[Freesurfer] mri_glmfi-sim multi-thread

2017-11-16 Thread Dowling, Kevin Francis 
Dear Freesurfer Experts,


My apologies for what might be a very simple question, but I have been unable 
to locate an answer in the archives/wiki. Our group is trying to cut down on 
our mri_glmfit-sim time (as we are hoping to run mri_glmfit-sim -sim mc-full, 
rather than -sim mc-z). I know that --bg will split up the larger number of 
simulations into n background jobs, but I also noted the warning that this 
option is not to be used on the Martinos launchpad computational cluster. As we 
are hoping to find a way to use launchpad, I was wondering if mri_glmfit-sim is 
multi-threaded (or can be multi-threaded similar to -parallel flag in 
recon-all)?


We are currently running Freesurfer 5.3, but can move up to 6.0 if needed. (Our 
specific command is: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../glmdir --sim 
mc-full 2.3 1000 mcfull1000_2.3 --sim-sign abs --cwpvalthresh .05)


Thank you in advance for your help!


Kind regards,

Kevin


Kevin F. Dowling
Clinical Research Coordinator
Brain Genomics Laboratory
Division of Psychiatric Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA, 02129
(p) 617.643.3215
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Re: [Freesurfer] [Talairach failed when striping skull]

2017-11-16 Thread Yi Li 
Dear Douglas,

This fails just on this one. Image seems good. I attached it in the previous 
mail but being held. Thanks!

Best Regards,
Yi


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Thursday, November 16, 2017 11:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [Talairach failed when striping skull]

does this fail on all your subjects or just this one? Have you looked at the 
input image to make sure that there is nothing wrong with it?


On 11/16/2017 11:32 AM, Yi Li wrote:
> Hi FS expert,
>
> When I run recon-all -autorecon1 -subjid , the Talaitach transform 
> failed. Please see the attached log file. Is there a way to correct the 
> error? Thanks!
>
> Best Regards,
> Yi
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Monday, November 13, 2017 5:48 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] [strip skull for unregistered images]
>
> Hi Yi
>
> yes, brainmask.mgz is the skull stripped image.
>
> And no, n3 is pretty gentle so I would think letting our normal intensity 
> normalization run would be fine (and better than not doing it)
>
> cheers
> Bruce
>
>
> On Mon, 13 Nov 2017, Yi Li
> wrote:
>
>> Hi Bruce,
>>
>> Thanks for the help! Is the skull-stripped image in Brainmask.mgz?
>>
>> Another question: since my raw image has gone through B1 correction
>> and
>> N3 normalization, will you suggest I omit the nu and normalize step in
>> -autorecon1?
>>
>> Best Regards,
>> Yi
>>
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
>> Fischl
>> Sent: Monday, November 13, 2017 10:50 AM
>> To: Freesurfer support list 
>> Subject: Re: [Freesurfer] [strip skull for unregistered images]
>>
>> Hi Yi
>>
>> autorecon1 should do the skull stripping, so there is no need for the
>> separate mri_mask call. The threshold of '5' is so to preserve edits
>> in which voxels are turned 'off' (they are set to 1 I believe, but we
>> reserve
>> 2-4 as additional 'off' values).
>>
>> The masking will not transform the voxel coordinates of the image
>>
>> cheers
>> Bruce
>>
>>
>>   On Mon, 13 Nov 2017, Yi Li wrote:
>>
>>> Dear FS experts,
>>>
>>>   
>>>
>>> I would like to strip skulls from unregistered images which have gone
>>> through GradWarp, B1-correction, N3 normalization and phantom-based scaling.
>>> I run the following two commands in freeSurfer:
>>>
>>> recon-all -autorecon1 -subjid 
>>>
>>> mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz
>>>
>>>   
>>>
>>> My questions are
>>>
>>> 1)  Currently I use 5 as threshold (-T 5). Is there a guidance
>>> for the setting of this parameter?
>>>
>>> 2)  In the output file T1.final.mgz, is the skull-stripped image
>>> represented in ijk space (image index space) or in XYZ space (via
>>> transformation matrix)?
>>>
>>> 3)  If the skull-stripped image is represented in XYZ space, how
>>> do I get it in ijk space?
>>>
>>>   
>>>
>>> Thanks in advance for the help!
>>>
>>>   
>>>
>>> Best Regards,
>>>
>>> Yi Li (PhD)
>>>
>>> Senior Computational Scientist
>>>
>>> Computational Sciences
>>>
>>> The Jackson Laboratory
>>>
>>> Farmington, CT 06032
>>>
>>> Tel: 860-837-2156
>>>
>>>   
>>>
>>> ---
>>>
>>> The information in this email, including attachments, may be
>>> confidential and is intended solely for the addressee(s). If you
>>> believe you received this email by mistake, please notify the sender
>>> by return email as soon as possible.
>>>
>> ---
>>
>> The information in this email, including attachments, may be confidential 
>> and is intended solely for the addressee(s). If you believe you received 
>> this email by mistake, please notify the sender by return email as soon as 
>> possible.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> ---
>
> The information in this email, including attachments, may be confidential and 
> is intended solely for the addressee(s). If you believe you received this 
> email by mistake, please notify the sender by return email as soon as 
> possible.
>
>
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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/

Re: [Freesurfer] make_average_subject error

2017-11-16 Thread Duran, Tugce 
Please see the attached log file. 

Thanks,
Tugce

On 11/16/17, 11:35 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N Greve"  wrote:

can you send the entire log file?


On 11/16/2017 11:32 AM, Duran, Tugce wrote:
>
> Dear FreeSurfer Experts,
>
> I’m recently getting an error in make_average_subject and can’t find 
> the reason.
>
> Please see the following for the error log from recon-all.log:
>
> *Loading aseg from 
> 
/gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISED_DEOBLIQUE_FREESURFER60_DEFAULT_KARST_10092017_RES/fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop/mri/aseg.presurf.hypos.mgz*
>
> *ASeg Vox2RAS: ---*
>
> *-1.0 0.0   0.0   128.0;*
>
> *0.0 0.0   1.0  -128.0;*
>
> *0.0 -1.0   0.0   128.0;*
>
> *0.0 0.0   0.0   1.0;*
>
> *mghRead(mri/norm.mgz, -1): could not open file*
>
> *-*
>
> **
>
> *Labeling Slice*
>
> *relabeling unlikely voxels in interior of white matter*
>
> *mri/norm.mgz: could not load norm volume from (null)*
>
> **
>
> *Linux i1.karst.uits.iu.edu 2.6.32-696.13.2.el6.x86_64 #1 SMP Fri Sep 
> 22 12:32:14 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux*
>
> **
>
> *recon-all -s 
> fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop 
> exited with ERRORS at Wed Nov 15 19:14:17 EST 2017*
>
> **
>
> **
>
> It appears that during the process it doesn’t create the norm.mgz file 
> to read or open it in the later processes (I think?). What can I do to 
> fix this error?
>
> Thanks,
>
> Tugce**
>
>
>
> ___
> 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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The information in this e-mail is intended only for the person to whom it is
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e-mail
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recon-all.log
Description: recon-all.log
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] [Talairach failed when striping skull]

2017-11-16 Thread Douglas N Greve 
does this fail on all your subjects or just this one? Have you looked at 
the input image to make sure that there is nothing wrong with it?


On 11/16/2017 11:32 AM, Yi Li wrote:
> Hi FS expert,
>
> When I run recon-all -autorecon1 -subjid , the Talaitach transform 
> failed. Please see the attached log file. Is there a way to correct the 
> error? Thanks!
>
> Best Regards,
> Yi
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Monday, November 13, 2017 5:48 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] [strip skull for unregistered images]
>
> Hi Yi
>
> yes, brainmask.mgz is the skull stripped image.
>
> And no, n3 is pretty gentle so I would think letting our normal intensity 
> normalization run would be fine (and better than not doing it)
>
> cheers
> Bruce
>
>
> On Mon, 13 Nov 2017, Yi Li
> wrote:
>
>> Hi Bruce,
>>
>> Thanks for the help! Is the skull-stripped image in Brainmask.mgz?
>>
>> Another question: since my raw image has gone through B1 correction
>> and
>> N3 normalization, will you suggest I omit the nu and normalize step in
>> -autorecon1?
>>
>> Best Regards,
>> Yi
>>
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
>> Fischl
>> Sent: Monday, November 13, 2017 10:50 AM
>> To: Freesurfer support list 
>> Subject: Re: [Freesurfer] [strip skull for unregistered images]
>>
>> Hi Yi
>>
>> autorecon1 should do the skull stripping, so there is no need for the
>> separate mri_mask call. The threshold of '5' is so to preserve edits
>> in which voxels are turned 'off' (they are set to 1 I believe, but we
>> reserve
>> 2-4 as additional 'off' values).
>>
>> The masking will not transform the voxel coordinates of the image
>>
>> cheers
>> Bruce
>>
>>
>>   On Mon, 13 Nov 2017, Yi Li wrote:
>>
>>> Dear FS experts,
>>>
>>>   
>>>
>>> I would like to strip skulls from unregistered images which have gone
>>> through GradWarp, B1-correction, N3 normalization and phantom-based scaling.
>>> I run the following two commands in freeSurfer:
>>>
>>> recon-all -autorecon1 -subjid 
>>>
>>> mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz
>>>
>>>   
>>>
>>> My questions are
>>>
>>> 1)  Currently I use 5 as threshold (-T 5). Is there a guidance
>>> for the setting of this parameter?
>>>
>>> 2)  In the output file T1.final.mgz, is the skull-stripped image
>>> represented in ijk space (image index space) or in XYZ space (via
>>> transformation matrix)?
>>>
>>> 3)  If the skull-stripped image is represented in XYZ space, how
>>> do I get it in ijk space?
>>>
>>>   
>>>
>>> Thanks in advance for the help!
>>>
>>>   
>>>
>>> Best Regards,
>>>
>>> Yi Li (PhD)
>>>
>>> Senior Computational Scientist
>>>
>>> Computational Sciences
>>>
>>> The Jackson Laboratory
>>>
>>> Farmington, CT 06032
>>>
>>> Tel: 860-837-2156
>>>
>>>   
>>>
>>> ---
>>>
>>> The information in this email, including attachments, may be
>>> confidential and is intended solely for the addressee(s). If you
>>> believe you received this email by mistake, please notify the sender
>>> by return email as soon as possible.
>>>
>> ---
>>
>> The information in this email, including attachments, may be confidential 
>> and is intended solely for the addressee(s). If you believe you received 
>> this email by mistake, please notify the sender by return email as soon as 
>> possible.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> ---
>
> The information in this email, including attachments, may be confidential and 
> is intended solely for the addressee(s). If you believe you received this 
> email by mistake, please notify the sender by return email as soon as 
> possible.
>
>
> ___
> 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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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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Re: [Freesurfer] make_average_subject error

2017-11-16 Thread Douglas N Greve 
can you send the entire log file?


On 11/16/2017 11:32 AM, Duran, Tugce wrote:
>
> Dear FreeSurfer Experts,
>
> I’m recently getting an error in make_average_subject and can’t find 
> the reason.
>
> Please see the following for the error log from recon-all.log:
>
> *Loading aseg from 
> /gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISED_DEOBLIQUE_FREESURFER60_DEFAULT_KARST_10092017_RES/fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop/mri/aseg.presurf.hypos.mgz*
>
> *ASeg Vox2RAS: ---*
>
> *-1.0 0.0   0.0   128.0;*
>
> *0.0 0.0   1.0  -128.0;*
>
> *0.0 -1.0   0.0   128.0;*
>
> *0.0 0.0   0.0   1.0;*
>
> *mghRead(mri/norm.mgz, -1): could not open file*
>
> *-*
>
> **
>
> *Labeling Slice*
>
> *relabeling unlikely voxels in interior of white matter*
>
> *mri/norm.mgz: could not load norm volume from (null)*
>
> **
>
> *Linux i1.karst.uits.iu.edu 2.6.32-696.13.2.el6.x86_64 #1 SMP Fri Sep 
> 22 12:32:14 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux*
>
> **
>
> *recon-all -s 
> fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop 
> exited with ERRORS at Wed Nov 15 19:14:17 EST 2017*
>
> **
>
> **
>
> It appears that during the process it doesn’t create the norm.mgz file 
> to read or open it in the later processes (I think?). What can I do to 
> fix this error?
>
> Thanks,
>
> Tugce**
>
>
>
> ___
> 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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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] [Talairach failed when striping skull]

2017-11-16 Thread Yi Li 
Hi FS expert,

When I run recon-all -autorecon1 -subjid , the Talaitach transform 
failed. Please see the attached log file. Is there a way to correct the error? 
Thanks!

Best Regards,
Yi


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, November 13, 2017 5:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [strip skull for unregistered images]

Hi Yi

yes, brainmask.mgz is the skull stripped image.

And no, n3 is pretty gentle so I would think letting our normal intensity 
normalization run would be fine (and better than not doing it)

cheers
Bruce


On Mon, 13 Nov 2017, Yi Li
wrote:

> Hi Bruce,
>
> Thanks for the help! Is the skull-stripped image in Brainmask.mgz?
>
> Another question: since my raw image has gone through B1 correction 
> and
> N3 normalization, will you suggest I omit the nu and normalize step in 
> -autorecon1?
>
> Best Regards,
> Yi
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Monday, November 13, 2017 10:50 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] [strip skull for unregistered images]
>
> Hi Yi
>
> autorecon1 should do the skull stripping, so there is no need for the 
> separate mri_mask call. The threshold of '5' is so to preserve edits 
> in which voxels are turned 'off' (they are set to 1 I believe, but we 
> reserve
> 2-4 as additional 'off' values).
>
> The masking will not transform the voxel coordinates of the image
>
> cheers
> Bruce
>
>
>  On Mon, 13 Nov 2017, Yi Li wrote:
>
>>
>> Dear FS experts,
>>
>>  
>>
>> I would like to strip skulls from unregistered images which have gone 
>> through GradWarp, B1-correction, N3 normalization and phantom-based scaling.
>> I run the following two commands in freeSurfer:
>>
>> recon-all -autorecon1 -subjid 
>>
>> mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz
>>
>>  
>>
>> My questions are
>>
>> 1)  Currently I use 5 as threshold (-T 5). Is there a guidance 
>> for the setting of this parameter?
>>
>> 2)  In the output file T1.final.mgz, is the skull-stripped image 
>> represented in ijk space (image index space) or in XYZ space (via 
>> transformation matrix)?
>>
>> 3)  If the skull-stripped image is represented in XYZ space, how 
>> do I get it in ijk space?
>>
>>  
>>
>> Thanks in advance for the help!
>>
>>  
>>
>> Best Regards,
>>
>> Yi Li (PhD)
>>
>> Senior Computational Scientist
>>
>> Computational Sciences
>>
>> The Jackson Laboratory
>>
>> Farmington, CT 06032
>>
>> Tel: 860-837-2156
>>
>>  
>>
>> ---
>>
>> The information in this email, including attachments, may be 
>> confidential and is intended solely for the addressee(s). If you 
>> believe you received this email by mistake, please notify the sender 
>> by return email as soon as possible.
>>
> ---
>
> The information in this email, including attachments, may be confidential and 
> is intended solely for the addressee(s). If you believe you received this 
> email by mistake, please notify the sender by return email as soon as 
> possible.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
---

The information in this email, including attachments, may be confidential and 
is intended solely for the addressee(s). If you believe you received this email 
by mistake, please notify the sender by return email as soon as possible.


talairach_avi.log
Description: talairach_avi.log
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] make_average_subject error

2017-11-16 Thread Duran, Tugce 
Dear FreeSurfer Experts,

I’m recently getting an error in make_average_subject and can’t find the reason.
Please see the following for the error log from recon-all.log:

Loading aseg from 
/gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISED_DEOBLIQUE_FREESURFER60_DEFAULT_KARST_10092017_RES/fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
0.0   0.0   1.0  -128.0;
0.0  -1.0   0.0   128.0;
0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from (null)

Linux i1.karst.uits.iu.edu 2.6.32-696.13.2.el6.x86_64 #1 SMP Fri Sep 22 
12:32:14 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 
fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop exited 
with ERRORS at Wed Nov 15 19:14:17 EST 2017


It appears that during the process it doesn’t create the norm.mgz file to read 
or open it in the later processes (I think?). What can I do to fix this error?

Thanks,
Tugce
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Re: [Freesurfer] Optseq and de convolution for rapid designs

2017-11-16 Thread Douglas N Greve 
I don't know about SPM, I would imagine you could do it somehow. FSL has 
an implementation. The deconvolution method is usually called "FIR" 
(finite impulse response)


On 11/16/2017 10:36 AM, fmri2013 wrote:
> Dear Douglas
>
> I will apprecite it if you can please clarify this simple question.
> If I optimise my design using Optseq, do you know if this de 
> convolution process is implemented in SPM or any other software? and 
> it is part of the processing behind the scenes? Or do I have to 
> account for this using a specific software.
>
> Many tha is
>
> Aser
>
>
> Sent from my Samsung Galaxy smartphone.
>
>  Original message 
> From: fmri2013 
> Date: 10/11/2017 19:30 (GMT+00:00)
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Optseq and de convolution for rapid designs
>
> Many thanks Douglas
>
> If I optimise my design using Optseq, do you know if this de 
> convolution process is implemented in SPM or any other software? and 
> it is part of the processing behind th3 scenes?  Or do I have to 
> account for this using a specific software.
>
> Aser
>
>
>
> Sent from my Samsung Galaxy smartphone.
>
>  Original message 
> From: Douglas Greve 
> Date: 10/11/2017 19:24 (GMT+00:00)
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Optseq and de convolution for rapid designs
>
> It is because the random jitter creates differential amounts of 
> overlap. Imagine if you have A=C+D and B=C-D. You know A and B, but 
> you want C and D. You have two equations and two unknowns, so you can 
> solve for C and D from A and B eventhough C and D "overlap" in A and B 
> and you never see C or D by themselves. This is a type of deconvolution
>
>
> On 11/10/17 11:38 AM, Aser A wrote:
>> Hi all
>>
>> I used Optseq  to optimize rapid event designs with multiple 
>> conditions . I have a theortical question : how it is possible to 
>> distingwoh the close by trials ? Is it by de convoution ? How is it 
>> possible to deal with overallped trials ?
>>
>> Is it because the conditions are random so that when averaging them 
>> the distingwoh is possible?
>>
>> Many thanks
>>
>> Aser
>>
>>
>>
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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
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Re: [Freesurfer] Optseq and de convolution for rapid designs

2017-11-16 Thread fmri2013 
Dear Douglas
I will apprecite it if you can please clarify this simple question. If I 
optimise my design using Optseq, do you know if this de convolution process is 
implemented in SPM or any other software? and it is part of the processing 
behind the scenes?  Or do I have to account for this using a specific software. 
Many tha is 
Aser

Sent from my Samsung Galaxy smartphone.
 Original message From: fmri2013  Date: 
10/11/2017  19:30  (GMT+00:00) To: Freesurfer support list 
 Subject: Re: [Freesurfer] Optseq and de 
convolution for rapid designs 
Many thanks Douglas  
If I optimise my design using Optseq, do you know if this de convolution 
process is implemented in SPM or any other software? and it is part of the 
processing behind th3 scenes?  Or do I have to account for this using a 
specific software. 
Aser


Sent from my Samsung Galaxy smartphone.
 Original message From: Douglas Greve 
 Date: 10/11/2017  19:24  (GMT+00:00) To: 
freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Optseq and de 
convolution for rapid designs 

It is because the random jitter creates differential amounts of
  overlap. Imagine if you have A=C+D and B=C-D. You know A and B,
  but you want C and D. You have two equations and two unknowns, so
  you can solve for C and D from A and B eventhough C and D
  "overlap" in A and B and you never see C or D by themselves. This
  is a type of deconvolution




On 11/10/17 11:38 AM, Aser A wrote:



  
Hi all



I used Optseq
   to optimize rapid event designs with multiple conditions . I
  have a theortical question : how it is possible to distingwoh
  the close by trials ? Is it by de convoution ? How is it
  possible to deal with overallped trials ? 



Is it because the
  conditions are random so that when averaging them the distingwoh is
  possible?



Many thanks 



Aser



  
  

  
  

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Re: [Freesurfer] optseq with dependent stim types in a single trial

2017-11-16 Thread Douglas N Greve 
Sorry, those kinds of constraints, ie, requiring some events to be in a 
certain order, are not possible in optseq.


On 11/15/2017 08:44 PM, Michelle VanTieghem wrote:
> Hello,
>
> I am using optseq to optimize a new task. I have been playing around 
> with the examples they have on the documentation. What I can't find is 
> information on how to set up the trial structure when 1 trial is 
> comprised of 3 different stimuli types:
> (choice 3sec --> effort (hard or easy) 3 sec --> feedback 2sec (reward 
> or no reward)
>
> I don't want to consider it all one long trial, because I do want to 
> model these 3 stim types separately with jitter between each of them. 
> So I'm not sure how to set this up within the structure of opt seq, or 
> if it's even possible.
>
> I also don't want to randomize the trial type itself (hard or easy) 
> because that is the participant choice.
>
> I'd greatly appreciate any input!
>
> Thanks,
> Michelle
>
>
> -- 
> Michelle VanTieghem
> PhD student in Psychology
> Developmental Affective Neuroscience Lab
> Columbia University
> mrv2...@columbia.edu 
>
>
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] feeding data not processed with longitudinal pipeline into Linear Mixed Effects (LME) model

2017-11-16 Thread Martin Reuter 
Hi Lara,

yes that is possible (and it also makes sense in early childhood as the 
longitudinal stream assumes no (or only minimal) head growing).

Best, Martin


Am 14.11.2017 um 19:03 schrieb Lara Foland-Ross:
> Hello Freesurfer experts,
>
> I have two longitudinal datasets. In each dataset, some participants have 
> only a single timepoint. For this reason, I aim to run the Linear Mixed 
> Effects (LME) Model described at 
> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels.
>
> I understand that it is recommended that before running LME, I process my 
> data using the longitudinal stream (e.g., 
> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing). However:
>
> 1. in one dataset, some participants were scanned several years apart in 
> early childhood, which caused the intra-subject registration to fail in the 
> longitudinal processing stream
>
> and
>
> 2. in the second dataset, editing of longitudinal timepoints was time 
> prohibitive - several hours of edits were spent per brain at the 
> cross-sectional level due to the use of an older sub-optimal pulse sequence. 
> And, several more hours are required for the editing of each base or 
> longitudinal timepoint.
>
> Given each of these circumstances, is it feasible/appropriate to run LME 
> using data that was not initially processed using the longitudinal processing 
> stream within Freesurfer?
>
> Thanks in advance!
> Lara
>
> Lara Foland-Ross, Ph.D.
> Research Associate and Imaging Lab Manager
> Center for Interdisciplinary Brain Sciences Research
> Stanford University School of Medicine
> 401 Quarry Road, Room 1356
> Stanford, CA 94305-5795
>
>
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