0.8428
> 20_167 051 0.8442
> 20_169 049 0.9407
> 20_169 050 0.9462
> 20_170 047 0.8921
> 20_170 048 0.9113
> 20_171 013 0.9060
> 20_171 014 0.9060
> 20_173 048 0.9193
> 20_173 049 0.9141
> 20_177 048 0.8695
> 20_177 049 0.8600
> 20_178 048 1.0327
> 20_178 049 0.8979
> 20_180 045 0.7999
> 20_180 046 0.8002
> 20_182 047 0.9135
> 20_182 048 0.9130
> 20_184 048 0.9842
> 20_184 049 0.9960
> 20_185 046 0.9640
> 20_185 047 0.9514
> 20_187 048 0.8134
> 20_187 049 0.8082
> 20_189 047 1.0063
> 20_189 048 0.9701
> 20_19  013 0.8485
> 20_19  014 0.8534
> 20_190 047 0.9279
> 20_190 048 0.9169
> 20_191 046 0.9586
> 20_191 047 0.9751
> 20_192 049 0.8544
> 20_193 013 0.9084
> 20_193 014 0.9110
> 20_194 047 0.9220
> 20_194 048 0.9166
> 20_195 048 0.9552
> 20_195 049 0.9508
> 20_196 047 0.9098
> 20_196 048 0.9011
> 20_199 048 0.8569
> 20_199 049 0.8567
> 20_20  013 0.8750
> 20_20  014 0.8749
> 20_201 048 0.8864
> 20_201 049 1.0040
> 20_202 048 0.8542
> 20_202 049 0.8516
> 20_203 048 1.0267
> 20_203 049 1.0060
> 20_204 048 0.8513
> 20_204 049 0.8588
> 20_208 014 0.9130
> 20_208 015 0.9329
> 20_209 047 1.0020
> 20_209 048 1.0120
> 20_21  027 0.9747
> 20_21  028 1.0081
> 20_210 048 0.8607
> 20_210 049 0.8564
> 20_220 047 0.
> 20_220 048 0.8903
> 20_222 047 0.9998
> 20_222 048 0.8597
> 20_224 013 0.8122
> 20_224 014 0.8107
> 20_226 013 0.7855
> 20_226 014 0.7845
> 20_227 013 0.9372
> 20_227 014 0.9818
> 20_231 047 0.8355
> 20_231 048 0.8506
> 20_232 048 0.9730
> 20_232 049 0.9591
> 20_234 048 0.9357
> 20_234 049 0.9429
> 20_235 048 0.7528
> 20_235 049 0.7483
> 20_236 047 0.8997
> 20_236 048 0.8922
> 20_239 049 0.8920
> 20_239 050 0.8817
> 20_24  013 0.8197
> 20_24  014 0.8280
> 20_240 047 0.9109
> 20_240 048 0.9231
> 20_243 013 0.8227
> 20_243 014 0.8333
> 20_245 045 0.8620
> 20_245 046 0.8635
> 20_246 047 0.8236
> 20_246 048

Re: [Freesurfer] FSFAST poor registration

2019-01-18 Thread Greve, Douglas N.,Ph.D.

What version of FS are you using? version 6 initializes with mri_coreg (the FS 
equivalent of spm_coreg). On whole-brain data, I've found this to be very 
robust. Is your data whole-brain?

On 1/18/19 5:10 AM, Keri Woods wrote:

External Email - Use Caution

Hi

I have a problem very similar to this one:

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html

I've tried the suggestions given there, but it didn't fix my problem.

I'm running the FSFAST preproc-sess stream and the quality of the registration 
is very poor for most of the subjects.

I've tried initializing the registration differently, using bbregister with 
--init-fsl, --init-spm and init-header, which didn't improve the results at all.

I've also tried register-sess with --init-fsl, --init-spm and init-header, as 
well as spmregister-sess and fslregister-sess.

Is there anything else I could try?

Using the SPM GUI, the registration was fine, so I thought that 
spmregister-sess would have been an improvement, but it wasn't. Is there anyway 
I can import the registration obtained using the SPM GUI?

Thanks for your help.

Thanks,
Keri







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[Freesurfer] FSFAST poor registration

2019-01-18 Thread Keri Woods

External Email - Use Caution

Hi

I have a problem very similar to this one:

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23206.html

I've tried the suggestions given there, but it didn't fix my problem.

I'm running the FSFAST preproc-sess stream and the quality of the
registration is very poor for most of the subjects.

I've tried initializing the registration differently, using bbregister
with --init-fsl,
--init-spm and init-header, which didn't improve the results at all.

I've also tried register-sess with --init-fsl, --init-spm and init-header,
as well as spmregister-sess and fslregister-sess.

Is there anything else I could try?

Using the SPM GUI, the registration was fine, so I thought that
spmregister-sess would have been an improvement, but it wasn't. Is there
anyway I can import the registration obtained using the SPM GUI?

Thanks for your help.

Thanks,
Keri
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Re: [Freesurfer] fsfast preproc-sess: viewing preproc surface outputs

2018-10-16 Thread Greve, Douglas N.,Ph.D.

You can load them in freeview through tksurferfv, something like
tksurferfv fsaverage lh inflated -aparc -ov 
fmcpr.odd.sm5.fsaverage.lh.nii.gz
There's not much to see:)



On 10/16/2018 03:00 PM, Jacob Matthews wrote:
>
> External Email - Use Caution
>
> Hi FS Team,
>
> We are running our first fsfast pipeline, and starting with a single 
> subject to test everything. We successfully ran preproc-sess with the 
> following command:
>
> preproc-sess -s 11987_20180731 -surface fsaverage lhrh -mni305 -fwhm 5 
> -per-run -sliceorder odd -fsd bold
>
> We wanted to check the outputs. It was clear how to view most 
> intermediate outputs, but we didn't know how to view the surface space 
> outputs:
> fmcpr.odd.sm5.fsaverage.rh.nii.gz
> fmcpr.odd.sm5.fsaverage.lh.nii.gz
>
> Loading them into freeview as surfaces fails. We thought perhaps they 
> needed to be loaded on top of an fsaverage surface, but didn't know 
> where to start this process.
>
> Thanks,
>
> Jacob Matthews
> MRI Specialist
> Rotman Research Institute
> Baycrest Hospital
> 416-785-2500 ext. 3322
>
>
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[Freesurfer] fsfast preproc-sess: viewing preproc surface outputs

2018-10-16 Thread Jacob Matthews

External Email - Use Caution

Hi FS Team,

We are running our first fsfast pipeline, and starting with a single
subject to test everything. We successfully ran preproc-sess with the
following command:

preproc-sess -s 11987_20180731 -surface fsaverage lhrh -mni305 -fwhm 5
-per-run -sliceorder odd -fsd bold

We wanted to check the outputs. It was clear how to view most intermediate
outputs, but we didn't know how to view the surface space outputs:
fmcpr.odd.sm5.fsaverage.rh.nii.gz
fmcpr.odd.sm5.fsaverage.lh.nii.gz

Loading them into freeview as surfaces fails. We thought perhaps they
needed to be loaded on top of an fsaverage surface, but didn't know where
to start this process.

Thanks,

Jacob Matthews
MRI Specialist
Rotman Research Institute
Baycrest Hospital
416-785-2500 ext. 3322
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Re: [Freesurfer] FSFAST, Beta values and Percent Signal Change questions

2018-04-17 Thread Douglas Greve




On 4/16/18 11:56 AM, Sarah Cole wrote:

Hi Doug,

I need your recommendations on two topics. I really appreciate your help.

1.) I have two runs of the same experiment, each for about 12 minutes. 
These 2 runs are different only in the presentation order of the 
stimuli. I also have one localizer session which first, I calculated 
my contrasts in it, found the active voxels with positive values, and 
made a mask of those voxels. Then, mapped the masks on those 2 runs 
and got the raw data within those voxels. So far, so good. Now, I am 
looking at the Beta values in these 2 runs for those active voxels, 
they are very different from each other. For example, in the first 
run, they are mostly positive but in the second run, they are mostly 
negative. My intuition was that they should be in the same ballpark. I 
cannot make sense of this. Do you have any suggestions on why this is 
happening?
Hard to say without a lot more details. Is this all happening on the 
fsaverage surface? Is your localizer the same paradigm as the two task 
runs? When you look at the maps of the 2 task runs, do they look the 
same? Is your mask in a region where the task has activation?



2.) To calculate the % signal change, is it ok to pick the baseline 
whatever is suitable to my research question. For example, if I need 
to know the % signal change relative to*the average signal in the 
first TR of a specific block*, can I use that as a baseline? Or does 
it always need to be the rest or the mean?
I'm not sure there is a hard and fast way to do this. Usually you want 
to make sure that there is no task in the baseline. But the task is such 
a small part of the overall signal that I don't think it matters.



Thank you so much and looking forward to hearing from you.

Sarah


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[Freesurfer] FSFAST, Beta values and Percent Signal Change questions

2018-04-16 Thread Sarah Cole

Hi Doug,

I need your recommendations on two topics. I really appreciate your help.

1.) I have two runs of the same experiment, each for about 12 minutes.
These 2 runs are different only in the presentation order of the stimuli. I
also have one localizer session which first, I calculated my contrasts in
it, found the active voxels with positive values, and made a mask of those
voxels. Then, mapped the masks on those 2 runs and got the raw data within
those voxels. So far, so good. Now, I am looking at the Beta values in
these 2 runs for those active voxels, they are very different from each
other. For example, in the first run, they are mostly positive but in the
second run, they are mostly negative. My intuition was that they should be
in the same ballpark. I cannot make sense of this. Do you have any
suggestions on why this is happening?


2.) To calculate the % signal change, is it ok to pick the baseline
whatever is suitable to my research question. For example, if I need to
know the % signal change relative to* the average signal in the first TR of
a specific block*, can I use that as a baseline? Or does it always need to
be the rest or the mean?


Thank you so much and looking forward to hearing from you.

Sarah
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Re: [Freesurfer] [FSFAST]

2018-04-09 Thread Walid Yassin

Thank you, i will!

Walid


> On Apr 10, 2018, at 8:03 AM, Douglas N. Greve  wrote:
> 
> You can do it with the tpexclude file. Do a search through the archives 
> for docs on how to use it
> 
> 
> On 04/09/2018 06:56 PM, Walid Yassin wrote:
>> Hello Doug,
>> 
>> Thank you for your previous answer.
>> I have another question in the mkanalysis. When I run mkanalysis is it 
>> possible to analyse only a part of my run?
>> I mean if my stimuli was 100s per run, can i tell mkanalysis to ignore 
>> the first 20s and the last 30s and analyse the 50 in the middle?
>> 
>> Walid
>> 
>> On Mar 21, 2018, at 0:10, Douglas Greve > > wrote:
>> 
>>> Sorry, yes you can use an A-B blocked paradigm. Run mkanalysis-sess 
>>> -help to get more info
>>> 
>>> 
>>> On 3/20/18 4:28 AM, Walid Yassin wrote:
 Hello all,
 
 I would like to pose my question again in case it got missed.
 
 Thank you.
 
 WY
 
 On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin 
 > wrote:
 
Hi Doug,
 
Is it possible to run retinotopy-like analysis to reveal areas
in the brain responsible for a certain phase of a presented stimuli?
Say, instead of presenting 0 - 360 degrees of rotating wedge per
cycle, we would like to present arbitrary scale of 0 - 100 of a
particular stimulus feature, that does not necessarily differ in
their retinotopic locations.
 
We thought, if we pretend that scale-0 is equivalent to a wedge
of 0 degree, and scale-50 is equivalent to a wedge of 180
degrees, and so on, we would be able to map the cortical area
corresponding to each value of the scale.
However, the retinotopy protocol of freesurfer requires the
input of a stimulus type “e.g. polar or eccen” and direction
“e.g. pos or neg”, so our analysis won’t work as we intend.
 
Running Freesurfer v5.3.0
 
Thank you
 
Walid
 
 
 
 
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>>> 
>>> The information in this e-mail is intended only for the person to 
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>>> and properly
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>> 
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Re: [Freesurfer] [FSFAST]

2018-04-09 Thread Douglas N. Greve

You can do it with the tpexclude file. Do a search through the archives 
for docs on how to use it


On 04/09/2018 06:56 PM, Walid Yassin wrote:
> Hello Doug,
>
> Thank you for your previous answer.
> I have another question in the mkanalysis. When I run mkanalysis is it 
> possible to analyse only a part of my run?
> I mean if my stimuli was 100s per run, can i tell mkanalysis to ignore 
> the first 20s and the last 30s and analyse the 50 in the middle?
>
> Walid
>
> On Mar 21, 2018, at 0:10, Douglas Greve  > wrote:
>
>> Sorry, yes you can use an A-B blocked paradigm. Run mkanalysis-sess 
>> -help to get more info
>>
>>
>> On 3/20/18 4:28 AM, Walid Yassin wrote:
>>> Hello all,
>>>
>>> I would like to pose my question again in case it got missed.
>>>
>>> Thank you.
>>>
>>> WY
>>>
>>> On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin 
>>> > wrote:
>>>
>>> Hi Doug,
>>>
>>> Is it possible to run retinotopy-like analysis to reveal areas
>>> in the brain responsible for a certain phase of a presented stimuli?
>>> Say, instead of presenting 0 - 360 degrees of rotating wedge per
>>> cycle, we would like to present arbitrary scale of 0 - 100 of a
>>> particular stimulus feature, that does not necessarily differ in
>>> their retinotopic locations.
>>>
>>> We thought, if we pretend that scale-0 is equivalent to a wedge
>>> of 0 degree, and scale-50 is equivalent to a wedge of 180
>>> degrees, and so on, we would be able to map the cortical area
>>> corresponding to each value of the scale.
>>> However, the retinotopy protocol of freesurfer requires the
>>> input of a stimulus type “e.g. polar or eccen” and direction
>>> “e.g. pos or neg”, so our analysis won’t work as we intend.
>>>
>>> Running Freesurfer v5.3.0
>>>
>>> Thank you
>>>
>>> Walid
>>>
>>>
>>>
>>>
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>>
>>
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>> 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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>> and properly
>> dispose of the e-mail.
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Re: [Freesurfer] [FSFAST]

2018-04-09 Thread Walid Yassin

Hello Doug,

Thank you for your previous answer.
I have another question in the mkanalysis. When I run mkanalysis is it possible 
to analyse only a part of my run?
I mean if my stimuli was 100s per run, can i tell mkanalysis to ignore the 
first 20s and the last 30s and analyse the 50 in the middle?

Walid

> On Mar 21, 2018, at 0:10, Douglas Greve  wrote:
> 
> Sorry, yes you can use an A-B blocked paradigm. Run mkanalysis-sess -help to 
> get more info
> 
>> On 3/20/18 4:28 AM, Walid Yassin wrote:
>> Hello all,
>> 
>> I would like to pose my question again in case it got missed.
>> 
>> Thank you.
>> 
>> WY
>> 
>>> On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin  
>>> wrote:
>>> Hi Doug,
>>> 
>>> Is it possible to run retinotopy-like analysis to reveal areas in the brain 
>>> responsible for a certain phase of a presented stimuli?
>>> Say, instead of presenting 0 - 360 degrees of rotating wedge per cycle, we 
>>> would like to present arbitrary scale of 0 - 100 of a particular stimulus 
>>> feature, that does not necessarily differ in their retinotopic locations.
>>> 
>>> We thought, if we pretend that scale-0 is equivalent to a wedge of 0 
>>> degree, and scale-50 is equivalent to a wedge of 180 degrees, and so on, we 
>>> would be able to map the cortical area corresponding to each value of the 
>>> scale.
>>> However, the retinotopy protocol of freesurfer requires the input of a 
>>> stimulus type “e.g. polar or eccen” and direction “e.g. pos or neg”, so our 
>>> analysis won’t work as we intend.
>>> 
>>> Running Freesurfer v5.3.0
>>> 
>>> Thank you
>>> 
>>> Walid
>> 
>> 
>> 
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> 
> The information in this e-mail is intended only for the person to whom it is
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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 properly
dispose of the e-mail.

Re: [Freesurfer] [Freesurfer/FSFAST]

2018-04-03 Thread Dave Yas

Oh, yes. I used mriconvert.

Sure! So ill convert it again (using mriconvert?), and run preproc-sess and 
send you the terminal output.

P.S. I can still view the file after conversion normally.


Thank you,


DWY



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve 
<dgr...@mgh.harvard.edu>
Sent: Wednesday, April 4, 2018 3:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]


but using what program? mri_convert? Can you try converting it again and 
sending me the terminal output?

On 4/3/18 11:38 PM, Dave Yas wrote:

By hand. I followed the FSFAST hierarchy and just simply created the files and 
named them.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas Greve 
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, April 4, 2018 3:34 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]


The version should not matter here.


How did you create 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii ?

On 4/3/18 7:51 PM, Dave Yas wrote:

Sorry i forgot to mention that i am using Freesurfer v5.3.0 (if that accounts 
for anything here).



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas Greve 
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Tuesday, April 3, 2018 11:42 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]


Is the disk full?

On 4/3/18 6:48 PM, Dave Yas wrote:

Yes, the file exists!

Here is the full output:



--
preproc-sess logfile is log/preproc-sess.sess01.log
--
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
Davey
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
Darwin DWYs-Mac-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 
18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
/Users/Studies/Directory/Study_Directory
/Applications/freesurfer/fsfast/bin/preproc-sess
-fsd bold -per-run -s sess01 -fwhm 5
Tue Apr  3 10:11:25 JST 2018
instem   f
mc   1 f fmcpr
stc  0 fmcpr
sm   1 fmcpr fmcpr.sm5
mask 1   brain
sess01 Template -
mktemplate-sess -s sess01 -d /Users/Studies/Directory/Study_Directory -fsd bold 
-update



Session: /Users/Studies/Directory/Study_Directory/sess01 
Tue Apr  3 10:11:25 JST 2018
Detected input format at nii
/Users/Studies/Directory/Study_Directory
mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz --frame 0
mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz --frame 0
INFO: using NIfTI-1 qform

Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii...


After that nothing happens..


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas Greve 
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Tuesday, April 3, 2018 1:17 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]


does that file exist? CAn you send the full terminal output?

On 4/2/18 9:53 PM, Dave Yas wrote:

Hi,


I am running preproc-sess on one subject.

I got the following error after running preproc-sess:


Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii

My PWD: /Users/Studies/Directory/Study_Directory

My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects

My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5

My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & 
subjectname.text/001/f.nii & paradigm file (.par)

Re: [Freesurfer] [Freesurfer/FSFAST]

2018-04-03 Thread Douglas Greve

but using what program? mri_convert? Can you try converting it again and 
sending me the terminal output?



On 4/3/18 11:38 PM, Dave Yas wrote:


By hand. I followed the FSFAST hierarchy and just simply created the 
files and named them.





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

*Sent:* Wednesday, April 4, 2018 3:34 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] [Freesurfer/FSFAST]

The version should not matter here.


How did you create 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii ?



On 4/3/18 7:51 PM, Dave Yas wrote:


Sorry i forgot to mention that i am using Freesurfer v5.3.0 (if that 
accounts for anything here).





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

*Sent:* Tuesday, April 3, 2018 11:42 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu>

*Subject:* Re: [Freesurfer] [Freesurfer/FSFAST]

Is the disk full?


On 4/3/18 6:48 PM, Dave Yas wrote:


Yes, the file exists!

Here is the full output:



--
preproc-sess logfile is log/preproc-sess.sess01.log
--
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
Davey
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
Darwin DWYs-Mac-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue 
Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64

/Users/Studies/Directory/Study_Directory
/Applications/freesurfer/fsfast/bin/preproc-sess
-fsd bold -per-run -s sess01 -fwhm 5
Tue Apr  3 10:11:25 JST 2018
instem   f
mc   1     f fmcpr
stc  0     fmcpr
sm   1 fmcpr fmcpr.sm5
mask 1   brain
sess01 Template -
mktemplate-sess -s sess01 -d 
/Users/Studies/Directory/Study_Directory -fsd bold -update



Session: /Users/Studies/Directory/Study_Directory/sess01 


Tue Apr  3 10:11:25 JST 2018
Detected input format at nii
/Users/Studies/Directory/Study_Directory
mri_convert 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz 
--frame 0
mri_convert 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz 
--frame 0

INFO: using NIfTI-1 qform

Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii...



After that nothing happens..



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

*Sent:* Tuesday, April 3, 2018 1:17 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu>

*Subject:* Re: [Freesurfer] [Freesurfer/FSFAST]

does that file exist? CAn you send the full terminal output?


On 4/2/18 9:53 PM, Dave Yas wrote:


Hi,


I am running preproc-sess on one subject.

I got the following error after running preproc-sess:


Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii


My PWD: /Users/Studies/Directory/Study_Directory

My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects

My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5

My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & 
subjectname.text/001/f.nii& paradigm file (.par)

       ~/002/f.nii & paradigm file

~/003/f.nii & paradigm file


Any help on the above?

I searched the previous mailing list and found someone who had the 
same problem but didn't reach a solution!




Thank you in advance,


DWY




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] [Freesurfer/FSFAST]

2018-04-03 Thread Dave Yas

By hand. I followed the FSFAST hierarchy and just simply created the files and 
named them.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve 
<dgr...@mgh.harvard.edu>
Sent: Wednesday, April 4, 2018 3:34 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]


The version should not matter here.


How did you create 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii ?

On 4/3/18 7:51 PM, Dave Yas wrote:

Sorry i forgot to mention that i am using Freesurfer v5.3.0 (if that accounts 
for anything here).



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas Greve 
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Tuesday, April 3, 2018 11:42 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]


Is the disk full?

On 4/3/18 6:48 PM, Dave Yas wrote:

Yes, the file exists!

Here is the full output:



--
preproc-sess logfile is log/preproc-sess.sess01.log
--
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
Davey
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
Darwin DWYs-Mac-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 
18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
/Users/Studies/Directory/Study_Directory
/Applications/freesurfer/fsfast/bin/preproc-sess
-fsd bold -per-run -s sess01 -fwhm 5
Tue Apr  3 10:11:25 JST 2018
instem   f
mc   1 f fmcpr
stc  0 fmcpr
sm   1 fmcpr fmcpr.sm5
mask 1   brain
sess01 Template -
mktemplate-sess -s sess01 -d /Users/Studies/Directory/Study_Directory -fsd bold 
-update



Session: /Users/Studies/Directory/Study_Directory/sess01 
Tue Apr  3 10:11:25 JST 2018
Detected input format at nii
/Users/Studies/Directory/Study_Directory
mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz --frame 0
mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz --frame 0
INFO: using NIfTI-1 qform

Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii...


After that nothing happens..


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas Greve 
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Tuesday, April 3, 2018 1:17 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]


does that file exist? CAn you send the full terminal output?

On 4/2/18 9:53 PM, Dave Yas wrote:

Hi,


I am running preproc-sess on one subject.

I got the following error after running preproc-sess:


Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii

My PWD: /Users/Studies/Directory/Study_Directory

My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects

My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5

My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & 
subjectname.text/001/f.nii & paradigm file (.par)

   
~/002/f.nii & paradigm file


   
~/003/f.nii & paradigm file


Any help on the above?

I searched the previous mailing list and found someone who had the same problem 
but didn't reach a solution!



Thank you in advance,


DWY




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] [Freesurfer/FSFAST]

2018-04-03 Thread Douglas Greve


The version should not matter here.


How did you create 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii ?



On 4/3/18 7:51 PM, Dave Yas wrote:


Sorry i forgot to mention that i am using Freesurfer v5.3.0 (if that 
accounts for anything here).





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

*Sent:* Tuesday, April 3, 2018 11:42 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] [Freesurfer/FSFAST]

Is the disk full?


On 4/3/18 6:48 PM, Dave Yas wrote:


Yes, the file exists!

Here is the full output:



--
preproc-sess logfile is log/preproc-sess.sess01.log
--
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
Davey
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
Darwin DWYs-Mac-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue 
Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64

/Users/Studies/Directory/Study_Directory
/Applications/freesurfer/fsfast/bin/preproc-sess
-fsd bold -per-run -s sess01 -fwhm 5
Tue Apr  3 10:11:25 JST 2018
instem   f
mc   1     f fmcpr
stc  0     fmcpr
sm   1 fmcpr fmcpr.sm5
mask 1   brain
sess01 Template -
mktemplate-sess -s sess01 -d /Users/Studies/Directory/Study_Directory 
-fsd bold -update



Session: /Users/Studies/Directory/Study_Directory/sess01 
Tue Apr  3 10:11:25 JST 2018
Detected input format at nii
/Users/Studies/Directory/Study_Directory
mri_convert 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz 
--frame 0
mri_convert 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz 
--frame 0

INFO: using NIfTI-1 qform

Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii...



After that nothing happens..



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

*Sent:* Tuesday, April 3, 2018 1:17 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu>

*Subject:* Re: [Freesurfer] [Freesurfer/FSFAST]

does that file exist? CAn you send the full terminal output?


On 4/2/18 9:53 PM, Dave Yas wrote:


Hi,


I am running preproc-sess on one subject.

I got the following error after running preproc-sess:


Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii


My PWD: /Users/Studies/Directory/Study_Directory

My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects

My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5

My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & 
subjectname.text/001/f.nii& paradigm file (.par)

                   ~/002/f.nii & paradigm file

                   ~/003/f.nii & paradigm file


Any help on the above?

I searched the previous mailing list and found someone who had the 
same problem but didn't reach a solution!




Thank you in advance,


DWY




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://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 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.

Re: [Freesurfer] [Freesurfer/FSFAST]

2018-04-03 Thread Dave Yas

Sorry i forgot to mention that i am using Freesurfer v5.3.0 (if that accounts 
for anything here).



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve 
<dgr...@mgh.harvard.edu>
Sent: Tuesday, April 3, 2018 11:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]


Is the disk full?

On 4/3/18 6:48 PM, Dave Yas wrote:

Yes, the file exists!

Here is the full output:



--
preproc-sess logfile is log/preproc-sess.sess01.log
--
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
Davey
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
Darwin DWYs-Mac-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 
18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
/Users/Studies/Directory/Study_Directory
/Applications/freesurfer/fsfast/bin/preproc-sess
-fsd bold -per-run -s sess01 -fwhm 5
Tue Apr  3 10:11:25 JST 2018
instem   f
mc   1 f fmcpr
stc  0 fmcpr
sm   1 fmcpr fmcpr.sm5
mask 1   brain
sess01 Template -
mktemplate-sess -s sess01 -d /Users/Studies/Directory/Study_Directory -fsd bold 
-update



Session: /Users/Studies/Directory/Study_Directory/sess01 
Tue Apr  3 10:11:25 JST 2018
Detected input format at nii
/Users/Studies/Directory/Study_Directory
mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz --frame 0
mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz --frame 0
INFO: using NIfTI-1 qform

Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii...


After that nothing happens..


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas Greve 
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Tuesday, April 3, 2018 1:17 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]


does that file exist? CAn you send the full terminal output?

On 4/2/18 9:53 PM, Dave Yas wrote:

Hi,


I am running preproc-sess on one subject.

I got the following error after running preproc-sess:


Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii

My PWD: /Users/Studies/Directory/Study_Directory

My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects

My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5

My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & 
subjectname.text/001/f.nii & paradigm file (.par)

   
~/002/f.nii & paradigm file


   
~/003/f.nii & paradigm file


Any help on the above?

I searched the previous mailing list and found someone who had the same problem 
but didn't reach a solution!



Thank you in advance,


DWY




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Re: [Freesurfer] [Freesurfer/FSFAST]

2018-04-03 Thread Dave Yas

Only ~80%, but there is space for this run..





From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve 
<dgr...@mgh.harvard.edu>
Sent: Tuesday, April 3, 2018 11:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]


Is the disk full?

On 4/3/18 6:48 PM, Dave Yas wrote:

Yes, the file exists!

Here is the full output:



--
preproc-sess logfile is log/preproc-sess.sess01.log
--
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
Davey
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
Darwin DWYs-Mac-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 
18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
/Users/Studies/Directory/Study_Directory
/Applications/freesurfer/fsfast/bin/preproc-sess
-fsd bold -per-run -s sess01 -fwhm 5
Tue Apr  3 10:11:25 JST 2018
instem   f
mc   1 f fmcpr
stc  0 fmcpr
sm   1 fmcpr fmcpr.sm5
mask 1   brain
sess01 Template -
mktemplate-sess -s sess01 -d /Users/Studies/Directory/Study_Directory -fsd bold 
-update



Session: /Users/Studies/Directory/Study_Directory/sess01 
Tue Apr  3 10:11:25 JST 2018
Detected input format at nii
/Users/Studies/Directory/Study_Directory
mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz --frame 0
mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz --frame 0
INFO: using NIfTI-1 qform

Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii...


After that nothing happens..


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas Greve 
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Tuesday, April 3, 2018 1:17 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]


does that file exist? CAn you send the full terminal output?

On 4/2/18 9:53 PM, Dave Yas wrote:

Hi,


I am running preproc-sess on one subject.

I got the following error after running preproc-sess:


Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii

My PWD: /Users/Studies/Directory/Study_Directory

My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects

My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5

My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & 
subjectname.text/001/f.nii & paradigm file (.par)

   
~/002/f.nii & paradigm file


   
~/003/f.nii & paradigm file


Any help on the above?

I searched the previous mailing list and found someone who had the same problem 
but didn't reach a solution!



Thank you in advance,


DWY




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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.

Re: [Freesurfer] [Freesurfer/FSFAST]

2018-04-03 Thread Douglas Greve


Is the disk full?


On 4/3/18 6:48 PM, Dave Yas wrote:


Yes, the file exists!

Here is the full output:



--
preproc-sess logfile is log/preproc-sess.sess01.log
--
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
Davey
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
Darwin DWYs-Mac-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 
19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64

/Users/Studies/Directory/Study_Directory
/Applications/freesurfer/fsfast/bin/preproc-sess
-fsd bold -per-run -s sess01 -fwhm 5
Tue Apr  3 10:11:25 JST 2018
instem   f
mc   1     f fmcpr
stc  0     fmcpr
sm   1 fmcpr fmcpr.sm5
mask 1   brain
sess01 Template -
mktemplate-sess -s sess01 -d /Users/Studies/Directory/Study_Directory 
-fsd bold -update



Session: /Users/Studies/Directory/Study_Directory/sess01 
Tue Apr  3 10:11:25 JST 2018
Detected input format at nii
/Users/Studies/Directory/Study_Directory
mri_convert 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz 
--frame 0
mri_convert 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz 
--frame 0

INFO: using NIfTI-1 qform

Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii...



After that nothing happens..



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

*Sent:* Tuesday, April 3, 2018 1:17 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] [Freesurfer/FSFAST]

does that file exist? CAn you send the full terminal output?


On 4/2/18 9:53 PM, Dave Yas wrote:


Hi,


I am running preproc-sess on one subject.

I got the following error after running preproc-sess:


Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii


My PWD: /Users/Studies/Directory/Study_Directory

My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects

My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5

My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & 
subjectname.text/001/f.nii& paradigm file (.par)

 ~/002/f.nii & paradigm file

   ~/003/f.nii & paradigm file


Any help on the above?

I searched the previous mailing list and found someone who had the 
same problem but didn't reach a solution!




Thank you in advance,


DWY




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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [Freesurfer/FSFAST]

2018-04-03 Thread Dave Yas

Yes, the file exists!

Here is the full output:



--
preproc-sess logfile is log/preproc-sess.sess01.log
--
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
Davey
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
Darwin DWYs-Mac-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 
18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
/Users/Studies/Directory/Study_Directory
/Applications/freesurfer/fsfast/bin/preproc-sess
-fsd bold -per-run -s sess01 -fwhm 5
Tue Apr  3 10:11:25 JST 2018
instem   f
mc   1 f fmcpr
stc  0 fmcpr
sm   1 fmcpr fmcpr.sm5
mask 1   brain
sess01 Template -
mktemplate-sess -s sess01 -d /Users/Studies/Directory/Study_Directory -fsd bold 
-update



Session: /Users/Studies/Directory/Study_Directory/sess01 
Tue Apr  3 10:11:25 JST 2018
Detected input format at nii
/Users/Studies/Directory/Study_Directory
mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz --frame 0
mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii 
/Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz --frame 0
INFO: using NIfTI-1 qform

Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii...


After that nothing happens..


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve 
<dgr...@mgh.harvard.edu>
Sent: Tuesday, April 3, 2018 1:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]


does that file exist? CAn you send the full terminal output?

On 4/2/18 9:53 PM, Dave Yas wrote:

Hi,


I am running preproc-sess on one subject.

I got the following error after running preproc-sess:


Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii

My PWD: /Users/Studies/Directory/Study_Directory

My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects

My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5

My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & 
subjectname.text/001/f.nii & paradigm file (.par)

   
~/002/f.nii & paradigm file


   
~/003/f.nii & paradigm file


Any help on the above?

I searched the previous mailing list and found someone who had the same problem 
but didn't reach a solution!



Thank you in advance,


DWY




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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [Freesurfer/FSFAST]

2018-04-03 Thread Douglas Greve


does that file exist? CAn you send the full terminal output?


On 4/2/18 9:53 PM, Dave Yas wrote:


Hi,


I am running preproc-sess on one subject.

I got the following error after running preproc-sess:


Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii


My PWD: /Users/Studies/Directory/Study_Directory

My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects

My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5

My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & 
subjectname.text/001/f.nii& paradigm file (.par)

                               ~/002/f.nii & paradigm file

                                               ~/003/f.nii & paradigm file


Any help on the above?

I searched the previous mailing list and found someone who had the 
same problem but didn't reach a solution!




Thank you in advance,


DWY




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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] [Freesurfer/FSFAST]

2018-04-02 Thread Dave Yas

Hi,


I am running preproc-sess on one subject.

I got the following error after running preproc-sess:


Error: niiRead(): error reading from 
/Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii

My PWD: /Users/Studies/Directory/Study_Directory

My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects

My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5

My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & 
subjectname.text/001/f.nii & paradigm file (.par)

   
~/002/f.nii & paradigm file


   
~/003/f.nii & paradigm file


Any help on the above?

I searched the previous mailing list and found someone who had the same problem 
but didn't reach a solution!



Thank you in advance,


DWY

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Re: [Freesurfer] [FSFAST]

2018-03-20 Thread Douglas Greve

Sorry, yes you can use an A-B blocked paradigm. Run mkanalysis-sess 
-help to get more info



On 3/20/18 4:28 AM, Walid Yassin wrote:

Hello all,

I would like to pose my question again in case it got missed.

Thank you.

WY

On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin > wrote:


Hi Doug,

Is it possible to run retinotopy-like analysis to reveal areas in
the brain responsible for a certain phase of a presented stimuli?
Say, instead of presenting 0 - 360 degrees of rotating wedge per
cycle, we would like to present arbitrary scale of 0 - 100 of a
particular stimulus feature, that does not necessarily differ in
their retinotopic locations.

We thought, if we pretend that scale-0 is equivalent to a wedge of
0 degree, and scale-50 is equivalent to a wedge of 180 degrees,
and so on, we would be able to map the cortical area corresponding
to each value of the scale.
However, the retinotopy protocol of freesurfer requires the input
of a stimulus type “e.g. polar or eccen” and direction “e.g. pos
or neg”, so our analysis won’t work as we intend.

Running Freesurfer v5.3.0

Thank you

Walid




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Re: [Freesurfer] [FSFAST]

2018-03-20 Thread Walid Yassin

Hello all,

I would like to pose my question again in case it got missed.

Thank you.

WY

On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin 
wrote:

> Hi Doug,
>
> Is it possible to run retinotopy-like analysis to reveal areas in the
> brain responsible for a certain phase of a presented stimuli?
> Say, instead of presenting 0 - 360 degrees of rotating wedge per cycle, we
> would like to present arbitrary scale of 0 - 100 of a particular stimulus
> feature, that does not necessarily differ in their retinotopic locations.
>
> We thought, if we pretend that scale-0 is equivalent to a wedge of 0
> degree, and scale-50 is equivalent to a wedge of 180 degrees, and so on, we
> would be able to map the cortical area corresponding to each value of the
> scale.
> However, the retinotopy protocol of freesurfer requires the input of a
> stimulus type “e.g. polar or eccen” and direction “e.g. pos or neg”, so our
> analysis won’t work as we intend.
>
> Running Freesurfer v5.3.0
>
> Thank you
>
> Walid
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[Freesurfer] [FSFAST]

2018-03-19 Thread Walid Yassin

Hi Doug,

Is it possible to run retinotopy-like analysis to reveal areas in the brain 
responsible for a certain phase of a presented stimuli?
Say, instead of presenting 0 - 360 degrees of rotating wedge per cycle, we 
would like to present arbitrary scale of 0 - 100 of a particular stimulus 
feature, that does not necessarily differ in their retinotopic locations.

We thought, if we pretend that scale-0 is equivalent to a wedge of 0 degree, 
and scale-50 is equivalent to a wedge of 180 degrees, and so on, we would be 
able to map the cortical area corresponding to each value of the scale.
However, the retinotopy protocol of freesurfer requires the input of a stimulus 
type “e.g. polar or eccen” and direction “e.g. pos or neg”, so our analysis 
won’t work as we intend. 

Running Freesurfer v5.3.0

Thank you

Walid
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Re: [Freesurfer] FSFAST

2018-02-05 Thread Ashley Cole

Only fmc.odd.sm5.nii.gz is in the same dimensions as the f.nii.gz. However,
I found a flag in the selxavg3 (-no-con-ok)that I do not need to specify a
contrast. If I am not mistaken, all is good now. Thank you for your
response.


On Sat, Feb 3, 2018 at 2:03 PM, Douglas Greve 
wrote:

> That file should be in the same dimensions, no?
>
> On 1/30/18 12:19 AM, Ashley Cole wrote:
>
> I just noticed that that file "fmc.odd.sm5.nii.gz" is created after
> selxavg3-sess. I was wondering how can I preprocess the functional image
> and have the output with the same dimension as the f.nii.gz without
> performing any contrasts. I just need to look at the signal in some ROIs
> without performing any contrasts. I hope this makes sense.
>
> Thanks,
> Ash
>
> On Mon, Jan 29, 2018 at 10:54 PM, Ashley Cole 
> wrote:
>
>> Hello,
>>
>> I have several nifti files. I have preprocessed some of them before. I
>> used this command:
>> preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305
>> -fwhm 5 -per-session -force
>>
>> The output files contained fmc.odd.sm5.self.lh.nii.gz,
>> fmc.odd.sm5.self.rh.nii.gz, fmc.odd.sm5.mni305.2mm.nii.gz, and
>> *fmc.odd.sm5.nii.gz*. Which this last one (fmc.odd.sm5.nii.gz) was the
>> file that I needed for my further analyses. However, when I run the same
>> command on another nifti file which was obtained from the same scanner and
>> the same session, the output doesn't have the fmc.odd.sm5.nii.gz.
>>
>> I ran it several times but it never gave me that file. Also, it doesn't
>> give me any errors.
>>
>> I appreciate any help.
>>
>> Ash
>>
>
>
>
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> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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Re: [Freesurfer] FSFAST

2018-02-03 Thread Douglas Greve


That file should be in the same dimensions, no?


On 1/30/18 12:19 AM, Ashley Cole wrote:
I just noticed that that file "fmc.odd.sm5.nii.gz" is created after 
selxavg3-sess. I was wondering how can I preprocess the functional 
image and have the output with the same dimension as the f.nii.gz 
without performing any contrasts. I just need to look at the signal in 
some ROIs without performing any contrasts. I hope this makes sense.


Thanks,
Ash

On Mon, Jan 29, 2018 at 10:54 PM, Ashley Cole > wrote:


Hello,

I have several nifti files. I have preprocessed some of them
before. I used this command:
preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh
-mni305 -fwhm 5 -per-session -force

The output files contained fmc.odd.sm5.self.lh.nii.gz,
fmc.odd.sm5.self.rh.nii.gz, fmc.odd.sm5.mni305.2mm.nii.gz, and
*fmc.odd.sm5.nii.gz*. Which this last one (fmc.odd.sm5.nii.gz) was
the file that I needed for my further analyses. However, when I
run the same command on another nifti file which was obtained from
the same scanner and the same session, the output doesn't have the
fmc.odd.sm5.nii.gz.

I ran it several times but it never gave me that file. Also, it
doesn't give me any errors.

I appreciate any help.

Ash




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Re: [Freesurfer] FSFAST

2018-01-29 Thread Ashley Cole

I just noticed that that file "fmc.odd.sm5.nii.gz" is created after
selxavg3-sess. I was wondering how can I preprocess the functional image
and have the output with the same dimension as the f.nii.gz without
performing any contrasts. I just need to look at the signal in some ROIs
without performing any contrasts. I hope this makes sense.

Thanks,
Ash

On Mon, Jan 29, 2018 at 10:54 PM, Ashley Cole 
wrote:

> Hello,
>
> I have several nifti files. I have preprocessed some of them before. I
> used this command:
> preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm
> 5 -per-session -force
>
> The output files contained fmc.odd.sm5.self.lh.nii.gz,
> fmc.odd.sm5.self.rh.nii.gz, fmc.odd.sm5.mni305.2mm.nii.gz, and
> *fmc.odd.sm5.nii.gz*. Which this last one (fmc.odd.sm5.nii.gz) was the
> file that I needed for my further analyses. However, when I run the same
> command on another nifti file which was obtained from the same scanner and
> the same session, the output doesn't have the fmc.odd.sm5.nii.gz.
>
> I ran it several times but it never gave me that file. Also, it doesn't
> give me any errors.
>
> I appreciate any help.
>
> Ash
>
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[Freesurfer] FSFAST

2018-01-29 Thread Ashley Cole

Hello,

I have several nifti files. I have preprocessed some of them before. I used
this command:
preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm
5 -per-session -force

The output files contained fmc.odd.sm5.self.lh.nii.gz,
fmc.odd.sm5.self.rh.nii.gz, fmc.odd.sm5.mni305.2mm.nii.gz, and
*fmc.odd.sm5.nii.gz*. Which this last one (fmc.odd.sm5.nii.gz) was the file
that I needed for my further analyses. However, when I run the same command
on another nifti file which was obtained from the same scanner and the same
session, the output doesn't have the fmc.odd.sm5.nii.gz.

I ran it several times but it never gave me that file. Also, it doesn't
give me any errors.

I appreciate any help.

Ash
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Re: [Freesurfer] fsfast

2017-08-02 Thread Douglas Greve

Those are two different things. The --seg is the name of the segmetation 
(eg, aparc+aseg.mgz). --segid is the index in that segmentation to use



On 8/2/17 5:23 PM, John Anderson wrote:

Thank you Doug,
One last question please
in the command

fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg 
mean.L_Posteriorcingulate.config

Instead of using segid. it is suggested in the help of fcseed that I 
can use the flag "seg segmentation" which is aparac+aseg by default.


if I run the command this way
fcseed-config -seg aparc+aseg -fcname 
aparc+aseg.dat -fsd bold -mean -cfg mean.aparc+aseg.config


the command always asks for a seedid? what I am doing wrong?






I still don't understand what you mean. in any event, fsfast is set up 
only to do seed-based FC.





 Original Message 
Subject: Re: fsfast
Local Time: August 2, 2017 5:14 PM
UTC Time: August 2, 2017 9:14 PM
From: john.ande...@protonmail.com
To: Freesurfer support list 

I mean instead of using seed like cingulate gyrus. Can I use the 
whole brain (e.g. wmparc.mgz)?



what do you mean by functional connectivity if it is not seed based.

 Original Message 
Subject: Re: fsfast
Local Time: August 2, 2017 5:01 PM
UTC Time: August 2, 2017 9:01 PM
From: john.ande...@protonmail.com
To: Freesurfer support list 

Hi Doug,

thank you for your response.
The steps in link that you provided is for a seed based functional 
connectivity analysis.


I aim to compare the functional connectivity between two groups 
without using seeds similar to what we do in surface based analysis 
between two groups to compare volume of or cortical thickness.. Is 
this possible with fMRI? Or FSfast can only run fMRI analysis 
depending on a seed of interest?


If FSFAST can compare functional connectivity between two groups 
then how can I create then I don't need the command fcseed-sess. As 
a result how the contrast will be created?


Thank you very much for any clarification.



Are you following these steps?

http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough

When you make your analysis, you need to include something like 
-taskreg L_Posteriorcingulate.dat


Then when you run isxconcat-sess, you include this as the contrast. 
See the wiki for more details



On 8/2/17 12:34 PM, John Anderson wrote:

Dear Dr Greve,

I am new to FSFAST so I highly appreciate your response.


I have resting state fMRI data and I am following the steps as 
reported in wiki. I want to study the difference in functional 
connectivity between two groups



My questions are regarding motion evaluation and the contrasts.


1. The attached figure is an output of "plot-twf-sess". Given the 
plotted data can we say that including run 003 is more reliable that 
all the other runs?



2. In the attached figure the command "plot-twf-sess" provides the 
maximum and minimum motion for every run on Y axes. I am wondering 
if there is any way to create a cutoff value of motion parameters 
for all the runs in the study were data can be included/excluded 
depending on lower/upper than this cutoff?



3. I used the following commands to study the differnc ein 
functional connectivity between two groups (each group has one run):


## preprocessing

preproc-sess -s $subj -stc up -fwhm 5 -surface fsaverage lh rh 
-mni305-2mm -fsd bold -per-run -init-spm



###**First-Level (Group) Analysis

mkanalysis-sess -analysis groupdiff-lh -surface fsaverage lh -fwhm 5 
-notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run



mkanalysis-sess -analysis groupdiff-rh -surface fsaverage rh -fwhm 5 
-notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run



mkanalysis-sess -analysis groupdiff-mni -mni305 2 -fwhm 5 -notsk 
-mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run



#Analyze First Level

selxavg3-sess -s $subj -a groupdiff-lh -no-con-ok

selxavg3-sess -s $subj -a groupdiff-rh -no-con-ok

selxavg3-sess -s $subj -a groupdiff-mni -no-con-ok


Now for the next step I need to concatenate the sessions using 
isxconcat but this command needs a contrast which I didn't create it 
in the previous step. Given that I am looking for a differnce in the 
functional connectivity between two groups how can I create the 
contrast for this anlaysis.




Thank you for any help and feedback!!

John



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The information in this

Re: [Freesurfer] fsfast

2017-08-02 Thread John Anderson

Thank you Doug,
One last question please
in the command
fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg 
mean.L_Posteriorcingulate.config
Instead of using segid. it is suggested in the help of fcseed that I can use 
the flag "seg segmentation" which is aparac+aseg by default.
if I run the command this way
fcseed-config -seg aparc+aseg -fcname aparc+aseg.dat -fsd bold -mean -cfg 
mean.aparc+aseg.config
the command always asks for a seedid? what I am doing wrong?

I still don't understand what you mean. in any event, fsfast is set up only to 
do seed-based FC.

>  Original Message 
> Subject: Re: fsfast
> Local Time: August 2, 2017 5:14 PM
> UTC Time: August 2, 2017 9:14 PM
> From: john.ande...@protonmail.com
> To: Freesurfer support list 
> I mean instead of using seed like cingulate gyrus. Can I use the whole brain 
> (e.g. wmparc.mgz)?
>
> what do you mean by functional connectivity if it is not seed based.
>
>>  Original Message 
>> Subject: Re: fsfast
>> Local Time: August 2, 2017 5:01 PM
>> UTC Time: August 2, 2017 9:01 PM
>> From: john.ande...@protonmail.com
>> To: Freesurfer support list 
>>
>> Hi Doug,
>>
>> thank you for your response.
>> The steps in link that you provided is for a seed based functional 
>> connectivity analysis.
>> I aim to compare the functional connectivity between two groups without 
>> using seeds similar to what we do in surface based analysis between two 
>> groups to compare volume of or cortical thickness.. Is this possible with 
>> fMRI? Or FSfast can only run fMRI analysis depending on a seed of interest?
>> If FSFAST can compare functional connectivity between two groups then how 
>> can I create then I don't need the command fcseed-sess. As a result how the 
>> contrast will be created?
>> Thank you very much for any clarification.
>> Are you following these steps?
>>
>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
>>
>> When you make your analysis, you need to include something like -taskreg 
>> L_Posteriorcingulate.dat
>>
>> Then when you run isxconcat-sess, you include this as the contrast. See the 
>> wiki for more details
>>
>> On 8/2/17 12:34 PM, John Anderson wrote:
>>
>> Dear Dr Greve,
>>
>> I am new to FSFAST so I highly appreciate your response.
>>
>> I have resting state fMRI data and I am following the steps as reported in 
>> wiki. I want to study the difference in functional connectivity between two 
>> groups
>>
>> My questions are regarding motion evaluation and the contrasts.
>>
>> 1. The attached figure is an output of "plot-twf-sess". Given the plotted 
>> data can we say that including run 003 is more reliable that all the other 
>> runs?
>>
>> 2. In the attached figure the command "plot-twf-sess" provides the maximum 
>> and minimum motion for every run on Y axes. I am wondering if there is any 
>> way to create a cutoff value of motion parameters for all the runs in the 
>> study were data can be included/excluded depending on lower/upper than this 
>> cutoff?
>>
>> 3. I used the following commands to study the differnc ein functional 
>> connectivity between two groups (each group has one run):
>>
>> ## preprocessing
>>
>> preproc-sess -s $subj -stc up -fwhm 5 -surface fsaverage lh rh -mni305-2mm 
>> -fsd bold -per-run -init-spm
>>
>> ### First-Level (Group) Analysis
>>
>> mkanalysis-sess -analysis groupdiff-lh -surface fsaverage lh -fwhm 5 -notsk 
>> -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
>>
>> mkanalysis-sess -analysis groupdiff-rh -surface fsaverage rh -fwhm 5 -notsk 
>> -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
>>
>> mkanalysis-sess -analysis groupdiff-mni -mni305 2 -fwhm 5 -notsk -mcextreg 
>> -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
>>
>> #Analyze First Level
>>
>> selxavg3-sess -s $subj -a groupdiff-lh -no-con-ok
>>
>> selxavg3-sess -s $subj -a groupdiff-rh -no-con-ok
>>
>> selxavg3-sess -s $subj -a groupdiff-mni -no-con-ok
>>
>> Now for the next step I need to concatenate the sessions using isxconcat but 
>> this command needs a contrast which I didn't create it in the previous step. 
>> Given that I am looking for a differnce in the functional connectivity 
>> between two groups how can I create the contrast for this anlaysis.
>>
>> Thank you for any help and feedback!!
>>
>> John
>>
>> ___
>>
>> Freesurfer mailing list
>>
>> Freesurfer@nmr.mgh.harvard.edu
>>
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Re: [Freesurfer] fsfast

2017-08-02 Thread Douglas Greve

I still don't understand what you mean. in any event, fsfast is set up 
only to do seed-based FC.



On 8/2/17 5:14 PM, John Anderson wrote:
I mean instead of using seed like cingulate gyrus. Can I use the whole 
brain (e.g. wmparc.mgz)?



what do you mean by functional connectivity if it is not seed based.

 Original Message 
Subject: Re: fsfast
Local Time: August 2, 2017 5:01 PM
UTC Time: August 2, 2017 9:01 PM
From: john.ande...@protonmail.com
To: Freesurfer support list 

Hi Doug,

thank you for your response.
The steps in link that you provided is for a seed based functional 
connectivity analysis.


I aim to compare the functional connectivity between two groups 
without using seeds similar to what we do in surface based analysis 
between two groups to compare volume of or cortical thickness.. Is 
this possible with fMRI? Or FSfast can only run fMRI analysis 
depending on a seed of interest?


If FSFAST can compare functional connectivity between two groups then 
how can I create then I don't need the command fcseed-sess. As a 
result how the contrast will be created?


Thank you very much for any clarification.



Are you following these steps?

http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough

When you make your analysis, you need to include something like 
-taskreg L_Posteriorcingulate.dat


Then when you run isxconcat-sess, you include this as the contrast. 
See the wiki for more details



On 8/2/17 12:34 PM, John Anderson wrote:

Dear Dr Greve,

I am new to FSFAST so I highly appreciate your response.


I have resting state fMRI data and I am following the steps as 
reported in wiki. I want to study the difference in functional 
connectivity between two groups



My questions are regarding motion evaluation and the contrasts.


1. The attached figure is an output of "plot-twf-sess". Given the 
plotted data can we say that including run 003 is more reliable that 
all the other runs?



2. In the attached figure the command "plot-twf-sess" provides the 
maximum and minimum motion for every run on Y axes. I am wondering if 
there is any way to create a cutoff value of motion parameters for 
all the runs in the study were data can be included/excluded 
depending on lower/upper than this cutoff?



3. I used the following commands to study the differnc ein functional 
connectivity between two groups (each group has one run):


## preprocessing

preproc-sess -s $subj -stc up -fwhm 5 -surface fsaverage lh rh 
-mni305-2mm -fsd bold -per-run -init-spm



###**First-Level (Group) Analysis

mkanalysis-sess -analysis groupdiff-lh -surface fsaverage lh -fwhm 5 
-notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run



mkanalysis-sess -analysis groupdiff-rh -surface fsaverage rh -fwhm 5 
-notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run



mkanalysis-sess -analysis groupdiff-mni -mni305 2 -fwhm 5 -notsk 
-mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run



#Analyze First Level

selxavg3-sess -s $subj -a groupdiff-lh -no-con-ok

selxavg3-sess -s $subj -a groupdiff-rh -no-con-ok

selxavg3-sess -s $subj -a groupdiff-mni -no-con-ok


Now for the next step I need to concatenate the sessions using 
isxconcat but this command needs a contrast which I didn't create it 
in the previous step. Given that I am looking for a differnce in the 
functional connectivity between two groups how can I create the 
contrast for this anlaysis.




Thank you for any help and feedback!!

John



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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 properly
dispose of the e-mail.

Re: [Freesurfer] fsfast

2017-08-02 Thread John Anderson

I mean instead of using seed like cingulate gyrus. Can I use the whole brain 
(e.g. wmparc.mgz)?

what do you mean by functional connectivity if it is not seed based.

>  Original Message 
> Subject: Re: fsfast
> Local Time: August 2, 2017 5:01 PM
> UTC Time: August 2, 2017 9:01 PM
> From: john.ande...@protonmail.com
> To: Freesurfer support list 
>
> Hi Doug,
>
> thank you for your response.
> The steps in link that you provided is for a seed based functional 
> connectivity analysis.
> I aim to compare the functional connectivity between two groups without using 
> seeds similar to what we do in surface based analysis between two groups to 
> compare volume of or cortical thickness.. Is this possible with fMRI? Or 
> FSfast can only run fMRI analysis depending on a seed of interest?
> If FSFAST can compare functional connectivity between two groups then how can 
> I create then I don't need the command fcseed-sess. As a result how the 
> contrast will be created?
> Thank you very much for any clarification.
> Are you following these steps?
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
>
> When you make your analysis, you need to include something like -taskreg 
> L_Posteriorcingulate.dat
>
> Then when you run isxconcat-sess, you include this as the contrast. See the 
> wiki for more details
>
> On 8/2/17 12:34 PM, John Anderson wrote:
>
> Dear Dr Greve,
>
> I am new to FSFAST so I highly appreciate your response.
>
> I have resting state fMRI data and I am following the steps as reported in 
> wiki. I want to study the difference in functional connectivity between two 
> groups
>
> My questions are regarding motion evaluation and the contrasts.
>
> 1. The attached figure is an output of "plot-twf-sess". Given the plotted 
> data can we say that including run 003 is more reliable that all the other 
> runs?
>
> 2. In the attached figure the command "plot-twf-sess" provides the maximum 
> and minimum motion for every run on Y axes. I am wondering if there is any 
> way to create a cutoff value of motion parameters for all the runs in the 
> study were data can be included/excluded depending on lower/upper than this 
> cutoff?
>
> 3. I used the following commands to study the differnc ein functional 
> connectivity between two groups (each group has one run):
>
> ## preprocessing
>
> preproc-sess -s $subj -stc up -fwhm 5 -surface fsaverage lh rh -mni305-2mm 
> -fsd bold -per-run -init-spm
>
> ### First-Level (Group) Analysis
>
> mkanalysis-sess -analysis groupdiff-lh -surface fsaverage lh -fwhm 5 -notsk 
> -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
>
> mkanalysis-sess -analysis groupdiff-rh -surface fsaverage rh -fwhm 5 -notsk 
> -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
>
> mkanalysis-sess -analysis groupdiff-mni -mni305 2 -fwhm 5 -notsk -mcextreg 
> -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
>
> #Analyze First Level
>
> selxavg3-sess -s $subj -a groupdiff-lh -no-con-ok
>
> selxavg3-sess -s $subj -a groupdiff-rh -no-con-ok
>
> selxavg3-sess -s $subj -a groupdiff-mni -no-con-ok
>
> Now for the next step I need to concatenate the sessions using isxconcat but 
> this command needs a contrast which I didn't create it in the previous step. 
> Given that I am looking for a differnce in the functional connectivity 
> between two groups how can I create the contrast for this anlaysis.
>
> Thank you for any help and feedback!!
>
> John
>
> ___
>
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Re: [Freesurfer] fsfast

2017-08-02 Thread Douglas Greve


what do you mean by functional connectivity if it is not seed based?


On 8/2/17 5:01 PM, John Anderson wrote:


Hi Doug,

thank you for your response.
The steps in link that you provided is for a seed based functional 
connectivity analysis.


I aim to compare the functional connectivity between two groups 
without using seeds similar to what we do in surface based analysis 
between two groups to compare volume of or cortical thickness.. Is 
this possible with fMRI? Or FSfast can only run fMRI analysis 
depending on a seed of interest?


If FSFAST can compare functional connectivity between two groups then 
how can I create then I don't need the command fcseed-sess. As a 
result how the contrast will be created?


Thank you very much for any clarification.



Are you following these steps?

http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough

When you make your analysis, you need to include something like 
-taskreg L_Posteriorcingulate.dat


Then when you run isxconcat-sess, you include this as the contrast. 
See the wiki for more details



On 8/2/17 12:34 PM, John Anderson wrote:

Dear Dr Greve,

I am new to FSFAST so I highly appreciate your response.


I have resting state fMRI data and I am following the steps as 
reported in wiki. I want to study the difference in functional 
connectivity between two groups



My questions are regarding motion evaluation and the contrasts.


1. The attached figure is an output of "plot-twf-sess". Given the 
plotted data can we say that including run 003 is more reliable that 
all the other runs?



2. In the attached figure the command "plot-twf-sess" provides the 
maximum and minimum motion for every run on Y axes. I am wondering if 
there is any way to create a cutoff value of motion parameters for all 
the runs in the study were data can be included/excluded depending on 
lower/upper than this cutoff?



3. I used the following commands to study the differnc ein functional 
connectivity between two groups (each group has one run):


## preprocessing

preproc-sess -s $subj -stc up -fwhm 5 -surface fsaverage lh rh 
-mni305-2mm -fsd bold -per-run -init-spm



###**First-Level (Group) Analysis

mkanalysis-sess -analysis groupdiff-lh -surface fsaverage lh -fwhm 5 
-notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run



mkanalysis-sess -analysis groupdiff-rh -surface fsaverage rh -fwhm 5 
-notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run



mkanalysis-sess -analysis groupdiff-mni -mni305 2 -fwhm 5 -notsk 
-mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run



#Analyze First Level

selxavg3-sess -s $subj -a groupdiff-lh -no-con-ok

selxavg3-sess -s $subj -a groupdiff-rh -no-con-ok

selxavg3-sess -s $subj -a groupdiff-mni -no-con-ok


Now for the next step I need to concatenate the sessions using 
isxconcat but this command needs a contrast which I didn't create it 
in the previous step. Given that I am looking for a differnce in the 
functional connectivity between two groups how can I create the 
contrast for this anlaysis.




Thank you for any help and feedback!!

John




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Re: [Freesurfer] fsfast

2017-08-02 Thread John Anderson

Hi Doug,

thank you for your response.
The steps in link that you provided is for a seed based functional connectivity 
analysis.
I aim to compare the functional connectivity between two groups without using 
seeds similar to what we do in surface based analysis between two groups to 
compare volume of or cortical thickness.. Is this possible with fMRI? Or FSfast 
can only run fMRI analysis depending on a seed of interest?
If FSFAST can compare functional connectivity between two groups then how can I 
create then I don't need the command fcseed-sess. As a result how the contrast 
will be created?
Thank you very much for any clarification.
Are you following these steps?

http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough

When you make your analysis, you need to include something like -taskreg 
L_Posteriorcingulate.dat

Then when you run isxconcat-sess, you include this as the contrast. See the 
wiki for more details

On 8/2/17 12:34 PM, John Anderson wrote:

Dear Dr Greve,

I am new to FSFAST so I highly appreciate your response.

I have resting state fMRI data and I am following the steps as reported in 
wiki. I want to study the difference in functional connectivity between two 
groups

My questions are regarding motion evaluation and the contrasts.

1. The attached figure is an output of "plot-twf-sess". Given the plotted data 
can we say that including run 003 is more reliable that all the other runs?

2. In the attached figure the command "plot-twf-sess" provides the maximum and 
minimum motion for every run on Y axes. I am wondering if there is any way to 
create a cutoff value of motion parameters for all the runs in the study were 
data can be included/excluded depending on lower/upper than this cutoff?

3. I used the following commands to study the differnc ein functional 
connectivity between two groups (each group has one run):

## preprocessing

preproc-sess -s $subj -stc up -fwhm 5 -surface fsaverage lh rh -mni305-2mm -fsd 
bold -per-run -init-spm

### First-Level (Group) Analysis

mkanalysis-sess -analysis groupdiff-lh -surface fsaverage lh -fwhm 5 -notsk 
-mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run

mkanalysis-sess -analysis groupdiff-rh -surface fsaverage rh -fwhm 5 -notsk 
-mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run

mkanalysis-sess -analysis groupdiff-mni -mni305 2 -fwhm 5 -notsk -mcextreg 
-polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run

#Analyze First Level

selxavg3-sess -s $subj -a groupdiff-lh -no-con-ok

selxavg3-sess -s $subj -a groupdiff-rh -no-con-ok

selxavg3-sess -s $subj -a groupdiff-mni -no-con-ok

Now for the next step I need to concatenate the sessions using isxconcat but 
this command needs a contrast which I didn't create it in the previous step. 
Given that I am looking for a differnce in the functional connectivity between 
two groups how can I create the contrast for this anlaysis.

Thank you for any help and feedback!!

John

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Re: [Freesurfer] fsfast

2017-08-02 Thread Douglas Greve


Are you following these steps?

http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough

When you make your analysis, you need to include something like 
-taskreg L_Posteriorcingulate.dat


Then when you run isxconcat-sess, you include this as the contrast. See 
the wiki for more details



On 8/2/17 12:34 PM, John Anderson wrote:

Dear Dr Greve,
I am new to FSFAST so I highly appreciate your response.

I have resting state fMRI data and I am following the steps as 
reported in wiki. I want to study the difference in functional 
connectivity between two groups


My questions are regarding motion evaluation and the contrasts.

1. The attached figure is an output of "plot-twf-sess".Given the 
plotted data can we say that including run 003 is more reliable that 
all the other runs?


2. In the attached figure the command "plot-twf-sess" provides the 
maximum and minimum motion for every run on Y axes. I am wondering if 
there is any way to create a cutoff value of motion parameters for all 
the runs in the study were data can be included/excluded depending on 
lower/upper than this cutoff?


3. I used the following commands to study the differnc ein functional 
connectivity between two groups (each group has one run):

## preprocessing
preproc-sess -s $subj -stc up -fwhm 5 -surface fsaverage lh rh 
-mni305-2mm -fsd bold -per-run -init-spm


###**First-Level (Group) Analysis
mkanalysis-sess -analysis groupdiff-lh -surface fsaverage lh -fwhm 5 
-notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run


mkanalysis-sess -analysis groupdiff-rh -surface fsaverage rh -fwhm 5 
-notsk -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run


mkanalysis-sess -analysis groupdiff-mni -mni305 2 -fwhm 5 -notsk 
-mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run


#Analyze First Level
selxavg3-sess -s $subj -a groupdiff-lh -no-con-ok
selxavg3-sess -s $subj -a groupdiff-rh -no-con-ok
selxavg3-sess -s $subj -a groupdiff-mni -no-con-ok

Now for the next step I need to concatenate the sessions using 
isxconcat but this command needs a contrast which I didn't create it 
in the previous step. Given that I am looking for a differnce in the 
functional connectivity between two groups how can I create the 
contrast for this anlaysis.



Thank you for any help and feedback!!
John


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Re: [Freesurfer] FSFAST (plot-twf-sess)

2017-08-02 Thread Douglas Greve

There are no easy ways to create a cut off. This is still a major 
question in fMRI analysis, esp for resting state.



On 7/31/17 2:58 PM, John Anderson wrote:

Dear Dr Greeve,
I am new to FSFAST so I highly appreciate your response.

I have resting state fMRI data and I am following the steps as 
reported in wiki.


My questions is regarding motion evaluation. The attached figure is an 
output of "plot-twf-sess".
1. Given the plotted data can we say that including run 003 is more 
reliable that all the other runs?
2. In the attached figure the command "plot-twf-sess" provide the 
maximum and minimum motion for every run on Y axes. I am wondering if 
there is any way to create a cutoff value of motion parameters for all 
the runs in the study were data can be included/excluded depending on 
lower/upper than this cutoff?


Thank you for help
John


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[Freesurfer] fsfast

2017-08-02 Thread John Anderson

Dear Dr Greve,
I am new to FSFAST so I highly appreciate your response.
I have resting state fMRI data and I am following the steps as reported in 
wiki. I want to study the difference in functional connectivity between two 
groups
My questions are regarding motion evaluation and the contrasts.
1. The attached figure is an output of "plot-twf-sess". Given the plotted data 
can we say that including run 003 is more reliable that all the other runs?
2. In the attached figure the command "plot-twf-sess" provides the maximum and 
minimum motion for every run on Y axes. I am wondering if there is any way to 
create a cutoff value of motion parameters for all the runs in the study were 
data can be included/excluded depending on lower/upper than this cutoff?
3. I used the following commands to study the differnc ein functional 
connectivity between two groups (each group has one run):
## preprocessing
preproc-sess -s $subj -stc up -fwhm 5 -surface fsaverage lh rh -mni305-2mm -fsd 
bold -per-run -init-spm
### First-Level (Group) Analysis
mkanalysis-sess -analysis groupdiff-lh -surface fsaverage lh -fwhm 5 -notsk 
-mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
mkanalysis-sess -analysis groupdiff-rh -surface fsaverage rh -fwhm 5 -notsk 
-mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
mkanalysis-sess -analysis groupdiff-mni -mni305 2 -fwhm 5 -notsk -mcextreg 
-polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run
#Analyze First Level
selxavg3-sess -s $subj -a groupdiff-lh -no-con-ok
selxavg3-sess -s $subj -a groupdiff-rh -no-con-ok
selxavg3-sess -s $subj -a groupdiff-mni -no-con-ok
Now for the next step I need to concatenate the sessions using isxconcat but 
this command needs a contrast which I didn't create it in the previous step. 
Given that I am looking for a differnce in the functional connectivity between 
two groups how can I create the contrast for this anlaysis.
Thank you for any help and feedback!!
John___
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[Freesurfer] FSFAST (plot-twf-sess)

2017-07-31 Thread John Anderson

Dear Dr Greeve,
I am new to FSFAST so I highly appreciate your response.
I have resting state fMRI data and I am following the steps as reported in wiki.
My questions is regarding motion evaluation. The attached figure is an output 
of "plot-twf-sess".
1. Given the plotted data can we say that including run 003 is more reliable 
that all the other runs?
2. In the attached figure the command "plot-twf-sess" provide the maximum and 
minimum motion for every run on Y axes. I am wondering if there is any way to 
create a cutoff value of motion parameters for all the runs in the study were 
data can be included/excluded depending on lower/upper than this cutoff?
Thank you for help
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Re: [Freesurfer] FSFAST Full Model Residuals?

2017-06-07 Thread Taylor, Johnmark

Actually, just noticed that this is an option in selxavg3-sess, never mind!

On Wed, Jun 7, 2017 at 9:07 PM, Taylor, Johnmark <
johnmarktay...@g.harvard.edu> wrote:

> Hello,
>
> I had a quick question. Is there a way to make FSFAST output a 4D volume
> of all the residuals? In other words: is there a way to see, for each voxel
> and timepoint, how much of the BOLD response was unexplained by the GLM? I
> know that it outputs a volume containing the residual variances, but I am
> interested in looking at the residuals in more detail. I see that there is
> a directory called "res", but for all of the GLMs I've run it appears to be
> empty...
>
> Thank you very much,
>
> JohnMark
>
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Re: [Freesurfer] FSFAST

2017-05-05 Thread Douglas Greve




On 5/5/17 5:06 AM, John Anderson wrote:

Dear Doug,
I have Bold fMRI data (6 minutes of acquisition which is equal to 180 
volume for every run). The total number for images is 140 (50 controls 
and 90 patients). I plan to use FSFAST (FS V6.0) to study:

1. The difference between the groups in global functional connectivity
2. Seed-based functional connectivity analysis depending on an ROI 
 for a difference in a voxel-wise analysis between PET images for the 
same subjects.

My questions are:
1. In this data set I have only one run for every subject. I am 
wondering if FSFAST  can analyze fMRI data (one run per subject).

Yes, no problem
2. FSFAST depends on  the recons, meaning it depends on the ROIs in 
wmparc, aseg and apare+aseg atlases. Can FSFAST accept an external ROI 
for seed based functional connectivity analysis?
Yes, just create an ROI as a mask in the conformed anatomical space and 
put the volume in the subject/mri folder. Then when you run fcseed-sess, 
spec that volume with -seg and specify the ROI code with -segid. Eg, if 
your volume was myroi.mgz and the value that the roi takes in that 
volume was 3, then -seg myroi.mgz -segid 3


I highly appreciate your advice
John






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[Freesurfer] FSFAST

2017-05-05 Thread John Anderson

Dear Doug,
I have Bold fMRI data (6 minutes of acquisition which is equal to 180 volume 
for every run). The total number for images is 140 (50 controls and 90 
patients). I plan to use FSFAST (FS V6.0) to study:
1. The difference between the groups in global functional connectivity
2. Seed-based functional connectivity analysis depending on an ROI for a 
difference in a voxel-wise analysis between PET images for the same subjects.
My questions are:
1. In this data set I have only one run for every subject. I am wondering if 
FSFAST can analyze fMRI data (one run per subject).
2. FSFAST depends on the recons, meaning it depends on the ROIs in wmparc, aseg 
and apare+aseg atlases. Can FSFAST accept an external ROI for seed based 
functional connectivity analysis?

I highly appreciate your advice
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Re: [Freesurfer] [FSFAST] Matlab parallel

2017-02-06 Thread Douglas N Greve

That should work (the env var is FSF_OUTPUT_FORMAT). You will also need 
to set it in your linux shell before running any of the scripts


On 02/03/2017 09:51 AM, Seung-Goo KIM wrote:
> Hi all,
>
> So this is a question about running FAST through matlab parallel 
> desktop: I know it is very funny (and inefficient) because I open up a 
> bash in the matlab to run a csh script that generates and runs a 
> matlab code, but just I’m familiar with matlab in doing many things 
> including string manipulation, so that’s how I’m doing now. If there 
> are matlab scripts that does a similar thing as csh scripts, it would 
> be nice.
>
> Anyway, I realized that I cannot run all the fitting with different 
> parameters and with the identical name of model (the GLM directory 
> name) at the same time because the code appears to refer to the 
> directory at $SUBJECTS_DIR.
>
> But I tried to run multiple subjects (with all different GLM names in 
> their own native spaces) through MATLAB on a server, it returns (seems 
> just one of random subject):
>
>> ERROR: could not read /tmp/tmp354512.nii
>> rm: cannot remove ‘/tmp/tmp354512.nii’: No such file or directory
>> ERROR: loading ${filename}.nii.gz as analyze
>
> So I traced back to the functions that return those errors (i.e., 
> load_nifti.m run in MRIread.m) and it seems to be something with the 
> temporary directory managed by matlab workers. The temporary file 
> seems to be only necessary for nii.gz file.
>
> If so, I would rather just use .nii file format (or maybe .mgz?) 
> format instead of dealing with the void complexity. Then can it be 
> done by just putting:
>
>> setenv(‘FSF_OUTPUTFORMAT’,’.mgz’) 
>
> before I run "preproc-sess" and "selxavg3-sess” in my scripts?
>
> Best regards,
> -- 
> Seung-Goo KIM
>
>
>
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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
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/

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Re: [Freesurfer] [FSFAST] Matlab parallel

2017-02-06 Thread Seung-Goo KIM

+Self-update: I figured out “.nii” works well. I thought “.mgz" should work 
well, but "preproc-sess” tried to read “template.mgz.nii” while it creates 
“template.nii”. So just the simple format “.nii” works well even in a harsh 
virtual environment (e.g.,matlab>parallel-workers>bash>csh>matlab).
-- 
Seung-Goo KIM

> On 2017-02-03, at 15:51, Seung-Goo KIM  wrote:
> 
> Hi all,
> 
> So this is a question about running FAST through matlab parallel desktop: I 
> know it is very funny (and inefficient) because I open up a bash in the 
> matlab to run a csh script that generates and runs a matlab code, but just 
> I’m familiar with matlab in doing many things including string manipulation, 
> so that’s how I’m doing now. If there are matlab scripts that does a similar 
> thing as csh scripts, it would be nice.
> 
> Anyway, I realized that I cannot run all the fitting with different 
> parameters and with the identical name of model (the GLM directory name) at 
> the same time because the code appears to refer to the directory at 
> $SUBJECTS_DIR. 
> 
> But I tried to run multiple subjects (with all different GLM names in their 
> own native spaces) through MATLAB on a server, it returns (seems just one of 
> random subject):
> 
>> ERROR: could not read /tmp/tmp354512.nii
>> rm: cannot remove ‘/tmp/tmp354512.nii’: No such file or directory
>> ERROR: loading ${filename}.nii.gz as analyze
> 
> So I traced back to the functions that return those errors (i.e., 
> load_nifti.m run in MRIread.m) and it seems to be something with the 
> temporary directory managed by matlab workers. The temporary file seems to be 
> only necessary for nii.gz file. 
> 
> If so, I would rather just use .nii file format (or maybe .mgz?) format 
> instead of dealing with the void complexity. Then can it be done by just 
> putting:
> 
>> setenv(‘FSF_OUTPUTFORMAT’,’.mgz’) 
> 
> 
> before I run "preproc-sess" and "selxavg3-sess” in my scripts?
> 
> Best regards,
> -- 
> Seung-Goo KIM
> 

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[Freesurfer] [FSFAST] Matlab parallel

2017-02-03 Thread Seung-Goo KIM

Hi all,

So this is a question about running FAST through matlab parallel desktop: I 
know it is very funny (and inefficient) because I open up a bash in the matlab 
to run a csh script that generates and runs a matlab code, but just I’m 
familiar with matlab in doing many things including string manipulation, so 
that’s how I’m doing now. If there are matlab scripts that does a similar thing 
as csh scripts, it would be nice.

Anyway, I realized that I cannot run all the fitting with different parameters 
and with the identical name of model (the GLM directory name) at the same time 
because the code appears to refer to the directory at $SUBJECTS_DIR. 

But I tried to run multiple subjects (with all different GLM names in their own 
native spaces) through MATLAB on a server, it returns (seems just one of random 
subject):

> ERROR: could not read /tmp/tmp354512.nii
> rm: cannot remove ‘/tmp/tmp354512.nii’: No such file or directory
> ERROR: loading ${filename}.nii.gz as analyze

So I traced back to the functions that return those errors (i.e., load_nifti.m 
run in MRIread.m) and it seems to be something with the temporary directory 
managed by matlab workers. The temporary file seems to be only necessary for 
nii.gz file. 

If so, I would rather just use .nii file format (or maybe .mgz?) format instead 
of dealing with the void complexity. Then can it be done by just putting:

> setenv(‘FSF_OUTPUTFORMAT’,’.mgz’) 


before I run "preproc-sess" and "selxavg3-sess” in my scripts?

Best regards,
-- 
Seung-Goo KIM

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Re: [Freesurfer] [FSFAST] Contrast percent map

2017-02-01 Thread Douglas Greve


you have the right idea, but it is

cespct = 100*contrast/baseline

The baseline is the mean offset of the fMRI, the contrast is the 
deviation from baseline



On 2/1/17 4:49 AM, Seung-Goo KIM wrote:

Dear all,

I wish to know how “cespct.nii.gz” is computed in selxavg3-sess. I 
thought it computes something like a relative change like:


cespct = (contrast-baseline)/baseline*100,

but I cannot figure out what was taken for the baseline. I thought it 
could be mean beta for constant terms (0-th polynomial) for each run, 
but my calculation was different from cespct.


I would take average intensity for each voxel I would greatly 
appreciate a detailed explanation how the program computes it.


Best regards,
--
Seung-Goo KIM



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[Freesurfer] [FSFAST] Contrast percent map

2017-02-01 Thread Seung-Goo KIM

Dear all,

I wish to know how “cespct.nii.gz” is computed in selxavg3-sess. I thought it 
computes something like a relative change like: 

cespct = (contrast-baseline)/baseline*100, 

but I cannot figure out what was taken for the baseline. I thought it could be 
mean beta for constant terms (0-th polynomial) for each run, but my calculation 
was different from cespct.

I would take average intensity for each voxel I would greatly appreciate a 
detailed explanation how the program computes it.

Best regards,
-- 
Seung-Goo KIM

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Re: [Freesurfer] FSFAST ROI atlas

2016-08-18 Thread Harms, Michael








Yes, the Gordon parcellation paper:

http://www.ncbi.nlm.nih.gov/pubmed/25316338





-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sabin Khadka <mr.sabinkha...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, August 18, 2016 at 8:55 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST ROI atlas





Hi Michael- Thanks very much for the file. Is there published paper or other documents that I could use as reference for these annotation?




Cheers,

Sabin Khadka




On Wed, Aug 17, 2016 at 12:53 PM, Harms, Michael 
<mha...@wustl.edu> wrote:





They are attached (assuming that the FS list allows small attachments).
There is a script that details exactly how it was done.





-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 
314-747-6173
St. Louis, MO  63110 Email: 
mha...@wustl.edu






From: Sabin Khadka <mr.sabinkha...@gmail.com>
Date: Wednesday, August 17, 2016 at 11:25 AM
To: Freesurfer support list <freesur...@nmr.mgh.harvard.edu>, "Harms, Michael" <mha...@wustl.edu>


Subject: Re: [Freesurfer] FSFAST ROI atlas









Hi Michael- Is there anyway I can get those Gordon parcellation annot files?




Cheers,

Sabin Khadka




On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael 
<mha...@wustl.edu> wrote:






FYI: I supplied a version of the “Gordon” parcellation in .annot format to Bruce a while back.  He had expressed an interest in possibly including it as part of FS 6.0.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 
314-747-6173
St. Louis, MO  63110 Email: 
mha...@wustl.edu







From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Doug Greve <gr...@nmr.mgh.harvard.edu>
Reply-To: "freesur...@nmr.mgh.harvard.edu" <freesur...@nmr.mgh.harvard.edu>
Date: Wednesday, August 17, 2016 at 9:55 AM
To: "freesur...@nmr.mgh.harvard.edu" <freesur...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST ROI atlas





I don't know anything about the Power atlas. For the HCP, if they have it in annotation format, then you can run mri_aparc2aseg to map it into the anatomical volume, then specify that volume when you run fcseed-config. To get the mri_aparc2aseg command line,
 look in the recon-all to find out how aparc+aseg.mgz is created


On 8/17/16 9:28 AM, Sabin Khadka wrote:



Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done.


Thanks for your help!





Cheers,

Sabin Khadka




On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
<gr...@nmr.mgh.harvard.edu> wrote:



I have not used them myself.



On 8/15/16 10:23 AM, Sabin Khadka wrote:








HI all- 


I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. 


However, I was wondering if anyone has used Power 
et.al 2011 rois and/or HCP's newly defined 180/per hemi rois to extract time series data. If so could you please advise me on how do it (if they are at all possible). 




Cheers,

Sabin Khadka





 



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__

Re: [Freesurfer] FSFAST ROI atlas

2016-08-18 Thread Sabin Khadka

Hi Michael- Thanks very much for the file. Is there published paper or
other documents that I could use as reference for these annotation?

Cheers,
Sabin Khadka

On Wed, Aug 17, 2016 at 12:53 PM, Harms, Michael <mha...@wustl.edu> wrote:

>
> They are attached (assuming that the FS list allows small attachments).
> There is a script that details exactly how it was done.
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From: Sabin Khadka <mr.sabinkha...@gmail.com>
> Date: Wednesday, August 17, 2016 at 11:25 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, "Harms,
> Michael" <mha...@wustl.edu>
>
> Subject: Re: [Freesurfer] FSFAST ROI atlas
>
> Hi Michael- Is there anyway I can get those Gordon parcellation annot
> files?
>
> Cheers,
> Sabin Khadka
>
> On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael <mha...@wustl.edu> wrote:
>
>>
>> FYI: I supplied a version of the “Gordon” parcellation in .annot format
>> to Bruce a while back.  He had expressed an interest in possibly including
>> it as part of FS 6.0.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Doug Greve <
>> gr...@nmr.mgh.harvard.edu>
>> Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesur...@nmr.mgh.harvard.ed
>> u>
>> Date: Wednesday, August 17, 2016 at 9:55 AM
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] FSFAST ROI atlas
>>
>> I don't know anything about the Power atlas. For the HCP, if they have it
>> in annotation format, then you can run mri_aparc2aseg to map it into the
>> anatomical volume, then specify that volume when you run fcseed-config. To
>> get the mri_aparc2aseg command line, look in the recon-all to find out how
>> aparc+aseg.mgz is created
>>
>> On 8/17/16 9:28 AM, Sabin Khadka wrote:
>>
>> Hi Doug- Do you think it is possible to use these atlas? If so could you
>> point me to steps that needed to be done.
>>
>> Thanks for your help!
>>
>> Cheers,
>> Sabin Khadka
>>
>> On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> I have not used them myself.
>>>
>>> On 8/15/16 10:23 AM, Sabin Khadka wrote:
>>>
>>> HI all-
>>>
>>> I am using FSFAST to extract ROI time series values for further
>>> connectivity analysis. I've used Desikan, Destriuex and DKT atlas.
>>>
>>> However, I was wondering if anyone has used Power et.al 2011 rois
>>> and/or HCP's newly defined 180/per hemi rois to extract time series data.
>>> If so could you please advise me on how do it (if they are at all
>>> possible).
>>>
>>> Cheers,
>>> Sabin Khadka
>>>
>>>
>>> ___
>>> 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.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 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.
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>>
>> The mater

Re: [Freesurfer] FSFAST ROI atlas

2016-08-17 Thread Sabin Khadka

Hi Michael- Is there anyway I can get those Gordon parcellation annot files?

Cheers,
Sabin Khadka

On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael <mha...@wustl.edu> wrote:

>
> FYI: I supplied a version of the “Gordon” parcellation in .annot format to
> Bruce a while back.  He had expressed an interest in possibly including it
> as part of FS 6.0.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Doug Greve <
> gr...@nmr.mgh.harvard.edu>
> Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu
> >
> Date: Wednesday, August 17, 2016 at 9:55 AM
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] FSFAST ROI atlas
>
> I don't know anything about the Power atlas. For the HCP, if they have it
> in annotation format, then you can run mri_aparc2aseg to map it into the
> anatomical volume, then specify that volume when you run fcseed-config. To
> get the mri_aparc2aseg command line, look in the recon-all to find out how
> aparc+aseg.mgz is created
>
> On 8/17/16 9:28 AM, Sabin Khadka wrote:
>
> Hi Doug- Do you think it is possible to use these atlas? If so could you
> point me to steps that needed to be done.
>
> Thanks for your help!
>
> Cheers,
> Sabin Khadka
>
> On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu
> > wrote:
>
>> I have not used them myself.
>>
>> On 8/15/16 10:23 AM, Sabin Khadka wrote:
>>
>> HI all-
>>
>> I am using FSFAST to extract ROI time series values for further
>> connectivity analysis. I've used Desikan, Destriuex and DKT atlas.
>>
>> However, I was wondering if anyone has used Power et.al 2011 rois and/or
>> HCP's newly defined 180/per hemi rois to extract time series data. If so
>> could you please advise me on how do it (if they are at all possible).
>>
>> Cheers,
>> Sabin Khadka
>>
>>
>> ___
>> 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.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 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.
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> ___
> 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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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
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Re: [Freesurfer] FSFAST ROI atlas

2016-08-17 Thread Harms, Michael








FYI: I supplied a version of the “Gordon” parcellation in .annot format to Bruce a while back.  He had expressed an interest in possibly including it as part of FS 6.0.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Doug Greve <gr...@nmr.mgh.harvard.edu>
Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, August 17, 2016 at 9:55 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST ROI atlas





I don't know anything about the Power atlas. For the HCP, if they have it in annotation format, then you can run mri_aparc2aseg to map it into the anatomical volume, then specify that volume when you run fcseed-config. To get the mri_aparc2aseg command line,
 look in the recon-all to find out how aparc+aseg.mgz is created


On 8/17/16 9:28 AM, Sabin Khadka wrote:


Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done.


Thanks for your help!




Cheers,

Sabin Khadka




On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
<gr...@nmr.mgh.harvard.edu> wrote:


I have not used them myself.



On 8/15/16 10:23 AM, Sabin Khadka wrote:







HI all- 


I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. 


However, I was wondering if anyone has used Power 
et.al 2011 rois and/or HCP's newly defined 180/per hemi rois to extract time series data. If so could you please advise me on how do it (if they are at all possible). 




Cheers,

Sabin Khadka





 


___
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Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___ Freesurfer mailing list 
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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 materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return 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
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] FSFAST ROI atlas

2016-08-17 Thread Douglas Greve

I don't know anything about the Power atlas. For the HCP, if they have 
it in annotation format, then you can run mri_aparc2aseg to map it into 
the anatomical volume, then specify that volume when you run 
fcseed-config. To get the mri_aparc2aseg command line, look in the 
recon-all to find out how aparc+aseg.mgz is created



On 8/17/16 9:28 AM, Sabin Khadka wrote:
Hi Doug- Do you think it is possible to use these atlas? If so could 
you point me to steps that needed to be done.


Thanks for your help!

Cheers,
Sabin Khadka

On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
> wrote:


I have not used them myself.


On 8/15/16 10:23 AM, Sabin Khadka wrote:

HI all-

I am using FSFAST to extract ROI time series values for further
connectivity analysis. I've used Desikan, Destriuex and DKT atlas.

However, I was wondering if anyone has used Power et.al
 2011 rois and/or HCP's newly defined 180/per hemi
rois to extract time series data. If so could you please advise
me on how do it (if they are at all possible).

Cheers,
Sabin Khadka


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu

https://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
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Re: [Freesurfer] FSFAST ROI atlas

2016-08-17 Thread Sabin Khadka

Hi Doug- Do you think it is possible to use these atlas? If so could you
point me to steps that needed to be done.

Thanks for your help!

Cheers,
Sabin Khadka

On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
wrote:

> I have not used them myself.
>
> On 8/15/16 10:23 AM, Sabin Khadka wrote:
>
> HI all-
>
> I am using FSFAST to extract ROI time series values for further
> connectivity analysis. I've used Desikan, Destriuex and DKT atlas.
>
> However, I was wondering if anyone has used Power et.al 2011 rois and/or
> HCP's newly defined 180/per hemi rois to extract time series data. If so
> could you please advise me on how do it (if they are at all possible).
>
> Cheers,
> Sabin Khadka
>
>
> ___
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>
>
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Re: [Freesurfer] FSFAST ROI atlas

2016-08-15 Thread Douglas Greve


I have not used them myself.


On 8/15/16 10:23 AM, Sabin Khadka wrote:

HI all-

I am using FSFAST to extract ROI time series values for further 
connectivity analysis. I've used Desikan, Destriuex and DKT atlas.


However, I was wondering if anyone has used Power et.al  
2011 rois and/or HCP's newly defined 180/per hemi rois to extract time 
series data. If so could you please advise me on how do it (if they 
are at all possible).


Cheers,
Sabin Khadka


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[Freesurfer] FSFAST ROI atlas

2016-08-15 Thread Sabin Khadka

HI all-

I am using FSFAST to extract ROI time series values for further
connectivity analysis. I've used Desikan, Destriuex and DKT atlas.

However, I was wondering if anyone has used Power et.al 2011 rois and/or
HCP's newly defined 180/per hemi rois to extract time series data. If so
could you please advise me on how do it (if they are at all possible).

Cheers,
Sabin Khadka
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Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3() failed\n

2016-07-09 Thread Douglas Greve

what do you mean nothing happens? After you hit the return key, it 
should either give you the path to the command or it should say Command 
not found.


doug


ps. Please remember to post to the list and not to us individually


On 7/8/16 7:16 PM, Erik Jahner wrote:
When I type "which matlab” in the command window, nothing happens. My 
$PATH structure is a s follows:


echo $PATH
/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin

Sorry if my response seems naïve, I’am new to running command 
lines although I’m trying learn.


Erik

Message: 6
Date: Fri, 8 Jul 2016 14:30:43 -0400
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu 
<mailto:gr...@nmr.mgh.harvard.edu>>

Subject: Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3()
failed\n
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID: <577ff153.1080...@nmr.mgh.harvard.edu 
<mailto:577ff153.1080...@nmr.mgh.harvard.edu>>

Content-Type: text/plain; charset=windows-1252; format=flowed

Is matlab in your path? What  happens if you type
which matlab
at the command line?

On 07/08/2016 12:34 AM, ERIK JAHNER wrote:


Hello FreeSurfer Developers,


This is Erik Jahner, I?m attempting to complete the final step in the
tutorial concerning FSFast Functional connectivity walkthrough
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough ), 


but for I get the following error when I run the following command:

selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lh


Mon Jul  4 11:01:41 PDT 2016

rawfunc2surf-sess completed



Started at Mon Jul 4 11:01:40 PDT 2016

Ended   at Mon Jul  4 11:01:41 PDT 2016

preproc-sess done

---

/Applications/freesurfer/LagStructure/subj439rest

Mon Jul  4 11:01:41 PDT 2016

anadir =
/Applications/freesurfer/LagStructure/subj439rest/rest/fc.lpccseed.surf.lh

DoGLMFit = 1

DoContrasts = 1

UpdateNeeded = 1

--

--- matlab output 

matlab: Command not found.

--

*ERROR: fast_selxavg3() failed\n*


I've searched the list and no similar errors have been reported. I
have tried to reinstall MATLAB; I have tried following the
instructions to install the runtime environment; I have tried redoing
all analysis from scratch. I have noticed that STEP 5 does not work
unless I change the -cfg from ?L_Posteriorcingulate.config?
to ?mean.L_Posteriorcingulate.config?. I don?t think this is the
problem, but I thought I would point it out.

My session directory is ?subj439rest?

Instead of titling the sub directory ?bold?, I titled it ?rest?


1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0

2) Platform: OSX Yousemite

3) uname -a: Darwin ERIKs-iMac.local 15.5.0 Darwin Kernel Version
15.5.0: Tue Apr 19 18:36:36 PDT 2016;
root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64

4) selxavg3-sess-rest-fc.lpccseed.surf.lh-160704110140.log: see attached

___

Here are the command lines I put in for steps 4-8, incase this is of
some use:

STEP 4

fcseed-config-segid 1010 -fcname L_Posteriorcingulate.dat -fsd rest
-mean-cfg mean.L_Posteriorcingulate.config

STEP 5

fcseed-sess-s subj439rest -cfg mean.L_Posteriorcingulate.config

STEP 6

 * fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config
 * fcseed-sess -s subj439rest -cfg wm.config

 * fcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config
 * fcseed-sess -s subj439rest -cfg vcsf.config

STEP7

mkanalysis-sess-analysis fc.lpccseed.surf.lh -surface fsaverage lh
-fwhm 5 -notask-taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5
-nuisreg wm.dat 5 -mcextreg-polyfit 5 -nskip 4 -fsd rest -TR 2 -per-run

STEP 8

selxavg3-sess-s subj439rest -a fc.lpccseed.surf.lh




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--
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gr...@nmr.mgh.harvard.edu <mailto: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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www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
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Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3() failed\n

2016-07-08 Thread Douglas N Greve

Is matlab in your path? What  happens if you type
which matlab
at the command line?

On 07/08/2016 12:34 AM, ERIK JAHNER wrote:
>
> Hello FreeSurfer Developers,
>
>
> This is Erik Jahner, I’m attempting to complete the final step in the 
> tutorial concerning FSFast Functional connectivity walkthrough 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
>  ), 
> but for I get the following error when I run the following command:
>
> selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lh
>
>
> Mon Jul  4 11:01:41 PDT 2016
>
> rawfunc2surf-sess completed
>
> 
>
> Started at Mon Jul 4 11:01:40 PDT 2016
>
> Ended   at Mon Jul  4 11:01:41 PDT 2016
>
> preproc-sess done
>
> ---
>
> /Applications/freesurfer/LagStructure/subj439rest
>
> Mon Jul  4 11:01:41 PDT 2016
>
> anadir = 
> /Applications/freesurfer/LagStructure/subj439rest/rest/fc.lpccseed.surf.lh
>
> DoGLMFit = 1
>
> DoContrasts = 1
>
> UpdateNeeded = 1
>
> --
>
> --- matlab output 
>
> matlab: Command not found.
>
> --
>
> *ERROR: fast_selxavg3() failed\n*
>
>
> I've searched the list and no similar errors have been reported. I 
> have tried to reinstall MATLAB; I have tried following the 
> instructions to install the runtime environment; I have tried redoing 
> all analysis from scratch. I have noticed that STEP 5 does not work 
> unless I change the -cfg from “L_Posteriorcingulate.config” 
> to “mean.L_Posteriorcingulate.config”. I don’t think this is the 
> problem, but I thought I would point it out.
>
> My session directory is “subj439rest”
>
> Instead of titling the sub directory “bold”, I titled it “rest”
>
>
> 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> 2) Platform: OSX Yousemite
>
> 3) uname -a: Darwin ERIKs-iMac.local 15.5.0 Darwin Kernel Version 
> 15.5.0: Tue Apr 19 18:36:36 PDT 2016; 
> root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
>
> 4) selxavg3-sess-rest-fc.lpccseed.surf.lh-160704110140.log: see attached
>
> ___
>
> Here are the command lines I put in for steps 4-8, incase this is of 
> some use:
>
> STEP 4
>
> fcseed-config-segid 1010 -fcname L_Posteriorcingulate.dat -fsd rest 
> -mean-cfg mean.L_Posteriorcingulate.config
>
> STEP 5
>
> fcseed-sess-s subj439rest -cfg mean.L_Posteriorcingulate.config
>
> STEP 6
>
>   * fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config
>   * fcseed-sess -s subj439rest -cfg wm.config
>
>   * fcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config
>   * fcseed-sess -s subj439rest -cfg vcsf.config
>
> STEP7
>
> mkanalysis-sess-analysis fc.lpccseed.surf.lh -surface fsaverage lh 
> -fwhm 5 -notask-taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 
> -nuisreg wm.dat 5 -mcextreg-polyfit 5 -nskip 4 -fsd rest -TR 2 -per-run
>
> STEP 8
>
> selxavg3-sess-s subj439rest -a fc.lpccseed.surf.lh
>
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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-- 
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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/

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[Freesurfer] FSFAST error: ERROR: fast_selxavg3() failed\n

2016-07-07 Thread ERIK JAHNER

Hello FreeSurfer Developers, This is Erik Jahner, I’m attempting to complete the final step in the tutorial concerning FSFast Functional connectivity walkthrough (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough ), but for I get the following error when I run the following command:selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lhMon Jul  4 11:01:41 PDT 2016rawfunc2surf-sess completed Started at Mon Jul 4 11:01:40 PDT 2016Ended   at Mon Jul  4 11:01:41 PDT 2016preproc-sess done---/Applications/freesurfer/LagStructure/subj439restMon Jul  4 11:01:41 PDT 2016anadir = /Applications/freesurfer/LagStructure/subj439rest/rest/fc.lpccseed.surf.lhDoGLMFit = 1DoContrasts = 1UpdateNeeded = 1- matlab output matlab: Command not found.--ERROR: fast_selxavg3() failed\n I've searched the list and no similar errors have been reported. I have tried to reinstall MATLAB; I have tried following the instructions to install the runtime environment; I have tried redoing all analysis from scratch. I have noticed that STEP 5 does not work unless I change the -cfg from “L_Posteriorcingulate.config” to “mean.L_Posteriorcingulate.config”. I don’t think this is the problem, but I thought I would point it out. My session directory is “subj439rest”Instead of titling the sub directory “bold”, I titled it “rest” 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.02) Platform: OSX Yousemite3) uname -a: Darwin ERIKs-iMac.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_644) selxavg3-sess-rest-fc.lpccseed.surf.lh-160704110140.log: see attached___Here are the command lines I put in for steps 4-8, incase this is of some use:STEP 4fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd rest -mean -cfg mean.L_Posteriorcingulate.configSTEP 5fcseed-sess  -s subj439rest -cfg mean.L_Posteriorcingulate.configSTEP 6fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config fcseed-sess -s subj439rest -cfg wm.configfcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config fcseed-sess -s subj439rest -cfg vcsf.configSTEP7mkanalysis-sess -analysis fc.lpccseed.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5  -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR 2 -per-runSTEP 8selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lhselxavg3-sess log file
/Applications/freesurfer/fsfast/bin/selxavg3-sess
-s subj439rest -a fc.lpccseed.surf.lh
$Id: selxavg3-sess,v 1.57.2.1 2011/12/09 20:06:47 greve Exp $
uid=0(root) gid=0(wheel) 
groups=0(wheel),701(com.apple.sharepoint.group.1),1(daemon),2(kmem),3(sys),4(tty),5(operator),8(procview),9(procmod),12(everyone),20(staff),29(certusers),61(localaccounts),80(admin),702(com.apple.sharepoint.group.2),33(_appstore),98(_lpadmin),100(_lpoperator),204(_developer),395(com.apple.access_ftp),101(com.apple.access_screensharing-disabled),399(com.apple.access_ssh)
/Applications/freesurfer/LagStructure
Darwin ERIKs-iMac.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 
18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
Mon Jul  4 11:01:40 PDT 2016
preproc-sess -s subj439rest -d /Applications/freesurfer/LagStructure -a 
fc.lpccseed.surf.lh -nolog
--
preproc-sess logfile is /dev/null
--
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
root
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
Darwin ERIKs-iMac.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 
18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
/Applications/freesurfer/LagStructure
/Applications/freesurfer/fsfast/bin/preproc-sess
-s subj439rest -d /Applications/freesurfer/LagStructure -a fc.lpccseed.surf.lh 
-nolog
Mon Jul  4 11:01:40 PDT 2016
instem   f 
mc   1 f fmcpr 
stc  0 fmcpr
sm   0   
mask 1   brain
subj439rest Template -
mktemplate-sess -s subj439rest -d /Applications/freesurfer/LagStructure -fsd 
rest -nolog -update
 
Session: /Applications/freesurfer/LagStructure/subj439rest 
Mon Jul  4 11:01:40 PDT 2016
Detected input format at nii.gz
subj439rest Update not needed
  Run: 007 
  Mon Jul  4 11:01:40 PDT 2016
  subj439rest 007 Update not needed
Mon Jul  4 11:01:40 PDT 2016
mktemplate-sess completed 
subj439rest Mask 
mkbrainmask-sess -maskstem brain -fsd rest -s subj439rest -d 
/Applications/freesurfer/LagStructure -nolog -update

/Applications/freesurfer/LagStructure/subj439rest 
Mon Jul  4 11

Re: [Freesurfer] FSFAST- Cerebellum

2016-07-06 Thread Douglas N Greve

What is the problem with the orientation? The little letters indicate 
that the orientation is correct. fslview ignores the orientation when 
displaying so it might come out upside down.

On 07/05/2016 01:35 PM, Sabin Khadka wrote:
>
> Hi Doug, As you suggested I mapped fmri into the anatomical space using
>
> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o 
> fmcpr.anat.nii.gz
>
> The orientation of fmcpr.anat.nii.gz seem to have some problem (see 
> below). However the label seems to be correct. I am a bit confused 
> here. Do I need to tranform the file somehow?
>
> fmcpr.nii.gz
>
> Inline image 1
>
> fmcpr.anat.nii.gz
>
> Inline image 2
>
>
>
> Cheers,
> Sabin Khadka
>
> On Thu, Jun 23, 2016 at 11:28 AM, Douglas Greve 
> > wrote:
>
> After you run preproc-sess, there will be a file called
> register.dof6.dat. Map fmri into the anatomical space, something like
>
> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat
> --o fmcpr.anat.nii.gz
>
> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
>
> However, I don't think that the aseg has those cerebellum
> parcellations.
>
> On 6/21/16 5:52 PM, Sabin Khadka wrote:
>> Hi Yeo- Thanks very much for your answer. Yes the data is in
>> mni305 space. I process my fmri data with
>>
>> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
>> -fwhm 6 -per-run -stc odd
>> and then to extract ROI time series values I did
>>
>> mri_segstats --annot fsaverage rh aparc --i
>> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid
>> 2000 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>>
>> and for cortical time series
>>
>> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
>> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12
>> --id 13 --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52
>> --id 53 --id 54 --id 58 --i
>> rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
>> subCorticalTimeSeries.txt
>>
>> Now I am not sure as how to extract cerebellum ROIs (time series
>> as described in Buckner et.al  2011)? If there are
>> any other additional steps I need to perform ? or if I have to
>> use some other scripts commands (other than mri_segstats).
>>
>>
>> Cheers,
>> Sabin Khadka
>>
>> On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo
>> > wrote:
>>
>> Hi Sabin,
>>
>> The structures 601-628 FreeSurferCololLUT.txt correspond to
>> anatomical
>> substructures of the cerebellum (e.g., Crus I, etc). Is that
>> what you
>> want? Or are you looking to use the functional parcels defined in
>> Buckner 2011?
>>
>> In addition, I do not know how mri_segstats works, so I
>> cannot verify
>> how you call the command is correct. Maybe others can provide
>> feedback
>> here.
>>
>> However, the Buckner cerebellar parcellations in
>> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is
>> in MNI152
>> space. From your command, I assume your data is in MNI305
>> space. So
>> you might need to transform the parcellation from MNI152 to
>> MNI305.
>>
>> Thanks,
>> Thomas
>>
>> On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka
>> >
>> wrote:
>> > Hi all,
>> >
>> > I am trying to extract mean time series BOLD data using
>> FSFAST from Cortical
>> > ROIs + sub cortical ROIs and cerebellum.
>> >
>> > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh
>> -mni305 -fwhm 6
>> > -per-run -stc oddmri_segstats --annot fsaverage lh
>> aparc --i
>> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz
>> --excludeid 1000
>> > --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
>> > mri_segstats --annot fsaverage rh aparc --i
>> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz
>> --excludeid 2000
>> > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>> >
>> > and for cortical time series
>> >
>> > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
>> > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id
>> 12 --id 13 --id
>> > 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53
>> --id 54 --id 58
>> > --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
>> > subCorticalTimeSeries.txt
>> >
>> > But I am not sure on how exactly to extract time series
>> from cerebellar
>> > regions. So if I want to extract time series from regions
>>

Re: [Freesurfer] FSFAST time series extraction

2016-07-06 Thread Sabin Khadka

Hi Doug,

Yes. Dr. Yeo Thomas helped me figuring out ways to extract ROI values from
Buckner 2011 7 Cerebellar network. Please see below for the steps I
performed to extract time series from Buckner 2011 7 Cerebellar networks.
If you could give your thoughts on the steps/process that'd be great.

*1. Run MNI152 1mm template through recon-all*
recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
Yeo2011_MNI152_FS
recon-all -all Yeo2011_MNI152_FS

*2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to
freesurfe nonlinear volumetric space*
mri_vol2vol --mov
$FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
\
--s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest

*3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear*
volumetric space to each subject:
mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ
BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o
Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph


*4. Create a cerebellum gray matter mask in the native subject's space by
applying mri_binarize to aparc2009s+aseg.mgz of the subject*

mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8  --o
cerebellum_mask_FSSub_m8.nii.gz #  For left
mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 47 --o
cerebellum_mask_FSSub_m47.nii.gz #  FOr right


*5. Using this mask to mask the Buckner cerebellum parcellations*

fslmaths Buckner2011_atlas_FSSub.nii.gz -mas
cerebellum_mask_FSSub_m8.nii.gz Buckner_atlas_FSSub_m8.nii.gz #  For
left
fslmaths Buckner2011_atlas_FSSub.nii.gz -mas
cerebellum_mask_FSSub_m47.nii.gz Buckner_atlas_FSSub_m47.nii.gz #  For
right

*6. Functional data to anatomical space*

mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
fmcpr.anat.nii.gz #  functional into anatomical space

*7. Extract L/R Cerebellar ROIs time series*

 mri_segstats --seg
{analysisrootdir}/analysis/Buckner_atlas_FSSub_m8.nii.gz   --ctab
$FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt
--excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_L.txt #
 extract Left Cerebellum time series
mri_segstats --seg
{analysisrootdir}/analysis/Buckner_atlas_FSSub_m47.nii.gz  --ctab
$FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt
--excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_R.txt #
 extract right Cerebellum time series

Cheers,
Sabin Khadka

On Tue, Jul 5, 2016 at 3:48 PM, Douglas N Greve 
wrote:

> has this question been answered?
>
> On 06/17/2016 09:42 AM, curry_sa...@yahoo.com wrote:
> > Hi all,
> >
> > I am trying to extract mean time series BOLD data using FSFAST from
> > Cortical ROIs + sub cortical ROIs and cerebellum.
> >
> > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
> > -fwhm 6 -per-run -stc oddmri_segstats --annot fsaverage lh aparc
> > --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid
> > 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
> > mri_segstats --annot fsaverage rh aparc --i
> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
> >
> > and for cortical time series
> >
> > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
> > --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id
> > 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz
> > --avgwf subCorticalTimeSeries.txt
> >
> > But I am not sure on how exactly to extract time series from
> > cerebellar regions. So if I want to extract time series from regions
> > as described in Buckner et.al 2011. Could I just use mri_segstats for
> > the labels 601-628 in FreeSurferCololLUT.txt? If not could you please
> > direct me to processes that I can use.
> >
> >
> >
> > Sent from Yahoo Mail. Get the ap 
> >
> >
> > ___
> > 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

Re: [Freesurfer] FSFAST time series extraction

2016-07-05 Thread Douglas N Greve

has this question been answered?

On 06/17/2016 09:42 AM, curry_sa...@yahoo.com wrote:
> Hi all,
>
> I am trying to extract mean time series BOLD data using FSFAST from 
> Cortical ROIs + sub cortical ROIs and cerebellum.
>
> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 
> -fwhm 6 -per-run -stc oddmri_segstats --annot fsaverage lh aparc 
> --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 
> 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
> mri_segstats --annot fsaverage rh aparc --i 
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 
> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>
> and for cortical time series
>
> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab 
> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 
> --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 
> 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz 
> --avgwf subCorticalTimeSeries.txt
>
> But I am not sure on how exactly to extract time series from 
> cerebellar regions. So if I want to extract time series from regions 
> as described in Buckner et.al 2011. Could I just use mri_segstats for 
> the labels 601-628 in FreeSurferCololLUT.txt? If not could you please 
> direct me to processes that I can use.
>
>
>
> Sent from Yahoo Mail. Get the ap 
>
>
> ___
> 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/

___
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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
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Re: [Freesurfer] FSFAST- Cerebellum

2016-06-30 Thread Thomas Yeo

Hi Sabin,

I think fslmeants should work. But you might need to first run
mri_binarize to convert Buckner_atlas_FSSub.nii.gz into individual
ROIs.

Also can you tell us which step generated the error "ERROR: must
specify a segmentation volume"? Is this the final step? Have you tried
overlaying Buckner_atlas_FSSub.nii.gz onto your individual subject in
freeview to check that the previous steps have worked?

Thanks,
Thomas

On Mon, Jun 27, 2016 at 6:53 PM, Sabin Khadka  wrote:
> Hi Thomas- On second thought is it valid to simply do if I want average time
> series of the cerebellum regions?
>
> fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >>
> avgCerebellum.txt
>
> Is this correct?
>
>
> Cheers,
> Sabin Khadka
>
> On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka 
> wrote:
>>
>> Hi Thomas and Doug-
>>
>> Thanks for you suggestions. Per your suggestions I performed following
>>
>> recon-all -i
>> $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz
>> -subjid Yeo2011_MNI152_FS
>>
>> recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS
>>
>> mri_vol2vol --mov
>> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>> \
>> --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
>> talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest
>>
>> mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ
>> BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o
>> Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph
>>
>> mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --match 47 --o
>> cerebellum_mask_FSSub.nii.gz
>>
>> fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub.nii.gz
>> Buckner_atlas_FSSub
>>
>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
>> fmcpr.anat.nii.gz
>>
>> mri_segstats --i Buckner_atlas_FSSub.nii.gz --i fmcpr.anat.nii.gz --avgwf
>> test.txt
>>
>> However, I got the following error
>> ERROR: must specify a segmentation volume
>>
>> Am I doing anything wrong here. Do you have any suggestions/fixes?
>>
>>
>> Cheers,
>> Sabin Khadka
>>
>> On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo  wrote:
>>>
>>> Hi Doug, thanks.
>>>
>>> Hi Sabin, you can use the following steps to transform the Buckner
>>> cerebellum atlas to your subject's native anatomical space and then
>>> follow Doug's instructions (taken and adapted from another user
>>> Bronwyn's email):
>>>
>>> 1. Run MNI152 1mm template through recon-all
>>> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
>>> Yeo2011_MNI152_FS
>>>
>>> 2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer
>>> nonlinear volumetric space
>>> mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ
>>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
>>> BucknerAtlas1mm_FSI.nii.gz --nearest
>>>
>>> 3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear
>>> volumetric space to each subject:
>>> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
>>> BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o
>>> Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph
>>>
>>> 4. Create a cerebellum gray matter mask in the native subject's space
>>> by applying mri_binarize to aparc+aseg.mgz of the subject
>>> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o
>>> cerebellum_mask_subjID.nii.gz
>>>
>>> 5. Using this mask to mask the Buckner cerebellum parcellations
>>> fslmaths Buckner2011_atlas_subjID.nii.gz -mas
>>> cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz
>>>
>>> Regards,
>>> Thomas
>>>
>>> On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve
>>>  wrote:
>>> > yes
>>> >
>>> >
>>> >
>>> > On 6/24/16 9:19 AM, Thomas Yeo wrote:
>>> >>
>>> >> Hi Doug,
>>> >>
>>> >> Would your mri_segstats command work if instead of aseg.mgz, Sabin
>>> >> passed in the cerbellum parcellation in the same anatomical space as
>>> >> aseg?
>>> >>
>>> >> --Thomas
>>> >>
>>> >> On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve
>>> >>  wrote:
>>> >>>
>>> >>> After you run preproc-sess, there will be a file called
>>> >>> register.dof6.dat.
>>> >>> Map fmri into the anatomical space, something like
>>> >>>
>>> >>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
>>> >>> fmcpr.anat.nii.gz
>>> >>>
>>> >>> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
>>> >>>
>>> >>> However, I don't think that the aseg has those cerebellum
>>> >>> parcellations.
>>> >>>
>>> >>> On 6/21/16 5:52 PM, Sabin Khadka wrote:
>>> >>>
>>> >>> Hi Yeo- Thanks very much for your answer. Yes the data is in mni305
>>> >>> space. I
>>> >>> process my fmri data with
>>> >>>
>>> >>> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
>>> >>> -fwhm 6
>>> >>>

Re: [Freesurfer] FSFAST- Cerebellum

2016-06-27 Thread Sabin Khadka

Hi Thomas- On second thought is it valid to simply do if I want average
time series of the cerebellum regions?

fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >>
avgCerebellum.txt

Is this correct?


Cheers,
Sabin Khadka

On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka 
wrote:

> Hi Thomas and Doug-
>
> Thanks for you suggestions. Per your suggestions I performed following
>
> recon-all -i
> $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz
> -subjid Yeo2011_MNI152_FS
>
> recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS
>
> mri_vol2vol --mov
> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> \
> --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
> talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest
>
> mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ
> BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o
> Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph
>
> mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --match 47 --o
> cerebellum_mask_FSSub.nii.gz
>
> fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub.nii.gz
> Buckner_atlas_FSSub
>
> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
> fmcpr.anat.nii.gz
>
> mri_segstats --i Buckner_atlas_FSSub.nii.gz --i fmcpr.anat.nii.gz --avgwf
> test.txt
>
> However, I got the following error
> ERROR: must specify a segmentation volume
>
> Am I doing anything wrong here. Do you have any suggestions/fixes?
>
>
> Cheers,
> Sabin Khadka
>
> On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo  wrote:
>
>> Hi Doug, thanks.
>>
>> Hi Sabin, you can use the following steps to transform the Buckner
>> cerebellum atlas to your subject's native anatomical space and then
>> follow Doug's instructions (taken and adapted from another user
>> Bronwyn's email):
>>
>> 1. Run MNI152 1mm template through recon-all
>> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
>> Yeo2011_MNI152_FS
>>
>> 2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer
>> nonlinear volumetric space
>> mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ
>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
>> BucknerAtlas1mm_FSI.nii.gz --nearest
>>
>> 3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear
>> volumetric space to each subject:
>> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
>> BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o
>> Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph
>>
>> 4. Create a cerebellum gray matter mask in the native subject's space
>> by applying mri_binarize to aparc+aseg.mgz of the subject
>> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o
>> cerebellum_mask_subjID.nii.gz
>>
>> 5. Using this mask to mask the Buckner cerebellum parcellations
>> fslmaths Buckner2011_atlas_subjID.nii.gz -mas
>> cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz
>>
>> Regards,
>> Thomas
>>
>> On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve
>>  wrote:
>> > yes
>> >
>> >
>> >
>> > On 6/24/16 9:19 AM, Thomas Yeo wrote:
>> >>
>> >> Hi Doug,
>> >>
>> >> Would your mri_segstats command work if instead of aseg.mgz, Sabin
>> >> passed in the cerbellum parcellation in the same anatomical space as
>> >> aseg?
>> >>
>> >> --Thomas
>> >>
>> >> On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve
>> >>  wrote:
>> >>>
>> >>> After you run preproc-sess, there will be a file called
>> >>> register.dof6.dat.
>> >>> Map fmri into the anatomical space, something like
>> >>>
>> >>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
>> >>> fmcpr.anat.nii.gz
>> >>>
>> >>> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
>> >>>
>> >>> However, I don't think that the aseg has those cerebellum
>> parcellations.
>> >>>
>> >>> On 6/21/16 5:52 PM, Sabin Khadka wrote:
>> >>>
>> >>> Hi Yeo- Thanks very much for your answer. Yes the data is in mni305
>> >>> space. I
>> >>> process my fmri data with
>> >>>
>> >>> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
>> -fwhm 6
>> >>> -per-run -stc odd
>> >>> and then to extract ROI time series values I did
>> >>>
>> >>> mri_segstats --annot fsaverage rh aparc --i
>> >>> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
>> >>> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>> >>>
>> >>> and for cortical time series
>> >>>
>> >>> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
>> >>> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
>> >>> --id
>> >>> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54
>> --id
>> >>> 58
>> >>> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
>> >>> subCorticalTimeSeries.txt

Re: [Freesurfer] FSFAST- Cerebellum

2016-06-27 Thread Sabin Khadka

Hi Thomas and Doug-

Thanks for you suggestions. Per your suggestions I performed following

recon-all -i
$FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz
-subjid Yeo2011_MNI152_FS

recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS

mri_vol2vol --mov
$FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
\
--s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest

mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ
BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o
Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph

mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --match 47 --o
cerebellum_mask_FSSub.nii.gz

fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub.nii.gz
Buckner_atlas_FSSub

mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
fmcpr.anat.nii.gz

mri_segstats --i Buckner_atlas_FSSub.nii.gz --i fmcpr.anat.nii.gz --avgwf
test.txt

However, I got the following error
ERROR: must specify a segmentation volume

Am I doing anything wrong here. Do you have any suggestions/fixes?


Cheers,
Sabin Khadka

On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo  wrote:

> Hi Doug, thanks.
>
> Hi Sabin, you can use the following steps to transform the Buckner
> cerebellum atlas to your subject's native anatomical space and then
> follow Doug's instructions (taken and adapted from another user
> Bronwyn's email):
>
> 1. Run MNI152 1mm template through recon-all
> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
> Yeo2011_MNI152_FS
>
> 2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer
> nonlinear volumetric space
> mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ
> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
> BucknerAtlas1mm_FSI.nii.gz --nearest
>
> 3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear
> volumetric space to each subject:
> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
> BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o
> Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph
>
> 4. Create a cerebellum gray matter mask in the native subject's space
> by applying mri_binarize to aparc+aseg.mgz of the subject
> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o
> cerebellum_mask_subjID.nii.gz
>
> 5. Using this mask to mask the Buckner cerebellum parcellations
> fslmaths Buckner2011_atlas_subjID.nii.gz -mas
> cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz
>
> Regards,
> Thomas
>
> On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve
>  wrote:
> > yes
> >
> >
> >
> > On 6/24/16 9:19 AM, Thomas Yeo wrote:
> >>
> >> Hi Doug,
> >>
> >> Would your mri_segstats command work if instead of aseg.mgz, Sabin
> >> passed in the cerbellum parcellation in the same anatomical space as
> >> aseg?
> >>
> >> --Thomas
> >>
> >> On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve
> >>  wrote:
> >>>
> >>> After you run preproc-sess, there will be a file called
> >>> register.dof6.dat.
> >>> Map fmri into the anatomical space, something like
> >>>
> >>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
> >>> fmcpr.anat.nii.gz
> >>>
> >>> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
> >>>
> >>> However, I don't think that the aseg has those cerebellum
> parcellations.
> >>>
> >>> On 6/21/16 5:52 PM, Sabin Khadka wrote:
> >>>
> >>> Hi Yeo- Thanks very much for your answer. Yes the data is in mni305
> >>> space. I
> >>> process my fmri data with
> >>>
> >>> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
> -fwhm 6
> >>> -per-run -stc odd
> >>> and then to extract ROI time series values I did
> >>>
> >>> mri_segstats --annot fsaverage rh aparc --i
> >>> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> >>> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
> >>>
> >>> and for cortical time series
> >>>
> >>> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> >>> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
> >>> --id
> >>> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id
> >>> 58
> >>> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
> >>> subCorticalTimeSeries.txt
> >>>
> >>> Now I am not sure as how to extract cerebellum ROIs (time series as
> >>> described in Buckner et.al 2011)? If there are any other additional
> steps
> >>> I
> >>> need to perform ? or if I have to use some other scripts commands
> (other
> >>> than mri_segstats).
> >>>
> >>>
> >>> Cheers,
> >>> Sabin Khadka
> >>>
> >>> On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo 
> >>> wrote:
> 
>  Hi Sabin,
> 
>  The structures 601-628

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