[Freesurfer] Unpacking ASL scans

[Nasiriavanaki, Zahra]

Dear Freesurfer developers


Hi


We collect a new ASL sequence at Bay 4 with Prisma. The scanner outputs a 3D 
mosaic. The problem is that unpacksdcmdir doesn't seem to work correctly on it 
so it results to an error!
Is there any command other than unpacksdcmdir for unpacking the ASL scans?

Thank you
Mona Nasiriavanaki


___
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.

[Freesurfer] Errors in scans

[Nasiriavanaki, Zahra]

Hi Freesufer developers

We are getting some errors in our resting state and ASL scans. Everything goes 
fine while we are scaning the subjects, but when we look at the data in BORGET, 
some of them come out with errors.
I copied one of the scaninfo files, so you can see the errors.
Is there anyway to not get errors? Or shall we just unpack the ok data and go 
on?

Thanks

1   localizer_64ch  ok  512 512   3   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716282052566788535
  2 AAHead_Scout  ok  160 160 128   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716283612565588717
  3 AAHead_Scout  ok  162 162   5   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716284031754889708
  4 AAHead_Scout  ok  162 162   3   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716284031832189712
  5 AAHead_Scout  ok  162 162   3   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716284031887889715
  6 MEMPRAGE  ok  256 256 176   4 
MR.1.3.12.2.1107.5.2.43.67026.2018062716353836176490274
  7 MEMPRAGE  ok  256 256 176   4 
MR.1.3.12.2.1107.5.2.43.67026.2018062716353836150890273
  8 MEMPRAGE  ok  256 256 176   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716353850258890299
  9 fMRI_DistortionMap_PA  ok   92  92  57   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716372672952394688
 10 fMRI_DistortionMap_AP  ok   92  92  57   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716380680499794923
 11 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062716403982376595295
 12 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062716480447089626419
 13 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062716552453255257555
 14 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062717024484181988697
 15 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062717100568938419838
 16 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062717172417291250987
 17 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062717244528886782134
 18 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062717320619207913274
 19 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.201806271739232204744422
 20 tgse_pcasl_optBS_M0_PLD2000  ok   96  96   1  22 
MR.1.3.12.2.1107.5.2.43.67026.2018062717460555193775829
 21 tgse_pcasl_optBS_M0_PLD2000 err   96  96   1   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062717461445002086101
 22 HCP_CMRR_SpinEchoFieldMap_AP  ok  104 104  72   3 
MR.1.3.12.2.1107.5.2.43.67026.2018062717461591061986321
 23 HCP_CMRR_SpinEchoFieldMap_PA  ok  104 104  72   3 
MR.1.3.12.2.1107.5.2.43.67026.2018062717461993800986977
 24 HCP_CMRR_fMRI_rest_AP err  104 104  72   1 
MR.1.3.12.2.1107.5.2.43.67026.201806271747377337919554
 25 HCP_CMRR_fMRI_rest_AP err  104 104  72 216 
MR.1.3.12.2.1107.5.2.43.67026.2018062717473793126919992
 26 HCP_CMRR_fMRI_rest_PA err  104 104  72   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062717540945183412846
 27 HCP_CMRR_fMRI_rest_PA  ok  104 104  72 488 
MR.1.3.12.2.1107.5.2.43.67026.2018062717541118019513248



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


___
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] Errors in scans

[Nasiriavanaki, Zahra]

Hi Doug


Thanks for your reply.

I have not unpacked the error ones!

I will go for it and let you know if there was a problem.




Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Thursday, June 28, 2018 9:57:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Errors in scans

Are the output volumes being created? Do they look ok? Sometimes
unpacksdcmdir will print out an error when there is not actually an
error there (eg, if it does not see the expected number of files, but
some times its expectation is wrong). In dcmunpack (the replacement for
unpacksdcmdir), I don't print out the ok/err because it it not always
reliable.

On 06/28/2018 11:35 AM, Nasiriavanaki, Zahra wrote:
>
> Hi Freesufer developers
>
>
> We are getting some errors in our resting state and ASL
> scans. Everything goes fine while we are scaning the subjects, but
> when we look at the data in BORGET, some of them come out with errors.
> I copied one of the scaninfo files, so you can see the errors.
> Is there anyway to not get errors? Or shall we just unpack the ok data
> and go on?
>
> Thanks
> 1   localizer_64ch  ok  512 512   3   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716282052566788535
>   2 AAHead_Scout  ok  160 160 128   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716283612565588717
>   3 AAHead_Scout  ok  162 162   5   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716284031754889708
>   4 AAHead_Scout  ok  162 162   3   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716284031832189712
>   5 AAHead_Scout  ok  162 162   3   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716284031887889715
>   6 MEMPRAGE  ok  256 256 176   4
> MR.1.3.12.2.1107.5.2.43.67026.2018062716353836176490274
>   7 MEMPRAGE  ok  256 256 176   4
> MR.1.3.12.2.1107.5.2.43.67026.2018062716353836150890273
>   8 MEMPRAGE  ok  256 256 176   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716353850258890299
>   9 fMRI_DistortionMap_PA  ok   92  92  57   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716372672952394688
>  10 fMRI_DistortionMap_AP  ok   92  92  57   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716380680499794923
>  11 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062716403982376595295
>  12 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062716480447089626419
>  13 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062716552453255257555
>  14 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062717024484181988697
>  15 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062717100568938419838
>  16 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062717172417291250987
>  17 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062717244528886782134
>  18 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062717320619207913274
>  19 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.201806271739232204744422
>  20 tgse_pcasl_optBS_M0_PLD2000  ok   96  96   1  22
> MR.1.3.12.2.1107.5.2.43.67026.2018062717460555193775829
> 21 tgse_pcasl_optBS_M0_PLD2000 err   96  96   1   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062717461445002086101
>  22 HCP_CMRR_SpinEchoFieldMap_AP  ok  104 104  72   3
> MR.1.3.12.2.1107.5.2.43.67026.2018062717461591061986321
>  23 HCP_CMRR_SpinEchoFieldMap_PA  ok  104 104  72   3
> MR.1.3.12.2.1107.5.2.43.67026.2018062717461993800986977
> 24 HCP_CMRR_fMRI_rest_AP err  104 104  72   1
> MR.1.3.12.2.1107.5.2.43.67026.201806271747377337919554
>  25 HCP_CMRR_fMRI_rest_AP err  104 104  72 216
> MR.1.3.12.2.1107.5.2.43.67026.2018062717473793126919992
> 26 HCP_CMRR_fMRI_rest_PA err  104 104  72   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062717540945183412846
>  27 HCP_CMRR_fMRI_rest_PA  ok  104 104  72 488
> MR.1.3.12.2.1107.5.2.43.67026.2018062717541118019513248
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

__

[Freesurfer] TPEF error

[Nasiriavanaki, Zahra]

Hi


I am running the connectivity analysis (seed to whole brain), and when I run 
selxavg command, I get this error:


ERROR: time points in 
/autofs/space/oprah_001/users/jvm27/looming/all_subjects/liur_loom2_c_sdp/rest/025/TPEF.txt
 exceed nframes (488)

and the time points do not exceed the number of frames! It is happening for 
most of my subjects.

I am copy ing my tpef file for this run.

Could you please let me know how I should solve it?


Thanks

Mona

TPEF file for run 025:

6
36
50
61
62
74
106
204
245
246
295
297
298
311
312
321
322
323
324
325
330
352
370
378
383
384
385
387
396
397
398
424
431
439
441
442
477
478
479
480











Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


___
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] TPEF error

[Nasiriavanaki, Zahra]

0.8


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Wednesday, July 18, 2018 2:38:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TPEF error

what is your TR?

On 07/18/2018 04:03 PM, Nasiriavanaki, Zahra wrote:
>
> Hi
>
>
> I am running the connectivity analysis (seed to whole brain), and when
> I run selxavg command, I get this error:
>
>
> ERROR: time points in
> /autofs/space/oprah_001/users/jvm27/looming/all_subjects/liur_loom2_c_sdp/rest/025/TPEF.txt
> exceed nframes (488)
>
> and the time points do not exceed the number of frames! It is
> happening for most of my subjects.
>
> I am copy ing my tpef file for this run.
>
> Could you please let me know how I should solve it?
>
>
> Thanks
>
> Mona
>
>
> TPEF file for run 025:
>
> 6
> 36
> 50
> 61
> 62
> 74
> 106
> 204
> 245
> 246
> 295
> 297
> 298
> 311
> 312
> 321
> 322
> 323
> 324
> 325
> 330
> 352
> 370
> 378
> 383
> 384
> 385
> 387
> 396
> 397
> 398
> 424
> 431
> 439
> 441
> 442
> 477
> 478
> 479
> 480
>
>
>
>
>
>
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
>
> ___
> 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
___
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] TPEF error

[Nasiriavanaki, Zahra]

Right!


Thank you Doug



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Wednesday, July 18, 2018 4:02:30 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TPEF error

Each entry in the TPEF is the time in seconds of the frame you want to
exclude. So, time=480 means frame 600 > your number of time points.

On 07/18/2018 04:42 PM, Nasiriavanaki, Zahra wrote:
>
> 0.8
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Douglas N. Greve
> 
> *Sent:* Wednesday, July 18, 2018 2:38:50 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] TPEF error
> what is your TR?
>
> On 07/18/2018 04:03 PM, Nasiriavanaki, Zahra wrote:
> >
> > Hi
> >
> >
> > I am running the connectivity analysis (seed to whole brain), and when
> > I run selxavg command, I get this error:
> >
> >
> > ERROR: time points in
> >
> /autofs/space/oprah_001/users/jvm27/looming/all_subjects/liur_loom2_c_sdp/rest/025/TPEF.txt
> > exceed nframes (488)
> >
> > and the time points do not exceed the number of frames! It is
> > happening for most of my subjects.
> >
> > I am copy ing my tpef file for this run.
> >
> > Could you please let me know how I should solve it?
> >
> >
> > Thanks
> >
> > Mona
> >
> >
> > TPEF file for run 025:
> >
> > 6
> > 36
> > 50
> > 61
> > 62
> > 74
> > 106
> > 204
> > 245
> > 246
> > 295
> > 297
> > 298
> > 311
> > 312
> > 321
> > 322
> > 323
> > 324
> > 325
> > 330
> > 352
> > 370
> > 378
> > 383
> > 384
> > 385
> > 387
> > 396
> > 397
> > 398
> > 424
> > 431
> > 439
> > 441
> > 442
> > 477
> > 478
> > 479
> > 480
> >
> >
> >
> >
> >
> >
> >
> >
> > *Zahra (Mona) Nasiriavanaki*
> >
> > Postdoctoral Research Fellow
> >
> > Martinos Center for Biomedical Imaging
> >
> > Massachusetts General Hospital
> >
> > 149 13th Street, 149-2615
> >
> > Charlestown, MA, USA, 02129
> >
> >
> >
> >
> >
> > ___
> > 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
>
>
> ___
> 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
___
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.

[Freesurfer] fcseed-config

[Nasiriavanaki, Zahra]

Hi all


I am running a seed to whole brain connectivity analysis. I am using the labels 
that I have made from functional ROIs.

When I run fcseed-config, It makes the configuration file but not the .dat 
files.

Here is my command:

fcseed-config -segid 1 -seg $SUBJECTS_DIR/${subj}/mri/lh.DIPS_sup2018.mgz 
-segid 1 -seg $SUBJECTS_DIR/${subj}/mri/lh.DIPS_inf2018.mgz -segid 1 -seg 
$SUBJECTS_DIR/${subj}/mri/rh.DIPS.2018.mgz -fcname bilateral_DIPS.dat -fsd rest 
-rlf restruns -mean -cfg ../all_subjects/${subj}/bilateral_DIPS.config 
-overwrite

I appreciate if someone tells me how to fix it.

Thanks
Mona



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


___
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] fcseed-config

[Nasiriavanaki, Zahra]

Right!

:)

Thanks


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
sha...@nmr.mgh.harvard.edu 
Sent: Thursday, July 26, 2018 9:10:19 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] fcseed-config

You need to run fcseed-sess to generate that.


> Hi all
>
>
> I am running a seed to whole brain connectivity analysis. I am using the
> labels that I have made from functional ROIs.
>
> When I run fcseed-config, It makes the configuration file but not the .dat
> files.
>
> Here is my command:
>
> fcseed-config -segid 1 -seg $SUBJECTS_DIR/${subj}/mri/lh.DIPS_sup2018.mgz
> -segid 1 -seg $SUBJECTS_DIR/${subj}/mri/lh.DIPS_inf2018.mgz -segid 1 -seg
> $SUBJECTS_DIR/${subj}/mri/rh.DIPS.2018.mgz -fcname bilateral_DIPS.dat -fsd
> rest -rlf restruns -mean -cfg
> ../all_subjects/${subj}/bilateral_DIPS.config -overwrite
>
> I appreciate if someone tells me how to fix it.
>
> Thanks
> Mona
>
>
>
> Zahra (Mona) Nasiriavanaki
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


_

Shahin Nasr

Assistant Prof. in Radiology
Harvard Medical School
Martinos Imaging Center, MGH
Bldg 149, 13th street,
Charlestown, MA 02129

___
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] FsPalm patch

[Nasiriavanaki, Zahra]

Hi


I downloaded it from this link.


https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide

PALM/UserGuide - FslWiki - University of 
Oxford
fsl.fmrib.ox.ac.uk
Downloading and installing PALM. To download latest packaged version, please 
click here.. Alternatively, visit the repository on GitHub.. PALM can run as a 
standalone command (i.e., executed directly from the command line/terminal), or 
inside Octave or Matlab.



Good luck

Mona



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tom Parker 

Sent: Friday, September 7, 2018 5:01:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FsPalm patch


External Email - Use Caution

Dear Freesurfer developers,

I am attempting to download the FsPalm patch 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm) using: the link described in 
the wiki - ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/PALM

However, there appears to be no directory at that location.

Please can you inform me how to install the FsPalm patch?

Many thanks
___
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.

[Freesurfer] Freesurfer 5.3 vs 6

[Nasiriavanaki, Zahra]

Dear Freesurfers


Hi


I have a bunch of data that is preprocessed in Freesurfer version 5.3 (both 
recon and preprocessing).

My question is whether I can do the first level and group analysis on this data 
using Freesurfer version 6? Or should I do everything in version 6 from the 
beginning?

I need to compare their results with my other data set in FS v 6.


Thanks

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] Freesurfer 5.3 vs 6

[Nasiriavanaki, Zahra]

Thank you very much Bruce!


Mona

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Friday, January 4, 2019 12:03:16 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 5.3 vs 6

Hi Mona

if you want to compare with another dataset processed with V6, you
probably have to reprocess everything in this one with V6 too otherwise
you will never know if the differences you are finding are algorithmic or
biological.

sorry
Bruce
On Fri, 4 Jan 2019, Nasiriavanaki, Zahra wrote:

>
> Dear Freesurfers
>
>
> Hi
>
>
> I have a bunch of data that is preprocessed in Freesurfer version 5.3 (both 
> recon and preprocessing).
>
> My question is whether I can do the first level and group analysis on this 
> data using Freesurfer
> version 6? Or should I do everything in version 6 from the beginning?
>
> I need to compare their results with my other data set in FS v 6.
>
>
> Thanks
>
> Mona
>
>
> Zahra (Mona) Nasiriavanaki
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] gammafit flag in mkanalysis-sess

[Nasiriavanaki, Zahra]

Hi Freesurfers


I have a few questions about gammafit flag in mkanalysis-sess command and I 
appreciate if you could respond whenever you had time.


-How should we decide which function is best to apply on hemodynamic response 
signal? I have used both spmhrf and gammafit and I see slightly different 
results.

-Does Freesurfer has a default function that applies on hemodynamic response 
signal if I don't use these flags?

-Where should I get gfdelta and gftau from?


Thanks

Mona



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] gammafit flag in mkanalysis-sess

[Nasiriavanaki, Zahra]

Thank you so much for your helpful reply Doug.


MOna


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Friday, January 4, 2019 2:26:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] gammafit flag in mkanalysis-sess



On 1/4/19 1:27 PM, Nasiriavanaki, Zahra wrote:

Hi Freesurfers


I have a few questions about gammafit flag in mkanalysis-sess command and I 
appreciate if you could respond whenever you had time.


-How should we decide which function is best to apply on hemodynamic response 
signal? I have used both spmhrf and gammafit and I see slightly different 
results.

Hard to say. Mostly, it does not make much of a difference, especially if you 
have a block design. In theory, you could see which one has the lowest residual 
error, but in general I would not agonize over it.

-Does Freesurfer has a default function that applies on hemodynamic response 
signal if I don't use these flags?

No, you have to supply one. I usually use --spmhrf 0

-Where should I get gfdelta and gftau from?

We always used delta=2.5 and tau=1.25. These are from Dale and Buckner, HBM 
1997, Selective Averaging of Rapidly Presented Individual Trials Using fMRI


Thanks

Mona



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





___
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] wm and vcsf nuisance regressors

[Nasiriavanaki, Zahra]

Dear Freesurfers


Hi

I am using white matter and CSF  external nuisance regressors in my 
mkanalysis-sess.

However, when I make these regressors, I use -mean in fcseed-config command, 
and so the .dat files only have one column (the mean values, I assume).

I looked up in the freesurfer archive and I saw that It is recommended to use  
-nuisreg wm.dat 5   and -nuisreg vcsf.dat 5.

My question is that what difference it makes to use mean of these regressors vs 
using only 5 of the columns.

I appreciate if you could please reply whenever you had time.


Thanks

Mona



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] wm and vcsf nuisance regressors

[Nasiriavanaki, Zahra]

Hi Doug


Thank you very much for your helpful reply.


Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Friday, January 18, 2019 11:34:04 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] wm and vcsf nuisance regressors

Hi Mona, when you run fcseed-config you can specify to use -mean or -pca npca. 
-mean produces the mean waveform. -pca will run a PCA on all  voxels and take 
the first npca components. In principle, using more components will fit more of 
the noise. But it can also make the design more poorly conditioned. In 
practice, I have not found it to make much of a difference (or even including 
or not including those regressors), especially for task-based analysis.

On 1/17/19 4:37 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers


Hi

I am using white matter and CSF  external nuisance regressors in my 
mkanalysis-sess.

However, when I make these regressors, I use -mean in fcseed-config command, 
and so the .dat files only have one column (the mean values, I assume).

I looked up in the freesurfer archive and I saw that It is recommended to use  
-nuisreg wm.dat 5   and -nuisreg vcsf.dat 5.

My question is that what difference it makes to use mean of these regressors vs 
using only 5 of the columns.

I appreciate if you could please reply whenever you had time.


Thanks

Mona



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





___
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] mri_vol2vol

[Nasiriavanaki, Zahra]

Dear Freesurfers


Hi

I am trying to project a subcortical volume , that I manually made, from 
fsaverage to individual subject's space.

I was wondering if it's ok if I use mri_vol2vol for this purpose. I copied my 
command below:


mri_vol2vol --mov ./${ROI}/ROI4.mgz  --targ 
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --o $SUBJECTS_DIR/${subj}/mri/${ROI}.mgz 
--talres 2 --interp nearest --regheader


Thanks

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] mri_vol2vol

[Nasiriavanaki, Zahra]

Thank you very much


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Monday, January 28, 2019 3:17:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol

that should work

On 1/28/19 2:44 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers


Hi

I am trying to project a subcortical volume , that I manually made, from 
fsaverage to individual subject's space.

I was wondering if it's ok if I use mri_vol2vol for this purpose. I copied my 
command below:


mri_vol2vol --mov ./${ROI}/ROI4.mgz  --targ 
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --o $SUBJECTS_DIR/${subj}/mri/${ROI}.mgz 
--talres 2 --interp nearest --regheader


Thanks

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





___
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] fcseedcor_multiple runs

[Nasiriavanaki, Zahra]

Dear Freesurfers


Hi


I have been doing seed to seed connectivity analysis using fcseedcor.

I have multiple runs for each subject, and based on the fcseedcor help, I am 
supposed to average runs before comparing across subjects.

So, does it mean I should average all seed.dat files and the regressors 
(including vscf,wm,global waveform, mcprextreg) across runs?

I appreciate your time and consideration.


Thanks

Mona



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] fcseedcor_multiple runs

[Nasiriavanaki, Zahra]

Thank you so much for your reply.

Yes, It does make a separate r and p for each run.

But, I would like to have one correlation coefficient for each subject, so I 
can compare them to each other.

Based on help, I should average runs before comparing across subjects. My 
question is how should I average runs? Should average the .dat files? the r 
values?


Thanks

Mona




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

Sent: Thursday, February 7, 2019 5:33:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fcseedcor_multiple runs

Looking at the help, it looks like it will produce a separate file for
each run for each session. Is that what you want?

On 2/1/19 9:41 AM, Nasiriavanaki, Zahra wrote:
>
> Dear Freesurfers
>
>
> Hi
>
>
> I have been doing seed to seed connectivity analysis using fcseedcor.
>
> I have multiple runs for each subject, and based on the fcseedcor
> help, I am supposed to average runs before comparing across subjects.
>
> So, does it mean I should average all seed.dat files and the
> regressors (including vscf,wm,global waveform, mcprextreg) across runs?
>
> I appreciate your time and consideration.
>
>
> Thanks
>
> Mona
>
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
> ___
> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] fcseedcor_multiple runs

[Nasiriavanaki, Zahra]

Dear Freesurfer experts


I have asked this question before and I really do appreciate if you could 
please reply whenever you had a chance.

I have been doing seed to seed connectivity analysis using fcseedcor.
I have multiple runs for each subject, and based on the fcseedcor help, I am 
supposed to average runs before comparing across subjects.
So, does it mean I should average timeseries across runs?or Should I average 
the acquired r values? (because after running fcseedcor, separate r and p 
values are made for each run).

Thanks so much
Mona





From: Nasiriavanaki, Zahra
Sent: Thursday, February 7, 2019 5:39:39 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fcseedcor_multiple runs


Thank you so much for your reply.

Yes, It does make a separate r and p for each run.

But, I would like to have one correlation coefficient for each subject, so I 
can compare them to each other.

Based on help, I should average runs before comparing across subjects. My 
question is how should I average runs? Should average the .dat files? the r 
values?


Thanks

Mona




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

Sent: Thursday, February 7, 2019 5:33:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fcseedcor_multiple runs

Looking at the help, it looks like it will produce a separate file for
each run for each session. Is that what you want?

On 2/1/19 9:41 AM, Nasiriavanaki, Zahra wrote:
>
> Dear Freesurfers
>
>
> Hi
>
>
> I have been doing seed to seed connectivity analysis using fcseedcor.
>
> I have multiple runs for each subject, and based on the fcseedcor
> help, I am supposed to average runs before comparing across subjects.
>
> So, does it mean I should average all seed.dat files and the
> regressors (including vscf,wm,global waveform, mcprextreg) across runs?
>
> I appreciate your time and consideration.
>
>
> Thanks
>
> Mona
>
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
> ___
> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] recon-all -hires

[Nasiriavanaki, Zahra]

Dear Freesurfer experts


I was running recon-all command with hires flag for our high resolution fMRI 
data, but it has been in a constant status since yesterday.

I copied the last few lines that are currently in my terminal. I had the same 
issue with another subject before, and I had to terminate the recon-all and run 
it without -hires.

Could you please let me know how I can solve this issue?


Thanks

Mona



#@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019
/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts

 cp ../surf/rh.orig.nofix ../surf/rh.orig


 cp ../surf/rh.inflated.nofix ../surf/rh.inflated

#@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019

 mris_fix_topology -rusage 
/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.lh.dat
 -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh

#@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019

 mris_fix_topology -rusage 
/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.rh.dat
 -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh

Waiting for PID 8994 of (8994 8997) to complete...



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

Re: [Freesurfer] recon-all -hires

[Nasiriavanaki, Zahra]

Hi Doug


Thank you very much for your reply.

Actually the recon finished today without any error. It just took so long to be 
done for only one subject (almost two days!)!

I checked the registration and It looks ok.

I will try -conf2hires for my other subject that -hires didn't work on it.


Thanks

Mona


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

Sent: Friday, February 22, 2019 1:07:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all -hires

sometimes the -hires flag does not work very well. For the subjects where it 
does complete, do the surfaces look ok? You can also use recon-all.v6.hires 
with the -conf2hires option (available in fs6 on our network).

On 2/21/19 2:36 PM, Nasiriavanaki, Zahra wrote:

Hi Bruce


Thank you very much for  your reply.

Here is my command:

recon-all -all -s ${subj} -i  ./${subj}/anat/016/mT1v2.nii -expert  
./scripts/expertopts/expert.opts -hires -mail zn025 -parallel

I also attached my .log file.


Thanks

MOna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Bruce Fischl 
<mailto:fis...@nmr.mgh.harvard.edu>
Sent: Thursday, February 21, 2019 2:23:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all -hires

Hi MOna


what was your full command line? And can you send us the recon-all.log
file?

cheers
Bruce
On Thu, 21 Feb 2019, Nasiriavanaki, Zahra wrote:

>
> Dear Freesurfer experts
>
>
> I was running recon-all command with hires flag for our high resolution fMRI 
> data, but it has been in a
> constant status since yesterday.
>
> I copied the last few lines that are currently in my terminal. I had the same 
> issue with another
> subject before, and I had to terminate the recon-all and run it without 
> -hires.
>
> Could you please let me know how I can solve this issue?
>
>
> Thanks
>
> Mona
>
>
>
> #@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019
> /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts
>
>  cp ../surf/rh.orig.nofix ../surf/rh.orig
>
>
>  cp ../surf/rh.inflated.nofix ../surf/rh.inflated
>
> #@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019
>
>  mris_fix_topology 
> -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh
>
> #@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019
>
>  mris_fix_topology 
> -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh
>
> Waiting for PID 8994 of (8994 8997) to complete...
>
>
>
>
>



___
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] projfrac question

[Nasiriavanaki, Zahra]

Dear Freesurfers


Hi

I was trying to look at the activation in different cortical layers in a single 
subject.

I ran my preproc-sess command three times, once without using -projfrac flag, 
once  -projfrac 0.5 and lastly -projfrac 0.2

The activation patterns are exactly the same.

My voxel sizes are 1.1*1.1*1.1 .

My question is:

1-Is it normal that the activations do not change at all the more I get closer 
to white matter?

2-when I use -projfrac 0.2 , does it mean that I am averaging the activation 
between white matter layer to 0.2 of gray matter layer? Or is it averaging the 
activation between pial surface to 0.2 gray matter?


I hope my questions are clear.


Thanks

Mona

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

Re: [Freesurfer] projfrac question

[Nasiriavanaki, Zahra]

Hi Doug


Thank you very much for your reply.

I was actually using -force and It did take a reasonable amount of time.

Then I ran the selxavg command to get the first level maps, and I guess It used 
the last preprocessd data which was from projfrac 0.2.


Thanks

Mona


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

Sent: Thursday, February 28, 2019 2:41:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] projfrac question

The projfrac function might not be working in the way that you think. It
might not actually be re-running anything. Did preproc-sess finish
faster than you would have expected? You can try deleting the projfrac
output and re-running. You can also run preproc-sess with -force, but
this will force it to re-run everything. If you want to use multiple
project fracs, then you should copy the functional tree to a new
location (if you use -p with cp, it will copy the modification time,
which will make preproc-sess run faster).

On 2/28/19 12:55 PM, Nasiriavanaki, Zahra wrote:
>
> Dear Freesurfers
>
>
> Hi
>
> I was trying to look at the activation in different cortical layers in
> a _single subject_.
>
> I ran my preproc-sess command three times, once without using
> -projfrac flag, once  -projfrac 0.5 and lastly -projfrac 0.2
>
> The activation patterns are exactly the same.
>
> My voxel sizes are 1.1*1.1*1.1 .
>
> My question is:
>
> 1-Is it normal that the activations do not change at all the more I
> get closer to white matter?
>
> 2-when I use -projfrac 0.2 , does it mean that I am averaging the
> activation between white matter layer to 0.2 of gray matter layer? Or
> is it averaging the activation between pial surface to 0.2 gray matter?
>
>
> I hope my questions are clear.
>
>
> Thanks
>
> Mona
>
>
>
> ___
> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] projfrac question

[Nasiriavanaki, Zahra]

I did not find mri_vol2surf.

Below is part of a log file, as you see  -projrfac has changed to 0.5 but not  
to 0.2.

mri_segreg --mov bold/020/tmp.bbregister.43919/template.nii --init-reg 
bold/020/tmp.bbregister.43919/reg.init.dat --out-reg 
bold/020/tmp.bbregister.43919/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 
--tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 
--gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR
cd /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T
mri_segreg --mov bold/020/tmp.bbregister.43919/template.nii --init-reg 
bold/020/tmp.bbregister.43919/reg.init.dat --out-reg 
bold/020/tmp.bbregister.43919/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 
--tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 
--gm-gt-wm 0.5


Thanks

Mona






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

Sent: Thursday, February 28, 2019 2:54:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] projfrac question

I would have thought that it would have changed. Can you look through
the logs and find the mri_vol2surf command and verify that the
--projfrac argument is changing?

On 2/28/19 2:51 PM, Nasiriavanaki, Zahra wrote:
>
> Hi Doug
>
>
> Thank you very much for your reply.
>
> I was actually using -force and It did take a reasonable amount of time.
>
> Then I ran the selxavg command to get the first level maps, and I
> guess It used the last preprocessd data which was from projfrac 0.2.
>
>
> Thanks
>
> Mona
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> *Sent:* Thursday, February 28, 2019 2:41:25 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] projfrac question
> The projfrac function might not be working in the way that you think. It
> might not actually be re-running anything. Did preproc-sess finish
> faster than you would have expected? You can try deleting the projfrac
> output and re-running. You can also run preproc-sess with -force, but
> this will force it to re-run everything. If you want to use multiple
> project fracs, then you should copy the functional tree to a new
> location (if you use -p with cp, it will copy the modification time,
> which will make preproc-sess run faster).
>
> On 2/28/19 12:55 PM, Nasiriavanaki, Zahra wrote:
> >
> > Dear Freesurfers
> >
> >
> > Hi
> >
> > I was trying to look at the activation in different cortical layers in
> > a _single subject_.
> >
> > I ran my preproc-sess command three times, once without using
> > -projfrac flag, once  -projfrac 0.5 and lastly -projfrac 0.2
> >
> > The activation patterns are exactly the same.
> >
> > My voxel sizes are 1.1*1.1*1.1 .
> >
> > My question is:
> >
> > 1-Is it normal that the activations do not change at all the more I
> > get closer to white matter?
> >
> > 2-when I use -projfrac 0.2 , does it mean that I am averaging the
> > activation between white matter layer to 0.2 of gray matter layer? Or
> > is it averaging the activation between pial surface to 0.2 gray matter?
> >
> >
> > I hope my questions are clear.
> >
> >
> > Thanks
> >
> > Mona
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard 
University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
mail.nmr.mgh.harvard.edu
To see the collection of prior postings to the list, visit the Freesurfer 
Archives.. A searchable archive which of messages PRIOR to March 2004 is at 
this site A searchable archive which includes messages AFTER March 2004 is at 
this site. Using 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


___
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

Re: [Freesurfer] projfrac question

[Nasiriavanaki, Zahra]

Yes, I found it.

I should mention that, this log file is the result of today's preprocessing  
(-projfrac 0.2) which I did in a separate folder, with all the previous 
preprocessing files being deleted.

As you see the -projfrac is still 0.5 !


  Fri Mar  1 11:32:16 EST 2019
mri_vol2surf --mov 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.nii.gz
 --reg 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
 --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.sm0.fsaverage.rh.nii.gz
 --noreshape --cortex --surfreg sphere.reg
srcvol = 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.nii.gz
srcreg = 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilin
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Input reg is LTA




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

Sent: Friday, March 1, 2019 11:09:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] projfrac question

that is part of the bbregister command. Can you find the commands related to 
mri_vol2surf?

On 2/28/19 3:51 PM, Nasiriavanaki, Zahra wrote:

I did not find mri_vol2surf.

Below is part of a log file, as you see  -projrfac has changed to 0.5 but not  
to 0.2.

mri_segreg --mov bold/020/tmp.bbregister.43919/template.nii --init-reg 
bold/020/tmp.bbregister.43919/reg.init.dat --out-reg 
bold/020/tmp.bbregister.43919/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 
--tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 
--gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR
cd /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T
mri_segreg --mov bold/020/tmp.bbregister.43919/template.nii --init-reg 
bold/020/tmp.bbregister.43919/reg.init.dat --out-reg 
bold/020/tmp.bbregister.43919/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 
--tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 
--gm-gt-wm 0.5


Thanks

Mona






From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, February 28, 2019 2:54:51 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] projfrac question

I would have thought that it would have changed. Can you look through
the logs and find the mri_vol2surf command and verify that the
--projfrac argument is changing?

On 2/28/19 2:51 PM, Nasiriavanaki, Zahra wrote:
>
> Hi Doug
>
>
> Thank you very much for your reply.
>
> I was actually using -force and It did take a reasonable amount of time.
>
> Then I ran the selxavg command to get the first level maps, and I
> guess It used the last preprocessd data which was from projfrac 0.2.
>
>
> Thanks
>
> Mona
>
> 
> *From:* 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>  on behalf of Greve, Douglas
> N.,Ph.D. <mailto:dgr...@mgh.harvard.edu>
> *Sent:* Thursday, February 28, 2019 2:41:25 PM
> *To:* freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] projfrac question
> The projfrac function might not be working in the way that you think. It
> might not actually be re-running anything. Did preproc-sess finish
> faster than you would have expected? You can try deleting the projfrac
> output and re-running. You can also run preproc-sess with -force, but
> this will force it to re-run everything. If you want to use multiple
> project fracs, then you should copy the functional tree to a new
> location (if you use -p with cp, it will copy the modification time,
> which will make preproc-sess run faster).
>
> On 2/28/19 12:55 PM, Nasiriavanaki, Zahra wrote:
> >
> > Dear Freesurfers
> >
> >
> > Hi
> >
> > I was trying to look at the activation in different cortical layers in
> > a _single subject_.
> >
> > I ran my preproc-sess command three times, once without using
> > -projfrac flag, once  -projfrac 0.5 and

Re: [Freesurfer] projfrac question

[Nasiriavanaki, Zahra]

Hi Doug


I re-analyzed one of my subjects from the very beginning with -projfrac 0.2. 
But still, in mri_vol2surf, the projfrac is 0.5 (copied below). Could you 
please let me know what I'm doing wrong?

Here is my command:

preproc-sess -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2 -surface fsaverage 
lhrh -fsd bold -d $dir/all_subjects -force


Thanks

Mona


mri_vol2surf --mov 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.nii.gz
 --reg 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/register.dof6.lta
 --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.sm0.fsaverage.rh.nii.gz
 --noreshape --cortex --surfreg sphere.reg
srcvol = 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.nii.gz
srcreg = 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/register.dof6.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilin
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Input reg is LTA






Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Nasiriavanaki, Zahra
Sent: Friday, March 1, 2019 11:52:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] projfrac question


Yes, I found it.

I should mention that, this log file is the result of today's preprocessing  
(-projfrac 0.2) which I did in a separate folder, with all the previous 
preprocessing files being deleted.

As you see the -projfrac is still 0.5 !


  Fri Mar  1 11:32:16 EST 2019
mri_vol2surf --mov 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.nii.gz
 --reg 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
 --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.sm0.fsaverage.rh.nii.gz
 --noreshape --cortex --surfreg sphere.reg
srcvol = 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.nii.gz
srcreg = 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilin
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Input reg is LTA




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

Sent: Friday, March 1, 2019 11:09:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] projfrac question

that is part of the bbregister command. Can you find the commands related to 
mri_vol2surf?

On 2/28/19 3:51 PM, Nasiriavanaki, Zahra wrote:

I did not find mri_vol2surf.

Below is part of a log file, as you see  -projrfac has changed to 0.5 but not  
to 0.2.

mri_segreg --mov bold/020/tmp.bbregister.43919/template.nii --init-reg 
bold/020/tmp.bbregister.43919/reg.init.dat --out-reg 
bold/020/tmp.bbregister.43919/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 
--tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 
--gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR
cd /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T
mri_segreg --mov bold/020/tmp.bbregister.43919/template.nii --init-reg 
bold/020/tmp.bbregister.43919/reg.init.dat --out-reg 
bold/020/tmp.bbregister.43919/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 
--tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 
--gm-gt-wm 0.5


Thanks

Mona






From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, February 28, 2019 2:54:51 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] projfrac question

I would have thought that it would have changed. Can you look through
the logs and find the mri_vol2surf command and verify that the
--projfrac argument is changing?

On 2/28/19 2:51 PM, Nasiriavanaki, Zahra wrote:
>
> Hi Doug
>
>
> Thank you very much for your reply.
>
> I was actually using -force and It did take a reasonable amount

Re: [Freesurfer] projfrac question

[Nasiriavanaki, Zahra]

Hi Doug


Thank you very much for your reply.

I ran one of my subjects with the command below and I got this error:

preproc-sess.test -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2 -surface 
fsaverage lhrh -fsd bold -d $dir/all_subjects -force

Does it mean I should run it with expert option flag?like the one in recon-all?


Thu Mar  7 10:10:00 EST 2019
mc-sess completed SUCCESSFULLY
inul_reunpack To Surface -
rawfunc2surf-sess -fwhm 0 -s inul_reunpack -d 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects -fsd bold 
-trgsubject fsaverage -per-run -projfrac 0.2
ERROR: experts key needed (-expkey)



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Wednesday, March 6, 2019 7:06:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] projfrac question

This does appear to be a bug. Are you using FS version 6? If so, I put a
test in that distriubtion called preproc-sess.test. Can you try running
that on a subject and see if you get the desired behavior?

On 3/6/19 1:31 PM, Nasiriavanaki, Zahra wrote:
>
> Hi Doug
>
>
> I re-analyzed one of my subjects from the very beginning with
> -projfrac 0.2. But still, in mri_vol2surf, the projfrac is 0.5 (copied
> below). Could you please let me know what I'm doing wrong?
>
> Here is my command:
>
> preproc-sess -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2 -surface
> fsaverage lhrh -fsd bold -d $dir/all_subjects -force
>
>
> Thanks
>
> Mona
>
>
> mri_vol2surf --mov
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.nii.gz
> --reg
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/register.dof6.lta
> --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.sm0.fsaverage.rh.nii.gz
> --noreshape --cortex --surfreg sphere.reg
> srcvol =
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.nii.gz
> srcreg =
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/register.dof6.lta
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = rh
> trgsubject = fsaverage
> surfreg = sphere.reg
> ProjFrac = 0.5
> thickness = thickness
> reshape = 0
> interp = trilin
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Input reg is LTA
>
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> 
> *From:* Nasiriavanaki, Zahra
> *Sent:* Friday, March 1, 2019 11:52:21 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] projfrac question
>
> Yes, I found it.
>
> I should mention that, this log file is the result of today's
> preprocessing  (-projfrac 0.2) which I did in a separate folder, with
> all the previous preprocessing files being deleted.
>
> As you see the -projfrac is still 0.5 !
>
>
>   Fri Mar  1 11:32:16 EST 2019
> mri_vol2surf --mov
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.nii.gz
> --reg
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
> --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.sm0.fsaverage.rh.nii.gz
> --noreshape --cortex --surfreg sphere.reg
> srcvol =
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.nii.gz
> srcreg =
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = rh
> trgsubject = fsaverage
> surfreg = sphere.reg
> ProjFrac = 0.5
> thickness = thickness
> reshape = 0
> interp = trilin
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Input reg is LTA
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> *Sent:* Friday, March 1, 2019 11:09:30 AM
> *To:* freesurfe

Re: [Freesurfer] projfrac question

[Nasiriavanaki, Zahra]

Dear Doug

Thank you so very much for your time and helps.
Yes It works perfectly.

Mona



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

Sent: Thursday, March 7, 2019 6:07:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] projfrac question

Can you try it again? this time use -projfrac 0.2 pf020  (ie, add
"pf020" after 0.2). Then when you use mkanalysis-sesss, add -expkey
pf020 to the command line. The pf020 will be included in the output file
name to make it unique. This allows you to use a single project folder
(ie, you don't need to copy to a new folder).

On 3/7/19 12:20 PM, Nasiriavanaki, Zahra wrote:
>
> Hi Doug
>
>
> Thank you very much for your reply.
>
> I ran one of my subjects with the command below and I got this error:
>
> preproc-sess.test -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2
> -surface fsaverage lhrh -fsd bold -d $dir/all_subjects -force
>
> Does it mean I should run it with expert option flag?like the one in
> recon-all?
>
>
> Thu Mar  7 10:10:00 EST 2019
> mc-sess completed SUCCESSFULLY
> inul_reunpack To Surface -
> rawfunc2surf-sess -fwhm 0 -s inul_reunpack -d
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects -fsd bold
> -trgsubject fsaverage -per-run -projfrac 0.2
> ERROR: experts key needed (-expkey)
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> *Sent:* Wednesday, March 6, 2019 7:06:44 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] projfrac question
> This does appear to be a bug. Are you using FS version 6? If so, I put a
> test in that distriubtion called preproc-sess.test. Can you try running
> that on a subject and see if you get the desired behavior?
>
> On 3/6/19 1:31 PM, Nasiriavanaki, Zahra wrote:
> >
> > Hi Doug
> >
> >
> > I re-analyzed one of my subjects from the very beginning with
> > -projfrac 0.2. But still, in mri_vol2surf, the projfrac is 0.5 (copied
> > below). Could you please let me know what I'm doing wrong?
> >
> > Here is my command:
> >
> > preproc-sess -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2 -surface
> > fsaverage lhrh -fsd bold -d $dir/all_subjects -force
> >
> >
> > Thanks
> >
> > Mona
> >
> >
> > mri_vol2surf --mov
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.nii.gz
> > --reg
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/register.dof6.lta
> > --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.sm0.fsaverage.rh.nii.gz
> > --noreshape --cortex --surfreg sphere.reg
> > srcvol =
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.nii.gz
> > srcreg =
> >
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/register.dof6.lta
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = rh
> > trgsubject = fsaverage
> > surfreg = sphere.reg
> > ProjFrac = 0.5
> > thickness = thickness
> > reshape = 0
> > interp = trilin
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > Done loading volume
> > Input reg is LTA
> >
> >
> >
> > *Zahra (Mona) Nasiriavanaki*
> >
> > Postdoctoral Research Fellow
> >
> > Martinos Center for Biomedical Imaging
> >
> > Massachusetts General Hospital
> >
> > 149 13th Street, 149-2615
> >
> > Charlestown, MA, USA, 02129
> >
> >
> >
> > 
> > *From:* Nasiriavanaki, Zahra
> > *Sent:* Friday, March 1, 2019 11:52:21 AM
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] projfrac question
> >
> > Yes, I found it.
> >
> > I should mention that, this log file is the result of today's
> > preprocessing  (-projfrac 0.2) which I did in a separate folder, with
> > all the previous preprocessing files being deleted.
> >
> > 

[Freesurfer] tkregister-sess

[Nasiriavanaki, Zahra]

Dear Freesurfers


Hi

I was checking the functional on structural data registration quality by using  
the below command.

tkregister-sess -s $subj -fsd bold -per-run -bbr-sum

I observed high values (around 0.9) for one of my subjects, and I figured out, 
that subject was registered to another subject's structural data by mistake.

I re-did the recon (in a new folder) and checked the registration again, the 
values are still the same! However when I check my log files, it seems that the 
recon is done correctly and the snapshots from QA_tools don't look bad.

I appreciate if you could please let me know what you think.


Thanks a lot

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] tkregister-sess

[Nasiriavanaki, Zahra]

I changed my SUBJECTS_DIR folder, but I did not delete the old one at that time.




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

Sent: Monday, March 18, 2019 12:34:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tkregister-sess

Did you delete the bad registration file and re-run the registration 
(preproc-sess)?

On 3/18/19 11:53 AM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers


Hi

I was checking the functional on structural data registration quality by using  
the below command.

tkregister-sess -s $subj -fsd bold -per-run -bbr-sum

I observed high values (around 0.9) for one of my subjects, and I figured out, 
that subject was registered to another subject's structural data by mistake.

I re-did the recon (in a new folder) and checked the registration again, the 
values are still the same! However when I check my log files, it seems that the 
recon is done correctly and the snapshots from QA_tools don't look bad.

I appreciate if you could please let me know what you think.


Thanks a lot

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





___
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] exact time of data acquisition per run

[Nasiriavanaki, Zahra]

Dear Freesurfer experts


Hi


I am trying to extract the time of data acquisition for each run from the 
functional data and compare it with my paradigm files.

I thought the numbers in DICOM file names (ie, 
MR.1.3.12.2.1107.5.2.43.67026.2019011316475911712728505 ) are correspondent 
with the date and time of data acquisition. But they don not exactly match with 
my paradigm files.

Do these numbers represent the exact time of data collection for each run?



Thanks

Mona




Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] exact time of data acquisition per run

[Nasiriavanaki, Zahra]

Great!

Thanks


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Sanchez, Juan (NYSPI) 

Sent: Wednesday, March 27, 2019 4:47:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] exact time of data acquisition per run


External Email - Use Caution

dcmdump the dicoms and the info will be in the hdr


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Nasiriavanaki, Zahra 

Sent: Wednesday, March 27, 2019 4:44:14 PM
To: Freesurfer support list
Subject: [Freesurfer] exact time of data acquisition per run


ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


Dear Freesurfer experts


Hi


I am trying to extract the time of data acquisition for each run from the 
functional data and compare it with my paradigm files.

I thought the numbers in DICOM file names (ie, 
MR.1.3.12.2.1107.5.2.43.67026.2019011316475911712728505 ) are correspondent 
with the date and time of data acquisition. But they don not exactly match with 
my paradigm files.

Do these numbers represent the exact time of data collection for each run?



Thanks

Mona




Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

[Freesurfer] mri_segstats

[Nasiriavanaki, Zahra]

Dear Freesurferers


I was trying to do a connectivity analysis using subnuclei of Amygdala.

I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf Amygdala) and I 
tried to use that in mri_segstats to extract the timeseries and then use it as 
a seed in my analysis. However when I looked at the results, the values are too 
high (around 800). Could you please let me know what I'm doing wrong?

P.S: the segmentation was basically done in MNI152-1mm and I moved it to 
MNI305-2mm by mri_vol2vol.



mri_vol2vol --mov MNI152template/MNI152_1/mri/reg.lh.HBT.mgz   --targ 
$SUBJECTS_DIR/fsaverage/mri.2mm/mni305.cor.mgz  --o 
$SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --interp nearest --regheade


mri_segstats --i $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz 
--seg $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt


Thanks  a lot

MOna

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

Re: [Freesurfer] mri_segstats

[Nasiriavanaki, Zahra]

Hi


I have not got the answer to my question yet, and I appreciate if you could 
please let me know what you think about it.


Thanks

Mona


From: Nasiriavanaki, Zahra
Sent: Tuesday, April 9, 2019 5:55:58 PM
To: Freesurfer support list
Subject: mri_segstats


Dear Freesurferers


I was trying to do a connectivity analysis using subnuclei of Amygdala.

I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf Amygdala) and I 
tried to use that in mri_segstats to extract the timeseries and then use it as 
a seed in my analysis. However when I looked at the results, the values are too 
high (around 800). Could you please let me know what I'm doing wrong?

P.S: the segmentation was basically done in MNI152-1mm and I moved it to 
MNI305-2mm by mri_vol2vol.



mri_vol2vol --mov MNI152template/MNI152_1/mri/reg.lh.HBT.mgz   --targ 
$SUBJECTS_DIR/fsaverage/mri.2mm/mni305.cor.mgz  --o 
$SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --interp nearest --regheade


mri_segstats --i $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz 
--seg $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt


Thanks  a lot

MOna

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

Re: [Freesurfer] mri_segstats

[Nasiriavanaki, Zahra]

Thank you for your reply.

The values of mri_segstats output text file (lateral.txt) are high. I attached 
it to this email.

mri_segstats --i $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz 
--seg $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt





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

Sent: Thursday, April 11, 2019 4:19:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats

The value of what is too  high?


On 4/11/19 4:07 PM, Nasiriavanaki, Zahra wrote:
>
> Hi
>
>
> I have not got the answer to my question yet, and I appreciate if you
> could please let me know what you think about it.
>
>
> Thanks
>
> Mona
>
> ----
> *From:* Nasiriavanaki, Zahra
> *Sent:* Tuesday, April 9, 2019 5:55:58 PM
> *To:* Freesurfer support list
> *Subject:* mri_segstats
>
> Dear Freesurferers
>
>
> I was trying to do a connectivity analysis using subnuclei of Amygdala.
>
> I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf
> Amygdala) and I tried to use that in mri_segstats to extract the
> timeseries and then use it as a seed in my analysis. However when I
> looked at the results, the values are too high (around 800). Could you
> please let me know what I'm doing wrong?
>
> P.S: the segmentation was basically done in MNI152-1mm and I moved it
> to MNI305-2mm by mri_vol2vol.
>
> mri_vol2vol --mov MNI152template/MNI152_1/mri/reg.lh.HBT.mgz --targ
> $SUBJECTS_DIR/fsaverage/mri.2mm/mni305.cor.mgz --o
> $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --interp nearest --regheade
>
> mri_segstats --i
> $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz --seg
> $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt
>
>
> Thanks  a lot
>
> MOna
>
>
>
> ___
> 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
  880.66492 
  879.35124 
  875.19926 
  878.23346 
  881.41143 
  878.01978 
  880.06932 
  882.16385 
  881.18868 
  884.87288 
  876.85369 
  879.21501 
  884.16000 
  881.42676 
  881.83217 
  880.46420 
  882.55352 
  883.94261 
  878.69354 
  882.01870 
  885.42943 
  881.85023 
  881.78761 
  880.89990 
  882.05140 
  881.49463 
  879.11290 
  881.71156 
  883.40625 
  885.35308 
  886.00897 
  884.20635 
  883.62201 
  884.86079 
  879.93472 
  880.38000 
  880.38240 
  879.34196 
  880.93785 
  889.45776 
  884.71200 
  877.96323 
  882.71370 
  886.57384 
  884.38491 
  886.27261 
  885.22180 
  884.92608 
  883.08029 
  882.82838 
  883.82696 
  886.61621 
  886.14899 
  882.42556 
  884.24720 
  885.83927 
  887.54077 
  888.56318 
  888.97052 
  887.70273 
  882.90662 
  888.15405 
  887.3 
  880.80367 
  887.67819 
  886.25526 
  884.89621 
  886.30670 
  890.39068 
  887.28961 
  887.74262 
  890.38000 
  885.77219 
  882.68568 
  883.08172 
  886.55909 
  888.62015 
  890.14195 
  885.46813 
  884.85042 
  887.99759 
  887.79979 
  888.65272 
  893.22492 
  888.57242 
  881.93206 
  885.05627 
  890.43585 
  890.70597 
  891.94003 
  891.08997 
  884.79187 
  882.68204 
  887.04860 
  892.99752 
  888.86018 
  888.93916 
  887.92639 
  891.26818 
  892.18812 
  892.25166 
  894.13254 
  891.26104 
  894.12174 
  895.34897 
  886.59572 
  888.05077 
  889.82544 
  888.03618 
  889.52830 
  889.12397 
  890.39206 
  893.30856 
  889.35844 
  890.10230 
  889.17691 
  890.90286 
  888.19625 
  889.39030 
  891.37744 
  888.89483 
  896.03565 
  903.50377 
  898.25897 
  890.16137 
  895.46996 
  894.20017 
  890.21543 
  894.12683 
  893.51801 
  893.27163 
  888.98254 
  889.72322 
  895.49739 
  897.36799 
  898.92711 
  891.67231 
  891.17966 
  894.54856 
  891.54128 
  888.39904 
  892.85606 
  891.19351 
  888.65139 
  892.89644 
  891.58232 
  889.17575 
  893.36888 
  895.90947 
  892.86331 
  895.31855 
  897.37581 
  898.34803 
  896.17875 
  894.53777 
  894.98599 
  891.79477 
  892.37661 
  893.70345 
  894.02283 
  896.38097 
  893.74852 
  890.68235 
  894.42961 
  892.66179 
  894.19767 
  893.99140 
  887.15148 
  894.65934 
  892.87306 
  886.91481 
  895.84461 
  896.43819 
  893.02697 
  897.91664 
  893.07503 
  889.62444 
  890.22281 
  895.30936 
  896.98467 
  896.73566 
  895.41997 
  890.49967 
  892.12631 
  895.65170 
  891.86272 
  893.40041 
  896.60271 
  895.78550 
  894.88053 
  895.03044 
  896.80774 
  888.46381 
  893.32973 
  904.80194 
  894.56621 
  893.66082 
  897.20610 
  899.85231 
  896.96227 
  891.115

Re: [Freesurfer] mri_segstats

[Nasiriavanaki, Zahra]

Thank you so very much.

Yes, the values look normal now.


Mona





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

Sent: Thursday, April 11, 2019 4:33:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats

You probably need to remove the mean. Add --avgwf-remove-mean to the
command line

On 4/11/19 4:29 PM, Nasiriavanaki, Zahra wrote:
>
> Thank you for your reply.
>
> The values of mri_segstatsoutput text file (lateral.txt) are high. I
> attached it to this email.
>
>
> mri_segstats --i
> $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz --seg
> $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> *Sent:* Thursday, April 11, 2019 4:19:00 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] mri_segstats
> The value of what is too  high?
>
>
> On 4/11/19 4:07 PM, Nasiriavanaki, Zahra wrote:
> >
> > Hi
> >
> >
> > I have not got the answer to my question yet, and I appreciate if you
> > could please let me know what you think about it.
> >
> >
> > Thanks
> >
> > Mona
> >
> > 
> > *From:* Nasiriavanaki, Zahra
> > *Sent:* Tuesday, April 9, 2019 5:55:58 PM
> > *To:* Freesurfer support list
> > *Subject:* mri_segstats
> >
> > Dear Freesurferers
> >
> >
> > I was trying to do a connectivity analysis using subnuclei of Amygdala.
> >
> > I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf
> > Amygdala) and I tried to use that in mri_segstats to extract the
> > timeseries and then use it as a seed in my analysis. However when I
> > looked at the results, the values are too high (around 800). Could you
> > please let me know what I'm doing wrong?
> >
> > P.S: the segmentation was basically done in MNI152-1mm and I moved it
> > to MNI305-2mm by mri_vol2vol.
> >
> > mri_vol2vol --mov MNI152template/MNI152_1/mri/reg.lh.HBT.mgz --targ
> > $SUBJECTS_DIR/fsaverage/mri.2mm/mni305.cor.mgz --o
> > $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --interp nearest --regheade
> >
> > mri_segstats --i
> > $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz --seg
> > $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt
> >
> >
> > Thanks  a lot
> >
> > MOna
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard 
University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
mail.nmr.mgh.harvard.edu
To see the collection of prior postings to the list, visit the Freesurfer 
Archives.. A searchable archive which of messages PRIOR to March 2004 is at 
this site A searchable archive which includes messages AFTER March 2004 is at 
this site. Using 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


___
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

Re: [Freesurfer] mri_segstats

[Nasiriavanaki, Zahra]

Following my previous question, I have one more question and I appreciate if 
you could please reply whenever you had time.

I extracted time series from a single resting state run using mri_segstats and 
compared it to the time series extracted from the same run using (fcseed-config 
& fcseed-sess).

The outputs are very different from each other. I'm wondering why they are 
different and which one I should use as a seed in the connectivity analysis?

mri_segstats --i  $subj/rest/009/fmcpr.siemens.sm5.mni305.2mm.nii.gz --seg 
SUBJECTS_DIR/$subj/mri/reg.lh.HBT2.mgz --id 7001 --avgwf-remove-mean --avgwf 
lh.lateral.txt

fcseed-config -segid 7001 -seg SUBJECTS_DIR/$subj/mri/reg.lh.HBT2.mgz -fcname 
lh.lateral.dat  -fsd rest -rlf restruns -mean -cfg lh.lateral.config -overwrite
fcseed-sess -s $subj -d . -cfg lh.lateral.config


Thanks

Mona


____
From: Nasiriavanaki, Zahra
Sent: Thursday, April 11, 2019 4:52:49 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_segstats


Thank you so very much.

Yes, the values look normal now.


Mona





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

Sent: Thursday, April 11, 2019 4:33:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats

You probably need to remove the mean. Add --avgwf-remove-mean to the
command line

On 4/11/19 4:29 PM, Nasiriavanaki, Zahra wrote:
>
> Thank you for your reply.
>
> The values of mri_segstatsoutput text file (lateral.txt) are high. I
> attached it to this email.
>
>
> mri_segstats --i
> $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz --seg
> $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> *Sent:* Thursday, April 11, 2019 4:19:00 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] mri_segstats
> The value of what is too  high?
>
>
> On 4/11/19 4:07 PM, Nasiriavanaki, Zahra wrote:
> >
> > Hi
> >
> >
> > I have not got the answer to my question yet, and I appreciate if you
> > could please let me know what you think about it.
> >
> >
> > Thanks
> >
> > Mona
> >
> > 
> > *From:* Nasiriavanaki, Zahra
> > *Sent:* Tuesday, April 9, 2019 5:55:58 PM
> > *To:* Freesurfer support list
> > *Subject:* mri_segstats
> >
> > Dear Freesurferers
> >
> >
> > I was trying to do a connectivity analysis using subnuclei of Amygdala.
> >
> > I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf
> > Amygdala) and I tried to use that in mri_segstats to extract the
> > timeseries and then use it as a seed in my analysis. However when I
> > looked at the results, the values are too high (around 800). Could you
> > please let me know what I'm doing wrong?
> >
> > P.S: the segmentation was basically done in MNI152-1mm and I moved it
> > to MNI305-2mm by mri_vol2vol.
> >
> > mri_vol2vol --mov MNI152template/MNI152_1/mri/reg.lh.HBT.mgz --targ
> > $SUBJECTS_DIR/fsaverage/mri.2mm/mni305.cor.mgz --o
> > $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --interp nearest --regheade
> >
> > mri_segstats --i
> > $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz --seg
> > $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt
> >
> >
> > Thanks  a lot
> >
> > MOna
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer Info Page - Harvard 
University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
mail.nmr.mgh.harvard.edu
To see the collection of prior postings to the list, visit the Freesurfer 
Archives.. A searchable archive which of messages PRIOR to March 2004 is at 
this site A searchable archive which includes messages AFTER March 2004 is at 
this site. Using 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


___
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

[Freesurfer] funcroi-table-sess

[Nasiriavanaki, Zahra]

Dear Freesurfer experts


Hi

I have a question about funcroi-table-sess, and I appreciate if you could 
please find a time to reply.

Is there anyway that funcroi-sess-table can give out the activation values in 
each timepoint separately? Right now I can get the average of activation in 
each subject (in a specific region of interest and a specific contrast) by 
using the below commands, and I was wondering if I can get the values in each 
timepoint.


funcroi-config  -label  ${lable}.label-roi ${subj}/${label_lh}.cfg
-analysis loom.lh  -force

funcroi-sess  -roi  all_subjects/${subj}/${label}.cfg -s all_subjects/$subj  -d 
.

funcroi-table-sess -roi  all_subjects/${subj}/${label}.cfg -s  
all_subjects/$subj -d .  -o 
all_subjects/$subj/ROI_analysis/${label_lh}_${contrast}.txt -c $contrast -m 
cespct


Thanks

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

[Freesurfer] spatial scale bar question

[Nasiriavanaki, Zahra]

Dear Freesurfers

Hi


I am trying to add a spatial scale bar to my cortical maps in tksurfer. 
However, as it's mentioned in Freesurfer forum before, the scale bar in 
tksurfer shrinks when you zoom in the brain.

I couldn't find a scale bar option in Freeview neither.

I appreciate if you could let me know how to get a scale bar.


Thanks

Mona

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

Re: [Freesurfer] spatial scale bar question

[Nasiriavanaki, Zahra]

Thanks for your reply.

I have overlaid the significance map on an inflated brain, and I don't see the 
scale bar icon anywhere.

tksurferfv fsaverage lh inflated -ov sig.nii.gz



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

Sent: Friday, May 10, 2019 3:27:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] spatial scale bar question

In freeview, it is just an icon above the image window. Click on it and it 
should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers

Hi


I am trying to add a spatial scale bar to my cortical maps in tksurfer. 
However, as it's mentioned in Freesurfer forum before, the scale bar in 
tksurfer shrinks when you zoom in the brain.

I couldn't find a scale bar option in Freeview neither.

I appreciate if you could let me know how to get a scale bar.


Thanks

Mona




___
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

Re: [Freesurfer] spatial scale bar question

[Nasiriavanaki, Zahra]

Yes Bruce.

It doesn't work.

I appreciate if you could let me know when you had any updates on it.


Thanks

Mona


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Friday, May 10, 2019 6:15:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] spatial scale bar question

I don't think it currently works in 3D mode as it is not trivial due to
perspective transforms. Ruopeng is trying some things
On Fri, 10 May 2019,
Greve, Douglas N.,Ph.D. wrote:

> here is a pick of it
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

[https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif]

>
>
> On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
>
>   Thanks for your reply.
>
>   I have overlaid the significance map on an inflated brain, and I don't 
> see the scale
>   bar icon anywhere.
>
>   tksurferfv fsaverage lh inflated -ov sig.nii.gz
>
>
> ___
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on
> behalf of Greve, Douglas N.,Ph.D. 
> Sent: Friday, May 10, 2019 3:27:15 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] spatial scale bar question
> In freeview, it is just an icon above the image window. Click on it and it 
> should give you a
> scale bar
>
> On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
>
>   Dear Freesurfers
>
>   Hi
>
>
>   I am trying to add a spatial scale bar to my cortical maps in tksurfer. 
> However,
>   as it's mentioned in Freesurfer forum before, the scale bar in tksurfer 
> shrinks
>   when you zoom in the brain.
>
>   I couldn't find a scale bar option in Freeview neither.
>
>   I appreciate if you could let me know how to get a scale bar.
>
>
>   Thanks
>
>   Mona
>
>
>
> ___
> 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
>
>
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] spatial scale bar question

[Nasiriavanaki, Zahra]

Great!
Thanks

> On May 13, 2019, at 9:56 AM, Bruce Fischl  wrote:
> 
> Hi Mona
> 
> sure. As I said it is a bit more complicated than it seems. Ruopeng will post 
> a note when something usable is in the dev version
> 
> Bruce
> 
> 
> On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote:
> 
>> Yes Bruce.
>> It doesn't work.
>> I appreciate if you could let me know when you had any updates on it.
>> Thanks
>> Mona
>> ___
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of
>> Bruce Fischl 
>> Sent: Friday, May 10, 2019 6:15:05 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] spatial scale bar question  
>> I don't think it currently works in 3D mode as it is not trivial due to
>> perspective transforms. Ruopeng is trying some things
>> On Fri, 10 May 2019,
>> Greve, Douglas N.,Ph.D. wrote:
>> > here is a pick of it
>> > https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif
>> [fv.colorbar.gif]
>> >
>> >
>> > On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
>> >
>> >   Thanks for your reply.
>> >
>> >   I have overlaid the significance map on an inflated brain, and I 
>> > don't see the scale
>> >   bar icon anywhere.
>> >
>> >   tksurferfv fsaverage lh inflated -ov sig.nii.gz
>> >
>> >
>> >__
>> _
>> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> >  on
>> > behalf of Greve, Douglas N.,Ph.D. 
>> > Sent: Friday, May 10, 2019 3:27:15 PM
>> > To: freesurfer@nmr.mgh.harvard.edu
>> > Subject: Re: [Freesurfer] spatial scale bar question  
>> > In freeview, it is just an icon above the image window. Click on it and it 
>> > should give you a
>> > scale bar
>> >
>> > On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
>> >
>> >   Dear Freesurfers 
>> >
>> >   Hi
>> >
>> >
>> >   I am trying to add a spatial scale bar to my cortical maps in 
>> > tksurfer. However,
>> >   as it's mentioned in Freesurfer forum before, the scale bar in 
>> > tksurfer shrinks
>> >   when you zoom in the brain.
>> >
>> >   I couldn't find a scale bar option in Freeview neither.
>> >
>> >   I appreciate if you could let me know how to get a scale bar.
>> >
>> >
>> >   Thanks
>> >
>> >   Mona
>> >
>> >
>> >
>> > ___
>> > 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
>> >
>> >
>> >
>> >
> ___
> 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

[Freesurfer] mkanalysis-sess refeventdur

[Nasiriavanaki, Zahra]

Hi Freesurfer experts


I am making an analysis in Freesurfer version 6 and I have a question about the 
"refeventdur" in mkanalysis-sess command.

My stimulus duration is 16 seconds, but for a specific analysis, I only want to 
include half of the stimulus duration (ex: the first 8 seconds only OR the last 
8 seconds only).

I was wondering if I can do this, by setting the "refeventdur" to 8 seconds.  
Will that work? and if it does, is it including the first 8 seconds or the last 
8 seconds?


Thanks

Mona



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] mkanalysis-sess refeventdur

[Nasiriavanaki, Zahra]

Got it.

Thank you very much for your reply


Mona


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

Sent: Monday, May 20, 2019 12:52:39 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mkanalysis-sess refeventdur

No, you'll need to change your paradigm file to have two distinct 8 sec
events rather than one 16 sec event.

On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote:
>
> Hi Freesurfer experts
>
>
> I am making an analysis in Freesurfer version 6 and I have a question
> about the "refeventdur" in mkanalysis-sess command.
>
> My stimulus duration is 16 seconds, but for a specific analysis, I
> only want to include half of the stimulus duration (ex: the first 8
> seconds only OR the last 8 seconds only).
>
> I was wondering if I can do this, by setting the "refeventdur" to 8
> seconds.  Will that work? and if it does, is it including the first 8
> seconds or the last 8 seconds?
>
>
> Thanks
>
> Mona
>
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
> ___
> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] QA_tools citation

[Nasiriavanaki, Zahra]

Dear Freesurfer experts

Hi

I was wondering how should I cite the Freesurfer QA_tools in a paper. I 
couldn’t find any references in the web page 
(https://surfer.nmr.mgh.harvard.edu/fswiki/QATools).

Thanks
Mona
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mis-registartion question

[Nasiriavanaki, Zahra]

I guess what I’m concerned about is the high values of tkregister-sess even 
though the registration looks normal.
I have checked tkregister values in other subjects with the same slab of 
functional data, and their values are within the normal range (~0.2-0.3), but 
for this subject the values of each run is about 0.95.

tkregister-sess -s $subj -fsd bold -per-run -bbr-sum

Thanks for your time



On Jun 28, 2019, at 3:11 PM, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:

I'm not sure I follow. From what I can see the registrations look ok. It looks 
like you only have a small slab of brain in the fMRI. What am I missing?

On 6/28/2019 10:41 AM, Nasiriavanaki, Zahra wrote:
Thank you so much for your reply.
I attached new images.
I scrolled through the brain and the worst registration is the last image 
attached.
I'm wondering what else could cause high values of tkregister-sess?



Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Friday, June 28, 2019 10:09:22 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mis-registartion question

It is hard to tell from those images, but the registration does not look that 
bad. It would be more informative to have images that are not on the midline.

On 6/27/2019 4:09 PM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers

Hi

I checked the functional to anatomical data registration using tkregister-sess 
-s $subj -fsd bold -per-run -bbr-sum. (The functional data is only collected 
from parietal and occipital lobes in 7T scanner).
The values obtained from tkregister-sess are too high (0.95) for 7 out of 8 
runs.
When I looked at the snapshots obtained from QA_tools, they looked ok (top row 
images). But, when I looked at the volumes of the individual runs using 
tkregister2 command, the registration doesn't look good (bottom row images).
tkregister2 --s $subj --mov  /$subj/bold/011/template.nii.gz --surf --reg 
new.dat --regheader .

I'm wondering if I need to do manual edits, and I appreciate any advice on that.



Thanks
Mona




Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129




___
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<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] mis-registration question

[Nasiriavanaki, Zahra]

Dear Freesurfers


Hi


I have a subject that the registration is not done correctly in two runs (run 
12 and run 15) .

The tkregister-sess values for this subject is shown below.

Subject 1 10 0.2628
Subject 1 11 0.3038
Subject 1 12 0.7639
Subject 1 13 0.3364
Subject 1 14 0.3346
Subject 1 15 0.9361
Subject 1 16 0.2584
Subject 1 17 0.2488


I attached the screen shots from tkregister2 to this email. The functional data 
is only collected in a slab of parietal and occipital lobe.

I appreciate if you let me know how to fix them.


Thanks

Mona


[cid:6833a8d0-828b-4f31-9b61-2a4a1c3a670d][cid:7d39f7e2-609a-43a5-a964-dd95f8179c30]





Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] mis-registration question

[Nasiriavanaki, Zahra]

Hi experts


I appreciate if you could help me with this question.


Thanks



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Nasiriavanaki, Zahra
Sent: Friday, August 2, 2019 12:17:53 PM
To: Freesurfer support list 
Subject: mis-registration question


Dear Freesurfers


Hi


I have a subject that the registration is not done correctly in two runs (run 
12 and run 15) .

The tkregister-sess values for this subject is shown below.

Subject 1 10 0.2628
Subject 1 11 0.3038
Subject 1 12 0.7639
Subject 1 13 0.3364
Subject 1 14 0.3346
Subject 1 15 0.9361
Subject 1 16 0.2584
Subject 1 17 0.2488


I attached the screen shots from tkregister2 to this email. The functional data 
is only collected in a slab of parietal and occipital lobe.

I appreciate if you let me know how to fix them.


Thanks

Mona


[cid:6833a8d0-828b-4f31-9b61-2a4a1c3a670d][cid:7d39f7e2-609a-43a5-a964-dd95f8179c30]





Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] mis-registration question

[Nasiriavanaki, Zahra]

Thanks for your reply.


preproc-sess -s $subj -per-run -nostc -fwhm 0 -surface fsaverage lhrh -fsd bold 
-init-header -d .


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Monday, August 5, 2019 1:01:07 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mis-registration question

what is your registration command?

On 8/2/2019 12:17 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers


Hi


I have a subject that the registration is not done correctly in two runs (run 
12 and run 15) .

The tkregister-sess values for this subject is shown below.

Subject 1 10 0.2628
Subject 1 11 0.3038
Subject 1 12 0.7639
Subject 1 13 0.3364
Subject 1 14 0.3346
Subject 1 15 0.9361
Subject 1 16 0.2584
Subject 1 17 0.2488


I attached the screen shots from tkregister2 to this email. The functional data 
is only collected in a slab of parietal and occipital lobe.

I appreciate if you let me know how to fix them.


Thanks

Mona


[cid:part1.4F74A672.38AE9526@mgh.harvard.edu][cid:part2.AC5CF7F1.14B22350@mgh.harvard.edu]





Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





___
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

Re: [Freesurfer] spatial scale bar question

[Nasiriavanaki, Zahra]

Hi Freesurfer experts


I wanted to follow up on my question about "spatial scale bar" for significancy 
maps in FS.

I appreciate if you let me know about the updates on that.


Thanks

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Monday, May 13, 2019 9:56:41 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] spatial scale bar question

Hi Mona

sure. As I said it is a bit more complicated than it seems. Ruopeng will
post a note when something usable is in the dev version

Bruce


On Mon, 13 May
2019, Nasiriavanaki, Zahra wrote:

>
> Yes Bruce.
>
> It doesn't work.
>
> I appreciate if you could let me know when you had any updates on it.
>
>
> Thanks
>
> Mona
>
> ___
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of
> Bruce Fischl 
> Sent: Friday, May 10, 2019 6:15:05 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] spatial scale bar question
> I don't think it currently works in 3D mode as it is not trivial due to
> perspective transforms. Ruopeng is trying some things
> On Fri, 10 May 2019,
> Greve, Douglas N.,Ph.D. wrote:
>
> > here is a pick of it
> > https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif
>
> [fv.colorbar.gif]
>
>
> >
> >
> > On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
> >
> >   Thanks for your reply.
> >
> >   I have overlaid the significance map on an inflated brain, and I 
> > don't see the scale
> >   bar icon anywhere.
> >
> >   tksurferfv fsaverage lh inflated -ov sig.nii.gz
> >
> >
> >__
> _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
> >  on
> > behalf of Greve, Douglas N.,Ph.D. 
> > Sent: Friday, May 10, 2019 3:27:15 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] spatial scale bar question
> > In freeview, it is just an icon above the image window. Click on it and it 
> > should give you a
> > scale bar
> >
> > On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
> >
> >   Dear Freesurfers
> >
> >   Hi
> >
> >
> >   I am trying to add a spatial scale bar to my cortical maps in 
> > tksurfer. However,
> >   as it's mentioned in Freesurfer forum before, the scale bar in 
> > tksurfer shrinks
> >   when you zoom in the brain.
> >
> >   I couldn't find a scale bar option in Freeview neither.
> >
> >   I appreciate if you could let me know how to get a scale bar.
> >
> >
> >   Thanks
> >
> >   Mona
> >
> >
> >
> > ___
> > 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
> >
> >
> >
> >
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] spatial scale bar question

[Nasiriavanaki, Zahra]

Hi Ruopeng


Thanks for your reply.

I have a question though. When I zoom in the 3D image, the scale bar numbers 
don't change. Shouldn't they change when I zoom in?


Thanks

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Friday, August 16, 2019 8:46:57 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] spatial scale bar question

Hi Mona,

If you are running the latest dev build, you can right click in the 3D view and 
choose “Show 3D scale”. The scale bars can only be placed at the boundary of 
the FOV.

Best,
Ruopeng

On Aug 15, 2019, at 4:30 PM, Nasiriavanaki, Zahra 
mailto:znasiriavan...@mgh.harvard.edu>> wrote:

Hi Freesurfer experts

I wanted to follow up on my question about "spatial scale bar" for significancy 
maps in FS.
I appreciate if you let me know about the updates on that.

Thanks
Mona


Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>>
Sent: Monday, May 13, 2019 9:56:41 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] spatial scale bar question

Hi Mona

sure. As I said it is a bit more complicated than it seems. Ruopeng will
post a note when something usable is in the dev version

Bruce


On Mon, 13 May
2019, Nasiriavanaki, Zahra wrote:

>
> Yes Bruce.
>
> It doesn't work.
>
> I appreciate if you could let me know when you had any updates on it.
>
>
> Thanks
>
> Mona
>
> ___
> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>  
> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
>  on behalf of
> Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>>
> Sent: Friday, May 10, 2019 6:15:05 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] spatial scale bar question
> I don't think it currently works in 3D mode as it is not trivial due to
> perspective transforms. Ruopeng is trying some things
> On Fri, 10 May 2019,
> Greve, Douglas N.,Ph.D. wrote:
>
> > here is a pick of it
> > https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif
>
> [fv.colorbar.gif]
>
>
> >
> >
> > On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
> >
> >   Thanks for your reply.
> >
> >   I have overlaid the significance map on an inflated brain, and I 
> > don't see the scale
> >   bar icon anywhere.
> >
> >   tksurferfv fsaverage lh inflated -ov sig.nii.gz
> >
> >
> >__
> _
> > From: 
> > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >  
> > mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
> >  on
> > behalf of Greve, Douglas N.,Ph.D. 
> > mailto:dgr...@mgh.harvard.edu>>
> > Sent: Friday, May 10, 2019 3:27:15 PM
> > To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> > Subject: Re: [Freesurfer] spatial scale bar question
> > In freeview, it is just an icon above the image window. Click on it and it 
> > should give you a
> > scale bar
> >
> > On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
> >
> >   Dear Freesurfers
> >
> >   Hi
> >
> >
> >   I am trying to add a spatial scale bar to my cortical maps in 
> > tksurfer. However,
> >   as it's mentioned in Freesurfer forum before, the scale bar in 
> > tksurfer shrinks
> >   when you zoom in the brain.
> >
> >   I couldn't find a scale bar option in Freeview neither.
> >
> >   I appreciate if you could let me know how to get a scale bar.
> >
> >
> >   Thanks
> >
> >   Mona
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.ed

Re: [Freesurfer] spatial scale bar question

[Nasiriavanaki, Zahra]

Thanks so much.


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ruopeng Wang 

Sent: Friday, August 16, 2019 10:42:08 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] spatial scale bar question

The 3D scale is also a 3d object in the view. When you zoom the view, the scale 
will also zoom. But the number should not change.

On Aug 16, 2019, at 10:25 AM, Nasiriavanaki, Zahra 
mailto:znasiriavan...@mgh.harvard.edu>> wrote:

Hi Ruopeng

Thanks for your reply.
I have a question though. When I zoom in the 3D image, the scale bar numbers 
don't change. Shouldn't they change when I zoom in?

Thanks
Mona

Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Ruopeng Wang 
mailto:rpw...@nmr.mgh.harvard.edu>>
Sent: Friday, August 16, 2019 8:46:57 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] spatial scale bar question

Hi Mona,

If you are running the latest dev build, you can right click in the 3D view and 
choose “Show 3D scale”. The scale bars can only be placed at the boundary of 
the FOV.

Best,
Ruopeng

On Aug 15, 2019, at 4:30 PM, Nasiriavanaki, Zahra 
mailto:znasiriavan...@mgh.harvard.edu>> wrote:

Hi Freesurfer experts

I wanted to follow up on my question about "spatial scale bar" for significancy 
maps in FS.
I appreciate if you let me know about the updates on that.

Thanks
Mona


Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>>
Sent: Monday, May 13, 2019 9:56:41 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] spatial scale bar question

Hi Mona

sure. As I said it is a bit more complicated than it seems. Ruopeng will
post a note when something usable is in the dev version

Bruce


On Mon, 13 May
2019, Nasiriavanaki, Zahra wrote:

>
> Yes Bruce.
>
> It doesn't work.
>
> I appreciate if you could let me know when you had any updates on it.
>
>
> Thanks
>
> Mona
>
> ___
> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>  
> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
>  on behalf of
> Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>>
> Sent: Friday, May 10, 2019 6:15:05 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] spatial scale bar question
> I don't think it currently works in 3D mode as it is not trivial due to
> perspective transforms. Ruopeng is trying some things
> On Fri, 10 May 2019,
> Greve, Douglas N.,Ph.D. wrote:
>
> > here is a pick of it
> > https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif
>
> [fv.colorbar.gif]
>
>
> >
> >
> > On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
> >
> >   Thanks for your reply.
> >
> >   I have overlaid the significance map on an inflated brain, and I 
> > don't see the scale
> >   bar icon anywhere.
> >
> >   tksurferfv fsaverage lh inflated -ov sig.nii.gz
> >
> >
> >__
> _
> > From: 
> > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >  
> > mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
> >  on
> > behalf of Greve, Douglas N.,Ph.D. 
> > mailto:dgr...@mgh.harvard.edu>>
> > Sent: Friday, May 10, 2019 3:27:15 PM
> > To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> > Subject: Re: [Freesurfer] spatial scale bar question
> > In freeview, it is just an icon above the image window. Click on it and it 
> > should give you a
> > scale bar
> >
> > On 5/10/2019 3:13 PM, Nasiriavanaki, Zahr

[Freesurfer] Opseq2 question

[Nasiriavanaki, Zahra]

Hi Freesurfer experts

I have a question about designing an event related task. We are designing a 
task for fear conditioning. Each stimuli presentation lasts 4 seconds. My 
question is if we set the TR to 2 (which is a multiply of 4), will it make the 
paradigm to have more power in signal detection? Or does it not matter if the 
TR and stimuli presentation be a multiply of each other or not?
I appreciate if you give me your comments on that.

Thanks a lot
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] Opseq2 question

[Nasiriavanaki, Zahra]

Hi Doug

Thank you very much for your reply. How does it make a difference if I use FIR? 
Could you please explain a little bit more?

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Tuesday, September 10, 2019 11:24 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Opseq2 question

If you are going to assume a shape to the hemodynamic response, then I
don't think it makes much difference. It will make a difference if you
are going to use an FIR.

On 9/9/19 10:49 AM, Nasiriavanaki, Zahra wrote:
> Hi Freesurfer experts
>
> I have a question about designing an event related task. We are
> designing a task for fear conditioning. Each stimuli presentation
> lasts 4 seconds. My question is if we set the TR to 2 (which is a
> multiply of 4), will it make the paradigm to have more power in signal
> detection? Or does it not matter if the TR and stimuli presentation be
> a multiply of each other or not?
> I appreciate if you give me your comments on that.
>
> Thanks a lot
> Mona
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
> ___
> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Opseq2 question

[Nasiriavanaki, Zahra]

Thank you so much.


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Tuesday, September 10, 2019 11:46 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Opseq2 question

The FIR assumes that your stimuli will be presented on a "clock", eg, on
a TR (not necessarily ever TR, but every time a stimulus is presented,
it starts on a TR). The "tick" of the clock can be the TR or it can be
an integer divisor of the TR (eg, TR/2 TR/3). The finer you make it, the
more flexibility you have as to when a stimulus can occur. But you loose
power based on the divisor, eg, TR/3 means that you'll have 1/3 the power.

On 9/10/19 11:35 AM, Nasiriavanaki, Zahra wrote:
> Hi Doug
>
> Thank you very much for your reply. How does it make a difference if I
> use FIR? Could you please explain a little bit more?
>
> Thanks
> Mona
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> *Sent:* Tuesday, September 10, 2019 11:24 AM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* Re: [Freesurfer] Opseq2 question
> If you are going to assume a shape to the hemodynamic response, then I
> don't think it makes much difference. It will make a difference if you
> are going to use an FIR.
>
> On 9/9/19 10:49 AM, Nasiriavanaki, Zahra wrote:
> > Hi Freesurfer experts
> >
> > I have a question about designing an event related task. We are
> > designing a task for fear conditioning. Each stimuli presentation
> > lasts 4 seconds. My question is if we set the TR to 2 (which is a
> > multiply of 4), will it make the paradigm to have more power in signal
> > detection? Or does it not matter if the TR and stimuli presentation be
> > a multiply of each other or not?
> > I appreciate if you give me your comments on that.
> >
> > Thanks a lot
> > Mona
> >
> > *Zahra (Mona) Nasiriavanaki*
> >
> > Postdoctoral Research Fellow
> >
> > Martinos Center for Biomedical Imaging
> >
> > Massachusetts General Hospital
> >
> > 149 13th Street, 149-2615
> >
> > Charlestown, MA, USA, 02129
> >
> >
> >
> >
> > ___
> > 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
>
> ___
> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mkcontrast-sess question

[Nasiriavanaki, Zahra]

Dear Freesurfer experts

Hi

I have a question about weighting different contrasts using mkcontrast-sess 
commmand.
I have single subject functional data with 18 different contrasts, and I am 
willing to weight the different contrasts as (for example) ascending linear. 
Something like:
 mkcontrast-sess -an $analysis   -a 1 -a 2 -a 3 -a 4 -a 10 -a 11 -a 12 -a 13 -a 
6 -a 7 -a 8 -a 9 -a 15 -a 16 -a 17 -a 18
 In which contrast number two weights twice as contrast number one and contrast 
number 3 weights twice as contrast number 2 and so on.  Is there any way I can 
do such a thing with mkcontrast-sess? or do you have any suggestion for such an 
analysis?

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] mkcontrast-sess question

[Nasiriavanaki, Zahra]

Hi Freesurferers

I appreciate if anyone could give me their thoughts on this question.

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Nasiriavanaki, Zahra
Sent: Friday, September 13, 2019 11:08 AM
To: Freesurfer support list 
Subject: mkcontrast-sess question

Dear Freesurfer experts

Hi

I have a question about weighting different contrasts using mkcontrast-sess 
commmand.
I have single subject functional data with 18 different contrasts, and I am 
willing to weight the different contrasts as (for example) ascending linear. 
Something like:
 mkcontrast-sess -an $analysis   -a 1 -a 2 -a 3 -a 4 -a 10 -a 11 -a 12 -a 13 -a 
6 -a 7 -a 8 -a 9 -a 15 -a 16 -a 17 -a 18
 In which contrast number two weights twice as contrast number one and contrast 
number 3 weights twice as contrast number 2 and so on.  Is there any way I can 
do such a thing with mkcontrast-sess? or do you have any suggestion for such an 
analysis?

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] mkcontrast-sess question

[Nasiriavanaki, Zahra]

Thanks a lot Doug!
It was exactly what I needed.

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Monday, September 16, 2019 10:13 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mkcontrast-sess question

Are you trying to do a parametric analysis? See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation

On 9/13/19 11:08 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurfer experts

Hi

I have a question about weighting different contrasts using mkcontrast-sess 
commmand.
I have single subject functional data with 18 different contrasts, and I am 
willing to weight the different contrasts as (for example) ascending linear. 
Something like:
 mkcontrast-sess -an $analysis   -a 1 -a 2 -a 3 -a 4 -a 10 -a 11 -a 12 -a 13 -a 
6 -a 7 -a 8 -a 9 -a 15 -a 16 -a 17 -a 18
 In which contrast number two weights twice as contrast number one and contrast 
number 3 weights twice as contrast number 2 and so on.  Is there any way I can 
do such a thing with mkcontrast-sess? or do you have any suggestion for such an 
analysis?

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





___
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

Re: [Freesurfer] PALM Analysis

[Nasiriavanaki, Zahra]

Hi Doug

I wanted to follow up this email and ask you a question. I see in the fspalm 
page, it says "You can use fspalm with both volume- and surface-based analyses; 
it will figure everything out".
Considering your reply to the below email, I'm wondering if we can use fspalm 
for subcortical analysis or not?

I appreciate very much any comments on it.

Thanks
Mona



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

Sent: Monday, September 2, 2019 10:32 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] PALM Analysis

Sorry, fsplam is only for surfaces.

On 9/2/2019 7:46 PM, Harikumar, Amritha wrote:
> Hi there,
>
> I am trying to run a Permutation Analysis of Linear Models (PALM) for 
> analyzing subcortical areas in the nucleus accumbens, caudate, and putamen. 
> Upon trying to run the script after reading the Freesurfer wiki, I am not 
> sure what it is referring to regarding applying fsPalm in MATLAB. My 
> questions are - do we a.) copy paste the existing fspalm command in Matlab 
> and run it after setting the two Freesurfer paths listed in the wiki, or what 
> is the correct procedure to run it? I tried running it in terminal as well, 
> but didn’t have any luck. My existing Matlab script has set up the two 
> Freesurfer paths, and is trying to run the fsPalm command for each 
> subcortical area of the three ROIs mentioned above, but that isn’t working 
> either. Any help in running fsPalm would be greatly appreciated!
>
> Thanks,
> Amritha
>
> Amritha Harikumar
> Clinical Research Coordinator
> Holt Emotion and Social Neuroscience Lab
> Department of Psychiatric Neuroimaging
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> ___
> 149 13th Street, Rm 2620A
> Charlestown, MA 02129
> Phone: 617-724-3283
>
>
>
>
> ___
> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] view labels in native space

[Nasiriavanaki, Zahra]

Hi Freesurfer experts

I have a few labels that correspond to activation clusters in fsaverage space 
for an individual subject. I used mri_label2label to transfer them to native 
space of the subject.

export SUBJECTS_DIR=/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR
mri_label2label --srclabel  ./first_levels/$subj/label/aparc/pos/lh-0001.label  
--trglabel lh-new.label  --srcsubject fsaverage --trgsubject ${subj} 
--regmethod surface --hemi lh

When I overlay the native label on top of the fsaverage significance map 
(tksurfer fsaverage lh inflated -ov sig.nii.gz), it looks like small dots all 
over the map.
Is this because I'm viewing the native label in fsaverage space?
Is there a way to view these labels in this subject's native space instead of 
fsaverage, something like tksurfer native(instead of fsaverage) lh inflated -ov 
sig.nii.gz?

Thank you very much in advance
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] view labels in native space

[Nasiriavanaki, Zahra]

Hi Doug

Thanks for your reply.
Could you pleas let me know how I can solve this issue?
How should I view those labels on the subject’s native space?

Thanks
Mona

On Oct 28, 2019, at 10:18 AM, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:

yes, the vertices in one subject do not have any correspondence to vertices in 
an other subject

On 10/25/19 12:08 PM, Nasiriavanaki, Zahra wrote:
Hi Freesurfer experts

I have a few labels that correspond to activation clusters in fsaverage space 
for an individual subject. I used mri_label2label to transfer them to native 
space of the subject.

export SUBJECTS_DIR=/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR
mri_label2label --srclabel  ./first_levels/$subj/label/aparc/pos/lh-0001.label  
--trglabel lh-new.label  --srcsubject fsaverage --trgsubject ${subj} 
--regmethod surface --hemi lh

When I overlay the native label on top of the fsaverage significance map 
(tksurfer fsaverage lh inflated -ov sig.nii.gz), it looks like small dots all 
over the map.
Is this because I'm viewing the native label in fsaverage space?
Is there a way to view these labels in this subject's native space instead of 
fsaverage, something like tksurfer native(instead of fsaverage) lh inflated -ov 
sig.nii.gz?

Thank you very much in advance
Mona


Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129




___
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

Re: [Freesurfer] view labels in native space

[Nasiriavanaki, Zahra]

Hi Tim

Thanks for you reply.
I did use the command you recommended (   tksurfer subject23 lh inflated -ov 
sig.nii.gz  )
But, I don't see any activation on it. However, when I use   (   tksurfer 
fsaverage lh inflated -ov sig.nii.gz  ), I see patches of activation.

Is it because my whole analysis is done on fsaverage and not native space?


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tim Schäfer 

Sent: Monday, October 28, 2019 10:28 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] view labels in native space

External Email - Use Caution

If I get the question correctly, all you have to do is:

1) not run mri_label2label at all
2) replace 'fsaverage' with the subject identifier in the command, e.g.:

  tksurfer subject23 lh inflated -ov sig.nii.gz

Best,

Tim

> On October 28, 2019 at 3:21 PM "Nasiriavanaki, Zahra" 
>  wrote:
>
>
> Hi Doug
>
> Thanks for your reply.
> Could you pleas let me know how I can solve this issue?
> How should I view those labels on the subject’s native space?
>
> Thanks
> Mona
>
> On Oct 28, 2019, at 10:18 AM, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> yes, the vertices in one subject do not have any correspondence to vertices 
> in an other subject
>
> On 10/25/19 12:08 PM, Nasiriavanaki, Zahra wrote:
> Hi Freesurfer experts
>
> I have a few labels that correspond to activation clusters in fsaverage space 
> for an individual subject. I used mri_label2label to transfer them to native 
> space of the subject.
>
> export 
> SUBJECTS_DIR=/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR
> mri_label2label --srclabel  
> ./first_levels/$subj/label/aparc/pos/lh-0001.label  --trglabel lh-new.label  
> --srcsubject fsaverage --trgsubject ${subj} --regmethod surface --hemi lh
>
> When I overlay the native label on top of the fsaverage significance map 
> (tksurfer fsaverage lh inflated -ov sig.nii.gz), it looks like small dots all 
> over the map.
> Is this because I'm viewing the native label in fsaverage space?
> Is there a way to view these labels in this subject's native space instead of 
> fsaverage, something like tksurfer native(instead of fsaverage) lh inflated 
> -ov sig.nii.gz?
>
> Thank you very much in advance
> Mona
>
>
> Zahra (Mona) Nasiriavanaki
> Postdoctoral Research Fellow
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street, 149-2615
> Charlestown, MA, USA, 02129
>
>
>
>
> ___
> 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

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

___
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

Re: [Freesurfer] flat maps in native space

[Nasiriavanaki, Zahra]

Hi Bruce

Thanks for your reply.
Well, two of my subjects have this problem. I have two subjects with correct 
flattened maps and for 3 other subjects "the mris_flatten"  is still running.
I attached the directory and I would appreciate if you could please take a look.

Thanks
MOna



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Friday, November 8, 2019 11:54 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] flat maps in native space

Hi Mona

that is pretty strange looking. Is the data somewhere local that we can
take a look at it? I would guess that one of the cuts left a connection
around, but would need to look at it to tell. Have you flattened other
subjects successfully?

cheers
Bruce


On Fri, 8 Nov 2019, Nasiriavanaki, Zahra
wrote:

> Hi Freesurfer experts
>
> I was trying to make flat maps for individual subjects, following instruction
> in 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch.
> For some of my subjects, the flat maps are distorted (attached image).
> Please let me know what you think.
>
> Thanks
> Mona
>
> [IMAGE]
>
> Zahra (Mona) Nasiriavanaki
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
>


new file
Description: new file
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] selxavg in native space vs fsaverage space

[Nasiriavanaki, Zahra]

Dear Freesurfer experts

Hi

I was trying to do selxavg in native space for individual subjects which I have 
analyzed them in "fsaverage" space before.
I have two sessions of functional data for each subject. In order to register 
them on one T1, I put the functional data from both sessions in one bold folder 
and registered all of them to one T1.
The maps that I acquired from these analysis are slightly different from 
"fsaverage" maps.  In "fsaverage" analysis, I analyzed each session separately 
(selxavg) and then concatenated (isxconcat) the two sessions at the end. I 
believe it is not possible to do this in "native" space, since I have to 
register all the functional data to one T1, right?
I need to know what is causing the differences in "native" and "fsaverage" maps?
I appreciate if you could reply.

Thanks a lot
Mona




Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] selxavg in native space vs fsaverage space

[Nasiriavanaki, Zahra]

Hi Doug

Thanks a lot for your reply.
what I mean by native space, is to register each subject's functional data on 
their own anatomical data.
yes, I was using --surf self in my preprocessing and mkanalysis, but since I 
was not using any smoothing, fwhm=0 in both native and fsaverage analysis, I 
thought the results should not differ.

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Wednesday, December 11, 2019 6:41 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] selxavg in native space vs fsaverage space

Hi Mona, not sure what you are trying to do. When you say "native"
space, do you mean native functional space or native anatmical space?
If you want to analyze the data on the native surface, you can use
--surf self when you run preproc-sess and mkanalysis-sess (instead of
specifying fsaverage) and analyze the session separately (which is
better if you are trying to do a longitudinal analysis).

it is hard to answer your other question about why there is a diff
between fsaverage and native space analyses without seeing what the
differences are and without knowing what the actual native space is.
They are different analyses, so they will not give exactly the same
results.

doug

On 12/11/19 11:30 AM, Nasiriavanaki, Zahra wrote:
> Dear Freesurfer experts
>
> Hi
>
> I was trying to do selxavg in native space for individual subjects
> which I have analyzed them in "fsaverage" space before.
> I have two sessions of functional data for each subject. In order to
> register them on one T1, I put the functional data from both sessions
> in one bold folder and registered all of them to one T1.
> The maps that I acquired from these analysis are slightly different
> from "fsaverage" maps.  In "fsaverage" analysis, I analyzed each
> session separately (selxavg) and then concatenated (isxconcat) the two
> sessions at the end. I believe it is not possible to do this in
> "native" space, since I have to register all the functional data to
> one T1, right?
> I need to know what is causing the differences in "native" and
> "fsaverage" maps?
> I appreciate if you could reply.
>
> Thanks a lot
> Mona
>
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
> ___
> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] flat maps in native space

[Nasiriavanaki, Zahra]

Thanks a lot for your reply Doug.
I will re-do my recon as you said.
Do you think the "blurriness" might be because of inadequate inflating of the 
surface? My expert option file was : mris_inflate -n 15 -w 10.
In addition to your recommendations, do you think I need to increase "n"?

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Wednesday, December 11, 2019 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] flat maps in native space

I'm not sure what is going on here, but I would guess that the v6 hires
stream is not behaving  very well. I would suggest using a patch I
created the HCP. If you are in the version 6 environment, you can run
recon-all.v6.hires the same way you did recon-all, but do not use -hires
and instead use -conf2hires

doug


On 12/9/19 6:17 PM, Nasiriavanaki, Zahra wrote:
> Dear Freesurfer experts
>
> Hi
>
> I have a follow up question regarding the flat maps in native space.
> I was trying to re-do the "making cuts and flattening the maps" step,
> but first I want to know if these individual maps looks ok to you.
> As you see in some parts of the brain the suci and gyri are *blurred
> *and this causes some of the cuts (the cut in Calcarine fissure) to be
> distorted (image attached). I'm not sure if this is normal to see the
> blurriness and distorted shape of the brain in individual maps or not.
> Is it possible that reconstruction hasn't been done well and that's
> causing this problem?
>
> Thanks a lot
> Mona
>
>
>
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> 
> *From:* Nasiriavanaki, Zahra 
> *Sent:* Friday, November 8, 2019 12:19 PM
> *To:* Bruce Fischl ; Freesurfer support
> list 
> *Subject:* Re: [Freesurfer] flat maps in native space
> Hi Bruce
>
> Thanks for your reply.
> Well, two of my subjects have this problem. I have two subjects with
> correct flattened maps and for 3 other subjects "the mris_flatten"  is
> still running.
> I attached the directory and I would appreciate if you could please
> take a look.
>
> Thanks
> MOna
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> *Sent:* Friday, November 8, 2019 11:54 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] flat maps in native space
> Hi Mona
>
> that is pretty strange looking. Is the data somewhere local that we can
> take a look at it? I would guess that one of the cuts left a connection
> around, but would need to look at it to tell. Have you flattened other
> subjects successfully?
>
> cheers
> Bruce
>
>
> On Fri, 8 Nov 2019, Nasiriavanaki, Zahra
> wrote:
>
> > Hi Freesurfer experts
> >
> > I was trying to make flat maps for individual subjects, following
> instruction
> > in
> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch.
> > For some of my subjects, the flat maps are distorted (attached image).
> > Please let me know what you think.
> >
> > Thanks
> > Mona
> >
> > [IMAGE]
> >
> > Zahra (Mona) Nasiriavanaki
> >
> > Postdoctoral Research Fellow
> >
> > Martinos Center for Biomedical Imaging
> >
> > Massachusetts General Hospital
> >
> > 149 13th Street, 149-2615
> >
> > Charlestown, MA, USA, 02129
> >
> >
> >
> >
> >
>
> ___
> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] flat maps in native space

[Nasiriavanaki, Zahra]

Hi

I was trying to run recon-all.v6.hires, but it doesn't give me permission. I am 
using a linux computer in Martinos center.
Could you please let me know how to solve it?

Thanks
Mona

[bee:Mona] (nmr-stable6-env) ./make_recon.sh osre_7T_all 009
./make_recon.sh: line 7: /usr/local/freesurfer/stable6/bin/recon-all.v6.hires: 
Permission denied


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Nasiriavanaki, Zahra 
Sent: Thursday, December 12, 2019 10:38 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] flat maps in native space

Thanks a lot for your reply Doug.
I will re-do my recon as you said.
Do you think the "blurriness" might be because of inadequate inflating of the 
surface? My expert option file was : mris_inflate -n 15 -w 10.
In addition to your recommendations, do you think I need to increase "n"?

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Wednesday, December 11, 2019 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] flat maps in native space

I'm not sure what is going on here, but I would guess that the v6 hires
stream is not behaving  very well. I would suggest using a patch I
created the HCP. If you are in the version 6 environment, you can run
recon-all.v6.hires the same way you did recon-all, but do not use -hires
and instead use -conf2hires

doug


On 12/9/19 6:17 PM, Nasiriavanaki, Zahra wrote:
> Dear Freesurfer experts
>
> Hi
>
> I have a follow up question regarding the flat maps in native space.
> I was trying to re-do the "making cuts and flattening the maps" step,
> but first I want to know if these individual maps looks ok to you.
> As you see in some parts of the brain the suci and gyri are *blurred
> *and this causes some of the cuts (the cut in Calcarine fissure) to be
> distorted (image attached). I'm not sure if this is normal to see the
> blurriness and distorted shape of the brain in individual maps or not.
> Is it possible that reconstruction hasn't been done well and that's
> causing this problem?
>
> Thanks a lot
> Mona
>
>
>
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> 
> *From:* Nasiriavanaki, Zahra 
> *Sent:* Friday, November 8, 2019 12:19 PM
> *To:* Bruce Fischl ; Freesurfer support
> list 
> *Subject:* Re: [Freesurfer] flat maps in native space
> Hi Bruce
>
> Thanks for your reply.
> Well, two of my subjects have this problem. I have two subjects with
> correct flattened maps and for 3 other subjects "the mris_flatten"  is
> still running.
> I attached the directory and I would appreciate if you could please
> take a look.
>
> Thanks
> MOna
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> *Sent:* Friday, November 8, 2019 11:54 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] flat maps in native space
> Hi Mona
>
> that is pretty strange looking. Is the data somewhere local that we can
> take a look at it? I would guess that one of the cuts left a connection
> around, but would need to look at it to tell. Have you flattened other
> subjects successfully?
>
> cheers
> Bruce
>
>
> On Fri, 8 Nov 2019, Nasiriavanaki, Zahra
> wrote:
>
> > Hi Freesurfer experts
> >
> > I was trying to make flat maps for individual subjects, following
> instruction
> > in
> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch.
> > For some of my subjects, the flat maps are distorted (attached image).
> > Please let me know what you think.
> >
> > Thanks
> > Mona
> >
> > [IMAGE]
> >
> > Zahra (Mona) Nasiriavanaki
> >
> > Postdoctoral Research Fellow
> >
> > Martinos Cen

Re: [Freesurfer] highres fMRI selxavg error

[Nasiriavanaki, Zahra]

I need to concatenate the two sessions. We scanned the subjects twice with the 
same task.
I need to see the maps for each session separately and also together.

Thanks

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Thursday, January 2, 2020 10:57 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] highres fMRI selxavg error

Why are you combining them into one bold folder?

On 12/30/2019 9:09 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurfer experts

Happy Holidays!
I have a subject with two highres fMRI scan sessions. Attached you can see an 
image, showing how I organized the sub-folders.
I preprocessed the bold1 and bold2 and then copied the preprocessed files to 
"bold from both sessions" folder.  I ran selxavg for bold1 and bold2 seperately 
and it went well.
However, when I ran selxavg for "bold from both sessions" folder, it gives the 
below error.
Could you please let me know what the problem is?Also if you have a better 
suggestion for how I should organize my subfolders/analysis, I appreciate that.

Thanks
Mona

>> >> >> >> /autofs/cluster/freesurfer/centos7_x86_64/stable6/fsfast/toolbox/fast_selxavg3.m
>> /autofs/cluster/freesurfer/centos7_x86_64/stable6/fsfast/toolbox/fast_ldanaflac.m
>> /autofs/cluster/freesurfer/centos7_x86_64/stable6/matlab/MRIread.m
>> >> >> starting fast_selxavg3b


#@# arap_7T_all ###
/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 12, skipping
 1 app.mat
 2 aw.mat
 3 caw.mat
 4 clo.mat
 5 faw.mat
 6 fem.mat
 7 fm.mat
 8 fmaw.mat
 9 mal.mat
10 maw.mat
11 oaw.mat
12 oc.mat
13 ocaw.mat
14 ope.mat
15 wit.mat
Excluding 6 points
nruns = 15
autostimdur =


outanadir = 
/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all/loom/loom_native.lh
Excluding 6 points
Excluding 0 points
Excluding 1 points
Excluding 5 points
Excluding 8 points
Excluding 3 points
Excluding 8 points
Excluding 4 points
Excluding 6 points
Excluding 10 points
Excluding 5 points
Excluding 5 points
Excluding 5 points
Excluding 5 points
Excluding 5 points
parfiles condition id list:  1  2  3  4  5  6  7  8
Found 41883/148565 (28.2) voxels in mask 1
Creating Design Matrix
 ... creation time =  0.040 sec
DoMCFit = 1
ntptot = 1350, nX = 219, DOF = 1131
Saving X matrix to 
/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all/loom/loom_native.lh/Xtmp.mat
XCond = 1873.07 (normalized)
Computing compensation for resdual AR1 bias
 1  -0.5  -0.456169(t=1.17104)
 2  -0.25  -0.261165(t=2.14097)
 3  0  -0.076309(t=2.3701)
 4  0.25  0.0914527(t=3.32529)
 5  0.5  0.225506(t=4.09175)
AR1 Correction M: 0.138222 1.44983
Computing contrast matrices
Computing contrasts
Loading previous GLM fit
Starting contrasts
app J=1 -
Error using *
Incorrect dimensions for matrix multiplication. Check that the number of
columns in the first matrix matches the number of rows in the second matrix. To
perform element wise multiplication, use '.*'.

Error in fast_fratiow (line 81)
ces = C*beta;

Error in fast_selxavg3b (line 1153)
 fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:));

>> --
ERROR: fast_selxavg3() failed\n




Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





___
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

Re: [Freesurfer] highres fMRI selxavg error

[Nasiriavanaki, Zahra]

I want to concatenate the two sessions which I guess is the same as combining 
them statistically.
Please note that it's all done in "self" space not fsaverage.


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Greve, Douglas N.,Ph.D. 
Sent: Thursday, January 2, 2020 11:46 AM
To: Nasiriavanaki, Zahra ; 
freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] highres fMRI selxavg error

When you say you need to see them together, what does that mean? Are you 
computing contrasts between the two sessions or you just want to combine them 
statistically?

On 1/2/2020 10:07 AM, Nasiriavanaki, Zahra wrote:
I need to concatenate the two sessions. We scanned the subjects twice with the 
same task.
I need to see the maps for each session separately and also together.

Thanks

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, January 2, 2020 10:57 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] highres fMRI selxavg error

Why are you combining them into one bold folder?

On 12/30/2019 9:09 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurfer experts

Happy Holidays!
I have a subject with two highres fMRI scan sessions. Attached you can see an 
image, showing how I organized the sub-folders.
I preprocessed the bold1 and bold2 and then copied the preprocessed files to 
"bold from both sessions" folder.  I ran selxavg for bold1 and bold2 seperately 
and it went well.
However, when I ran selxavg for "bold from both sessions" folder, it gives the 
below error.
Could you please let me know what the problem is?Also if you have a better 
suggestion for how I should organize my subfolders/analysis, I appreciate that.

Thanks
Mona

>> >> >> >> /autofs/cluster/freesurfer/centos7_x86_64/stable6/fsfast/toolbox/fast_selxavg3.m
>> /autofs/cluster/freesurfer/centos7_x86_64/stable6/fsfast/toolbox/fast_ldanaflac.m
>> /autofs/cluster/freesurfer/centos7_x86_64/stable6/matlab/MRIread.m
>> >> >> starting fast_selxavg3b


#@# arap_7T_all ###
/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 12, skipping
 1 app.mat
 2 aw.mat
 3 caw.mat
 4 clo.mat
 5 faw.mat
 6 fem.mat
 7 fm.mat
 8 fmaw.mat
 9 mal.mat
10 maw.mat
11 oaw.mat
12 oc.mat
13 ocaw.mat
14 ope.mat
15 wit.mat
Excluding 6 points
nruns = 15
autostimdur =


outanadir = 
/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all/loom/loom_native.lh
Excluding 6 points
Excluding 0 points
Excluding 1 points
Excluding 5 points
Excluding 8 points
Excluding 3 points
Excluding 8 points
Excluding 4 points
Excluding 6 points
Excluding 10 points
Excluding 5 points
Excluding 5 points
Excluding 5 points
Excluding 5 points
Excluding 5 points
parfiles condition id list:  1  2  3  4  5  6  7  8
Found 41883/148565 (28.2) voxels in mask 1
Creating Design Matrix
 ... creation time =  0.040 sec
DoMCFit = 1
ntptot = 1350, nX = 219, DOF = 1131
Saving X matrix to 
/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all/loom/loom_native.lh/Xtmp.mat
XCond = 1873.07 (normalized)
Computing compensation for resdual AR1 bias
 1  -0.5  -0.456169(t=1.17104)
 2  -0.25  -0.261165(t=2.14097)
 3  0  -0.076309(t=2.3701)
 4  0.25  0.0914527(t=3.32529)
 5  0.5  0.225506(t=4.09175)
AR1 Correction M: 0.138222 1.44983
Computing contrast matrices
Computing contrasts
Loading previous GLM fit
Starting contrasts
app J=1 -
Error using *
Incorrect dimensions for matrix multiplication. Check that the number of
columns in the first matrix matches the number of rows in the second matrix. To
perform element wise multiplication, use '.*'.

Error in fast_fratiow (line 81)
ces = C*beta;

Error in fast_selxavg3b (line 1153)
 fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:));

>> --
ERROR: fast_selxavg3() failed\n




Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospit

Re: [Freesurfer] highres fMRI selxavg error

[Nasiriavanaki, Zahra]

Thanks a lot for your reply.

I have one more question about selxavg error and I appreciate if you could 
reply.
I have another subject which has been scanned in 7T.  When I run selxavg, it 
doesn't go through for the left and right hemi, but it gets perfectly done for 
subcortex. I attached the log file.
We have collected the functional data in a slab of the brain containing 
subcortical areas and the insular cortex (at least this is what we aimed for). 
Looking at the data with tkregister2 command, I can't say if the insular cortex 
is included or not. Also, if it is included, then should we see the insular 
activation in cortical maps or subcortical ones?
tkregister2 --s ylug_ass_sess01 --mov  
$all_subjects/ylug_ass_sess01/bold/010/template.nii.gz --surf --reg new.dat 
--regheader

Thanks a lot
Mona




Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Greve, Douglas N.,Ph.D. 
Sent: Thursday, January 2, 2020 1:18 PM
To: Nasiriavanaki, Zahra ; 
freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] highres fMRI selxavg error

The easiest thing to do is to probably do the concatenation by hand, eg,
mri_concat subj/sess01/analysis/contrast/ces.nii.gz 
subj/sess01/analysis/contrast/ces.nii.gz --o ces.sess01+sess02.nii.gz
mri_concat subj/sess01/analysis/contrast/cesvar.nii.gz 
subj/sess01/analysis/contrast/cesvar.nii.gz --o cesvar.sess01+sess02.nii.gz

Create a dof file by adding together the dofs for each individual analysis as 
indicated by these values. Just put this number into a text file, eg, 
dof.sess01+sess02.dat
cat subj/sess01/analysis/dof.dat subj/sess01/analysis/dof.dat

Create a mask
fscalc subj/sess01/analysis/mask.nii.gz and  subj/sess01/analysis/mask.nii.gz 
-o mask.sess01+sess02.nii.gz

Then run glmfit like
mri_glmfit --surface subject lh --y ces.sess01+sess02.nii.gz --yffxvar 
cesvar.sess01+sess02.nii.gz --ffxdofdat dof.sess01+sess02.dat --mask 
mask.sess01+sess02.nii.gz --osgm --o ffx/subject/analysis/contrast/osgm





On 1/2/2020 11:20 AM, Nasiriavanaki, Zahra wrote:
I want to concatenate the two sessions which I guess is the same as combining 
them statistically.
Please note that it's all done in "self" space not fsaverage.


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, January 2, 2020 11:46 AM
To: Nasiriavanaki, Zahra 
<mailto:znasiriavan...@mgh.harvard.edu>; 
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] highres fMRI selxavg error

When you say you need to see them together, what does that mean? Are you 
computing contrasts between the two sessions or you just want to combine them 
statistically?

On 1/2/2020 10:07 AM, Nasiriavanaki, Zahra wrote:
I need to concatenate the two sessions. We scanned the subjects twice with the 
same task.
I need to see the maps for each session separately and also together.

Thanks

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, January 2, 2020 10:57 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] highres fMRI selxavg error

Why are you combining them into one bold folder?

On 12/30/2019 9:09 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurfer experts

Happy Holidays!
I have a subject with two highres fMRI scan sessions. Attached you can see an 
image, showing how I organized the sub-folders.
I preprocessed the bold1 and bold2 and then copied the preprocessed files to 
"bold from both sessions" folder.  I ran selxavg for bold1 and bold2 seperately 
and it went well.
However, when I ran selxavg for "bold from both sessions" folder, it gives the 
below error.
Could you please let me know what the problem is?Also if you have a better 
suggestion for how I should organize my subfolders/analysis, I appreciate that.

Thanks
Mona

>> >> >> >> /autofs/cluster/freesurfer/centos7_x86_64/stable6/fsfast/toolbox/fast_selxavg3.m
>> /autofs/cluster/freesurfer/centos7_x86_64/stable6/fsfast/toolbox/fast_lda

Re: [Freesurfer] highres fMRI selxavg error

[Nasiriavanaki, Zahra]

I did run it from the shell and figured out what the problem was!

Thanks a lot!!
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Greve, Douglas N.,Ph.D. 
Sent: Thursday, January 2, 2020 3:25 PM
To: Nasiriavanaki, Zahra ; 
freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] highres fMRI selxavg error

It appears to be dying on this command
mris_fwhm --mask 
/autofs/space/oprah_001/users/zn025/fearcond_7T/all_subjects/ylug_ass_sess01/bold/cond.lh/mask.nii
Can you run it from the shell and send the terminal output?


On 1/2/2020 2:13 PM, Nasiriavanaki, Zahra wrote:
Thanks a lot for your reply.

I have one more question about selxavg error and I appreciate if you could 
reply.
I have another subject which has been scanned in 7T.  When I run selxavg, it 
doesn't go through for the left and right hemi, but it gets perfectly done for 
subcortex. I attached the log file.
We have collected the functional data in a slab of the brain containing 
subcortical areas and the insular cortex (at least this is what we aimed for). 
Looking at the data with tkregister2 command, I can't say if the insular cortex 
is included or not. Also, if it is included, then should we see the insular 
activation in cortical maps or subcortical ones?
tkregister2 --s ylug_ass_sess01 --mov  
$all_subjects/ylug_ass_sess01/bold/010/template.nii.gz --surf --reg new.dat 
--regheader

Thanks a lot
Mona




Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, January 2, 2020 1:18 PM
To: Nasiriavanaki, Zahra 
<mailto:znasiriavan...@mgh.harvard.edu>; 
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] highres fMRI selxavg error

The easiest thing to do is to probably do the concatenation by hand, eg,
mri_concat subj/sess01/analysis/contrast/ces.nii.gz 
subj/sess01/analysis/contrast/ces.nii.gz --o ces.sess01+sess02.nii.gz
mri_concat subj/sess01/analysis/contrast/cesvar.nii.gz 
subj/sess01/analysis/contrast/cesvar.nii.gz --o cesvar.sess01+sess02.nii.gz

Create a dof file by adding together the dofs for each individual analysis as 
indicated by these values. Just put this number into a text file, eg, 
dof.sess01+sess02.dat
cat subj/sess01/analysis/dof.dat subj/sess01/analysis/dof.dat

Create a mask
fscalc subj/sess01/analysis/mask.nii.gz and  subj/sess01/analysis/mask.nii.gz 
-o mask.sess01+sess02.nii.gz

Then run glmfit like
mri_glmfit --surface subject lh --y ces.sess01+sess02.nii.gz --yffxvar 
cesvar.sess01+sess02.nii.gz --ffxdofdat dof.sess01+sess02.dat --mask 
mask.sess01+sess02.nii.gz --osgm --o ffx/subject/analysis/contrast/osgm





On 1/2/2020 11:20 AM, Nasiriavanaki, Zahra wrote:
I want to concatenate the two sessions which I guess is the same as combining 
them statistically.
Please note that it's all done in "self" space not fsaverage.


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, January 2, 2020 11:46 AM
To: Nasiriavanaki, Zahra 
<mailto:znasiriavan...@mgh.harvard.edu>; 
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] highres fMRI selxavg error

When you say you need to see them together, what does that mean? Are you 
computing contrasts between the two sessions or you just want to combine them 
statistically?

On 1/2/2020 10:07 AM, Nasiriavanaki, Zahra wrote:
I need to concatenate the two sessions. We scanned the subjects twice with the 
same task.
I need to see the maps for each session separately and also together.

Thanks

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, January 2, 2020 10:57 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] highres fMRI selxavg error

Why are you combining

Re: [Freesurfer] mis-registration question

[Nasiriavanaki, Zahra]

Dear Freesurfer experts

I have a follow up question about mis-registration and I appreciate if you 
could please reply.
I am having trouble fixing the registration for one of my subjects in highres 
scan.
The tkregister-sess values looked bad (around 0.8). So I checked the 
registration with tkregister2 and it looked off too.
I ran this command: "register-sess -s $subj -per-run -delete-dat -dof 6 -fsd 
bold4 -init-header -bbr-xopts bbr.xopts -d $all_subjects", with  --brute1max 20 
--brute1delta 4 ! which took a long while to finish! but still the registration 
is off.
Could you please help me with that?

Thanks
MOna



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Monday, August 5, 2019 1:53 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mis-registration question

Can you send a pointer to the data so I can have a look? Include the folder 
were you run tkregister-sess from as well as the $SUBJECTS_DIR

On 8/5/2019 1:33 PM, Nasiriavanaki, Zahra wrote:

Thanks for your reply.


preproc-sess -s $subj -per-run -nostc -fwhm 0 -surface fsaverage lhrh -fsd bold 
-init-header -d .


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Monday, August 5, 2019 1:01:07 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mis-registration question

what is your registration command?

On 8/2/2019 12:17 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers


Hi


I have a subject that the registration is not done correctly in two runs (run 
12 and run 15) .

The tkregister-sess values for this subject is shown below.

Subject 1 10 0.2628
Subject 1 11 0.3038
Subject 1 12 0.7639
Subject 1 13 0.3364
Subject 1 14 0.3346
Subject 1 15 0.9361
Subject 1 16 0.2584
Subject 1 17 0.2488


I attached the screen shots from tkregister2 to this email. The functional data 
is only collected in a slab of parietal and occipital lobe.

I appreciate if you let me know how to fix them.


Thanks

Mona


[cid:part1.1D7D76D6.30EA461F@mgh.harvard.edu][cid:part2.3980DB9D.DA94E372@mgh.harvard.edu]





Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





___
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

Re: [Freesurfer] highres fMRI selxavg error

[Nasiriavanaki, Zahra]

Dear Freesurfer experts

Hi

I have a follow up question on this topic.
I am getting this error "Error using /Matrix dimensions must agree. Error in 
fast_selxavg3b (line 566) RescaleFactor = flac0.inorm/gmean;", when I run 
selxavg for one of my subjects. I attached the log file and copied the terminal 
output below.
Discussing it previously, we found out the problem being "global.meanval.dat 
and global.waveform.dat" files becoming empty after running selxavg!
Listening to Doug's recommendation, I did run everything from scratch.
After doing the preprocessing step, I realized the registration of functional 
on anatomical data is not correct using this command: "tkregister-sess -s $subj 
-fsd bold -per-run -bbr-sum".
So I had to run "register-sess -s $subj -per-run -delete-dat -dof 6 -fsd bold 
-init-header -bbr-xopts bbr.xopts -d ." multiple times to make the registration 
correct (with --brute1max starting from 8 and every time I increased it. The 
last time I ran this command, --brute1max was set to 28).  I got normal values 
for "tkregister-sess" and  I ran selxavg and got the error that I attached.
My question is: Do you think running "register-sess" multiple times is causing 
this issue? and I appreciate any suggestions about how to solve this issue.

P.S:This is highres functional MRI data; the functional data is only acquired 
from parietal and occipital lobes; out of several subjects; analysis is run in 
subject's native space.

Thanks a lot
Mona

#@# osre_7T_all ###
/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/osre_7T_all
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 12, skipping
 1 far.mat
 2 far_vs_near.mat
 3 far_vs_nodis.mat
 4 near.mat
 5 near_vs_far.mat
 6 near_vs_nodis.mat
 7 no_disparity.mat
Excluding 5 points
nruns = 8
autostimdur =


outanadir = 
/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/osre_7T_all/bold3/vis1_native.rh
Excluding 5 points
Excluding 6 points
Excluding 6 points
Excluding 7 points
Excluding 8 points
parfiles condition id list:  1  2  3
Found 1881/138983 ( 1.4) voxels in mask 1
Creating Design Matrix
 ... creation time =  0.020 sec
DoMCFit = 1
ntptot = 640, nX = 107, DOF = 533
Saving X matrix to 
/autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/osre_7T_all/bold3/vis1_native.rh/Xtmp.mat
XCond = 448.137 (normalized)
Computing compensation for resdual AR1 bias
 1  -0.5  -0.4499(t=0.059341)
 2  -0.25  -0.255889(t=0.147506)
 3  0  -0.0718039(t=0.175004)
 4  0.25  0.0955918(t=0.257562)
 5  0.5  0.229844(t=0.289084)
AR1 Correction M: 0.131515 1.4543
Computing contrast matrices
OLS Beta Pass
  run 1t= 0.0
reading data ... 0.629912
Global Mean
  run 2t= 0.8
reading data ... 0.666993
Global Mean
  run 3t= 0.8
reading data ... 0.640162
Global Mean
  run 4t= 0.8
reading data ... 0.646836
Global Mean
  run 5t= 0.8
reading data ... 0.642453
Global Mean
  run 6t= 0.8
reading data ... 0.64432
Global Mean
  run 7t= 0.8
reading data ... 0.63922
Global Mean
  run 8t= 0.8
reading data ... 0.63597
Global Mean
Global In-Mask Mean =  (35.6878)
Error using /
Matrix dimensions must agree.

Error in fast_selxavg3b (line 566)
RescaleFactor = flac0.inorm/gmean;

>> --
ERROR: fast_selxavg3() failed\n




Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Nasiriavanaki, Zahra 
Sent: Thursday, January 2, 2020 3:40 PM
To: Greve, Douglas N.,Ph.D. ; 
freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] highres fMRI selxavg error

I did run it from the shell and figured out what the problem was!

Thanks a lot!!
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Greve, Douglas N.,Ph.D. 
Sent: Thursday, January 2, 2020 3:25 PM
To: Nasiriavanaki, Zahra ; 
freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] highres fMRI selxavg error

It appears to be dying on this command
mris_fwhm --mask 
/autofs/space/oprah_001/users/zn025/fearcond_7T/all_subjects/ylug_ass_sess01/bold/cond.lh/mask.nii
Can you run it from the shell and send the terminal output?


On 1/2/2020 2:13 PM, Nasiriavanaki, Zahra wrote:
Thanks a lot for your reply.

I have one more question about selxavg error and I appreciate if you could 
reply.
I have another subject which has been scanned in 7T.  When I run selxav

[Freesurfer] activation timeseries

[Nasiriavanaki, Zahra]

Dear Freesurfer experts

I want to extract "activation timeseries (BOLD signal changes in each time 
point) " from a predefined ROI  in a single subject task fMRI data. Previously, 
I extracted these values from fmcpr.sm0.self.lh.nii.gz  by using mri_segstats, 
but the data seems to be too noisy.
I searched the forum and found this solution (mri_glmfit --y fmc.nii --qa 
--glmdir qa.glm --save-yhat This will detrend the time series (removing mean, 
linear, and quadratic

trends). With --save-yhat, one of the outputs will be yhat.mgh (the detrended 
time series). If  you have a task, the task will still be in 
there.https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18901.html

I ran this command: mri_glmfit --y fmcpr.nii.gz --qa --glmdir qa.glm --save-yhat
and then this command to extract the timeseries:  mri_segstats --i yhat.mgh 
--slabel arap_7T_all lh $SUBJECTS_DIR/arap_7T_all/lh.label --id 1 
--avgwf-remove-mean --avgwf ./lh.01.txt
I got this error: ERROR: dimension mismatch between input volume and seg  input 
174 174 51  seg   148565 1 1
I would like to know if this is the right way to extract timeseries from a task 
data. and if yes, how can I fix the error.

Thanks a lot
Mona


Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

[Freesurfer] make average subject/ highres fMRI data

[Nasiriavanaki, Zahra]

Dear Freesurfer experts

Hi

I got an error when I was trying to make an average subject. I attached the log 
file.
I appreciate if you could please let me know what the problem is.
make_average_subject --out avgsubject --subjects subj1 subj2 subj 3

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

Linux bee.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 
23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s avgsubject exited with ERRORS at Mon Feb 10 10:43:37 EST 2020

For more details, see the log file 
/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


Mon Feb 10 10:40:43 EST 2020
/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject
/usr/local/freesurfer/stable6/bin/recon-all
-s avgsubject -cortribbon -aparc2aseg
subjid avgsubject
setenv SUBJECTS_DIR /autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR
FREESURFER_HOME /usr/local/freesurfer/stable6
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6
build-stamp.txt: freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb
Linux bee.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksizeunlimited
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  65535 
memorylocked 64 kbytes
maxproc  772023 
maxlocks unlimited
maxsignal772023 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:  19783356810569768 4984420  456692   182279380   186057864
Swap:  62499836   4684862452988


program versions used
$Id: recon-all,v 1.580.2.15 2016/12/08 22:02:41 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2020/02/10-15:40:43-GMT  BuildTimeStamp: Dec 29 2016 04:02:37  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: zn025  Machine: bee.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 3.10.0-1062.4.3.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2020/02/10-15:40:44-GMT  BuildTimeStamp: Dec 29 2016 04:02:37  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: zn025  Machine: bee.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 3.10.0-1062.4.3.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2020/02/10-15:40:44-GMT  BuildTimeStamp: Dec 29 2016 04:02:37  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: zn025  Machine: bee.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 3.10.0-1062.4.3.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/02/10-15:40:44-GMT  BuildTimeStamp: Dec 29 2016 04:02:37  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: zn025  Machine: bee.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 3.10.0-1062.4.3.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2020/02/10-15:40:44-GMT  BuildTimeStamp: Dec 29 2016 04:02:37  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: zn025  Machine: bee.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 3.10.0-1062.4.3.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2020/02/10-15:40:44-GMT  BuildTimeStamp: Dec 29 2016 04:02:37  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: zn025  Machine: bee.nmr.mgh.harvard.edu  Platform: Linux  PlatformVersion: 3.10.0-1062.4.3.el7.x86_64  CompilerName: GCC  CompilerVersion: 40800 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  Tim

Re: [Freesurfer] make average subject/ highres fMRI data

[Nasiriavanaki, Zahra]

Hi

I would like to follow up on this question and would appreciate if you could 
reply.

Thanks!
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: Nasiriavanaki, Zahra
Sent: Monday, February 10, 2020 12:11 PM
To: Freesurfer support list 
Subject: make average subject/ highres fMRI data

Dear Freesurfer experts

Hi

I got an error when I was trying to make an average subject. I attached the log 
file.
I appreciate if you could please let me know what the problem is.
make_average_subject --out avgsubject --subjects subj1 subj2 subj 3

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

Linux bee.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 
23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s avgsubject exited with ERRORS at Mon Feb 10 10:43:37 EST 2020

For more details, see the log file 
/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

[Freesurfer] mri_glmfit --no-prune

[Nasiriavanaki, Zahra]

Hi Freesurferers

I am running mri_glmfit on a group data using --no-prune flag. i 'm getting the 
below error.
I appreciate if you could let me know what the issue is.

Loading y from 
/autofs/space/oprah_001/users/zn025/looming_3T/group_levels/patients_20/loom.lh/aw/ces.nii.gz
   ... done reading.
Saving design matrix to main2.wls/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1
Matrix condition is 1
Found 149955 points in label.
Found 149955 voxels in mask
Saving mask to main2.wls/mask.nii.gz
Reshaping mriglm->mask...
search space = 74612.583051
ERROR: MRInormWeights: value less than or eq to 0.
  c=336, r=0, s=0, v=0


Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] mri_glmfit --no-prune

[Nasiriavanaki, Zahra]

Dear Doug

Thanks a lot for your reply.
So, how can I solve this issue?

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Tuesday, February 18, 2020 6:52 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_glmfit --no-prune

The ces stack has had the medial wall  masked out so all the values there are 
0. When you specify --wls, it normalizes the weights across subject. However, 
in the medial wall, all the weights are 0 (can't divide by 0, so it throws an 
error.

On 2/18/2020 5:35 PM, Nasiriavanaki, Zahra wrote:
Hi Freesurferers

I am running mri_glmfit on a group data using --no-prune flag. i 'm getting the 
below error.
I appreciate if you could let me know what the issue is.

Loading y from 
/autofs/space/oprah_001/users/zn025/looming_3T/group_levels/patients_20/loom.lh/aw/ces.nii.gz
   ... done reading.
Saving design matrix to main2.wls/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1
Matrix condition is 1
Found 149955 points in label.
Found 149955 voxels in mask
Saving mask to main2.wls/mask.nii.gz
Reshaping mriglm->mask...
search space = 74612.583051
ERROR: MRInormWeights: value less than or eq to 0.
  c=336, r=0, s=0, v=0


Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





___
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

Re: [Freesurfer] mri_glmfit --no-prune

[Nasiriavanaki, Zahra]

Hi

I got the answer.
If I don't use  the weighted list squares, it will go through!

Thanks again
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Nasiriavanaki, Zahra 

Sent: Wednesday, February 19, 2020 10:27 AM
To: Greve, Douglas N.,Ph.D. ; 
freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_glmfit --no-prune

Dear Doug

Thanks a lot for your reply.
So, how can I solve this issue?

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Tuesday, February 18, 2020 6:52 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_glmfit --no-prune

The ces stack has had the medial wall  masked out so all the values there are 
0. When you specify --wls, it normalizes the weights across subject. However, 
in the medial wall, all the weights are 0 (can't divide by 0, so it throws an 
error.

On 2/18/2020 5:35 PM, Nasiriavanaki, Zahra wrote:
Hi Freesurferers

I am running mri_glmfit on a group data using --no-prune flag. i 'm getting the 
below error.
I appreciate if you could let me know what the issue is.

Loading y from 
/autofs/space/oprah_001/users/zn025/looming_3T/group_levels/patients_20/loom.lh/aw/ces.nii.gz
   ... done reading.
Saving design matrix to main2.wls/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1
Matrix condition is 1
Found 149955 points in label.
Found 149955 voxels in mask
Saving mask to main2.wls/mask.nii.gz
Reshaping mriglm->mask...
search space = 74612.583051
ERROR: MRInormWeights: value less than or eq to 0.
  c=336, r=0, s=0, v=0


Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





___
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] timeseries question

[Nasiriavanaki, Zahra]

Hi Freesurferes

I have extracted timeseries from a task fMRI using the command below:
mri_segstats --i fmcpr.sm0.self.rh.nii.gz --slabel $subj rh  rh.label --id 1 
--avgwf-remove-mean --avgwf ./rh.txt

My question is: Is the temporal drift being counted in considering that I used 
preprocessed data as the input?

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] timeseries question

[Nasiriavanaki, Zahra]

Hi

I wanted to follow up on this question and clarify it a little bit more.
My question is if the temporal drift (hemodynamic response delay) has been 
counted in considering that I used the preprocessed data as the input?
I deeply appreciate any help.

Thanks
Mona





On Feb 28, 2020, at 5:50 PM, Nasiriavanaki, Zahra 
mailto:znasiriavan...@mgh.harvard.edu>> wrote:

Hi Freesurferes

I have extracted timeseries from a task fMRI using the command below:
mri_segstats --i fmcpr.sm0.self.rh.nii.gz --slabel $subj rh  rh.label --id 1 
--avgwf-remove-mean --avgwf ./rh.txt

My question is: Is the temporal drift being counted in considering that I used 
preprocessed data as the input?

Thanks
Mona

Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129

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

[Freesurfer] selxavg3-sess not working

[Nasiriavanaki, Zahra]

Hi Freesurferers

I am trying to run selxavg3-sess for a single subject (3T fMRI data). Oddly, 
the  terminal output shows that it doesn't need updating for preprocessing and 
ends with this:  "Started at Thu Mar 12 10:48:09 EDT 2020
Ended   at Thu Mar 12 10:48:12 EDT 2020 preproc-sess done".  It seems that it 
just checks the preprocessing, but does not initiate the selxavg analysis. 
There is no error neither selxavg log file.

my command: selxavg3-sess -s $subj -d ../all_subjects -analysis loom.lh  -force

I appreciate any comments on this issue.

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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

Re: [Freesurfer] selxavg3-sess not working

[Nasiriavanaki, Zahra]

Hi Doug

Thanks for your reply.
Yes, I did.
I run the command from the folder where my analysis which I call loom.lh is 
located.

selxavg3-sess -s $subj -d ../all_subjects -analysis loom.lh  -force

On Mar 13, 2020, at 6:41 PM, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:

Did you pass it an analysis? There is not one in that command line

On 3/12/2020 11:28 AM, Nasiriavanaki, Zahra wrote:
Hi Freesurferers

I am trying to run selxavg3-sess for a single subject (3T fMRI data). Oddly, 
the  terminal output shows that it doesn't need updating for preprocessing and 
ends with this:  "Started at Thu Mar 12 10:48:09 EDT 2020
Ended   at Thu Mar 12 10:48:12 EDT 2020 preproc-sess done".  It seems that it 
just checks the preprocessing, but does not initiate the selxavg analysis. 
There is no error neither selxavg log file.

my command: selxavg3-sess -s $subj -d ../all_subjects -analysis loom.lh  -force

I appreciate any comments on this issue.

Thanks
Mona

Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129




___
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] extracting values of each voxel within an ROI

[Nasiriavanaki, Zahra]

Hi all

Is there any command for extracting the fmri activation from all voxels in an 
ROI?
I know I can use funcroi-config, funcroi-sess and funcroi-table-sess to extract 
the average activation in a specific ROI from a specific contrast. But what if 
I want to extract the values of each voxel within that ROI?
 
I appreciate any comments on this.

Thanks
Mona
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] extracting values of each voxel within an ROI

[Nasiriavanaki, Zahra]

Hi Doug

Thank you very much for your reply.
I am doing these analysis in each subject’s self space, and my ROI is a 
handmade cortical label in ascci format.
In this case, would the indices be the vertex Id in the label file?
also, instead of  f=MRIread('f.nii.gz’); can I use “sig.nii.gz” to get the 
threshold of each voxel (sig.nii.gz is the result of selxavg for a specific 
contrast)?

Thanks
Mona


> On Mar 20, 2020, at 10:49 AM, Douglas N. Greve  wrote:
> 
> Do you mean all the voxels separately? I don't think I have anything, 
> but you can do it in matlab with something like
> seg = MRIread('seg.nii.gz');
> indices= find(seg.vol == IndexOfYourROI);
> f = MRIread('f.nii.gz');
> fmat = fast_vol2mat(f);
> froi = fmat(:,indices);
> 
> this assumes taht f.nii.gz and seg.nii.gz are in vox-for-vox registration
> 
> 
> 
> On 3/18/2020 5:13 PM, Nasiriavanaki, Zahra wrote:
>> Hi all
>> 
>> Is there any command for extracting the fmri activation from all voxels in 
>> an ROI?
>> I know I can use funcroi-config, funcroi-sess and funcroi-table-sess to 
>> extract the average activation in a specific ROI from a specific contrast. 
>> But what if I want to extract the values of each voxel within that ROI?
>> 
>> I appreciate any comments on this.
>> 
>> Thanks
>> Mona
>> ___
>> 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


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

Re: [Freesurfer] selxavg3-sess not working

[Nasiriavanaki, Zahra]

Hi Doug

Thanks for your reply. Unfortunately I am still having problem. It’s so odd, 
because it has never happened with my other subjects before.
I attached the log files and I appreciate if you could please take a look.
command: selxavg3-sess -s $subj -d ../all_subjects -analysis loom.lh



On Mar 20, 2020, at 10:26 AM, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:

oh, sorry, I misread your earlier email. The -force in selxavg3-sess only 
applies to the post processing. If  you want to redo the preprocessing, then 
run preproc-sess -force

On 3/13/2020 7:28 PM, Nasiriavanaki, Zahra wrote:
Hi Doug

Thanks for your reply.
Yes, I did.
I run the command from the folder where my analysis which I call loom.lh is 
located.

selxavg3-sess -s $subj -d ../all_subjects -analysis loom.lh  -force

On Mar 13, 2020, at 6:41 PM, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:

Did you pass it an analysis? There is not one in that command line

On 3/12/2020 11:28 AM, Nasiriavanaki, Zahra wrote:
Hi Freesurferers

I am trying to run selxavg3-sess for a single subject (3T fMRI data). Oddly, 
the  terminal output shows that it doesn't need updating for preprocessing and 
ends with this:  "Started at Thu Mar 12 10:48:09 EDT 2020
Ended   at Thu Mar 12 10:48:12 EDT 2020 preproc-sess done".  It seems that it 
just checks the preprocessing, but does not initiate the selxavg analysis. 
There is no error neither selxavg log file.

my command: selxavg3-sess -s $subj -d ../all_subjects -analysis loom.lh  -force

I appreciate any comments on this issue.

Thanks
Mona

Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129





___
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<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



selxavg3-sess-bold-loom.lh-200320115858.log
Description: selxavg3-sess-bold-loom.lh-200320115858.log
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] averaging timecourses

[Nasiriavanaki, Zahra]

Hi Freesurfer experts

I have extracted the time course of a task fMRI data in a specific contrast and 
within a specific ROI, in 7 subjects. 
Consider my specific ROI has 1200 voxels and I extracted the time course for a 
duration of 5 TRs. After extracting the timecourse, I have a matrix of 1200x5 
for each subject. 
To calculate the average timecourse, I concatenated the matrices for the 7 
subjects and made one matrix of 8400x5. Then I averaged across columns which 
gives me one mean per column. I also calculated the standard error for each 
column.
My question is if this voxel wise way of averaging and calculating the standard 
error is statistically correct or not.
I deeply appreciate any comments on this.

Thanks a lot 
Mona
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] cortical thickness

[Nasiriavanaki, Zahra]

Hi Freesurfer experts

I have a question about the way FS calculates cortical thickness and I 
appreciate if you could please respond.
I calculated the cortical thickness using read_curv script in a specific ROI in 
parietal lobe. 
The mean thickness at that area was 2.4. Does this number show the cortical 
thickness in millimeter? 

Thanks
MOna
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] cortical thickness

[Nasiriavanaki, Zahra]

Thanks for your response Bruce.
Does FS calculate the distance between the surface and CSF border in Euclidean 
and then converts it into mm?

Thanks
Mona


> On Jul 6, 2020, at 12:40 PM, Fischl, Bruce  wrote:
> 
> yes
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Nasiriavanaki, Zahra
> Sent: Monday, July 6, 2020 12:31 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] cortical thickness
> 
> Hi Freesurfer experts
> 
> I have a question about the way FS calculates cortical thickness and I 
> appreciate if you could please respond.
> I calculated the cortical thickness using read_curv script in a specific ROI 
> in parietal lobe. 
> The mean thickness at that area was 2.4. Does this number show the cortical 
> thickness in millimeter? 
> 
> Thanks
> MOna
> ___
> 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


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

Re: [Freesurfer] cortical thickness

[Nasiriavanaki, Zahra]

I got my answer. Thanks so much


> On Jul 6, 2020, at 1:31 PM, Fischl, Bruce  wrote:
> 
> I'm not sure I understand your question. We compute the distance between 
> minimum distances between the white and pial in mm, then compute the minimum 
> between the pial and the white, then average them (all in mm)
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Nasiriavanaki, Zahra
> Sent: Monday, July 6, 2020 1:00 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] cortical thickness
> 
> Thanks for your response Bruce.
> Does FS calculate the distance between the surface and CSF border in 
> Euclidean and then converts it into mm?
> 
> Thanks
> Mona
> 
> 
>> On Jul 6, 2020, at 12:40 PM, Fischl, Bruce  wrote:
>> 
>> yes
>> 
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  On Behalf Of Nasiriavanaki, Zahra
>> Sent: Monday, July 6, 2020 12:31 PM
>> To: Freesurfer support list 
>> Subject: [Freesurfer] cortical thickness
>> 
>> Hi Freesurfer experts
>> 
>> I have a question about the way FS calculates cortical thickness and I 
>> appreciate if you could please respond.
>> I calculated the cortical thickness using read_curv script in a specific ROI 
>> in parietal lobe. 
>> The mean thickness at that area was 2.4. Does this number show the cortical 
>> thickness in millimeter? 
>> 
>> Thanks
>> MOna
>> ___
>> 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
> 
> 
> ___
> 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


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

[Freesurfer] high pass filter cutoff

[Nasiriavanaki, Zahra]

Hi Freesurferers

Could you please let me know how I should calculate the high pass filter 
cutoff? I have seen a bunch of different formulas (i.e 1.5*the stimulation 
period)?
My task is a block-designed task, each stimuli takes 16 seconds and is followed 
by the next stimuli without an ITI. TR=2, number of conditions=8.
I have used a hpf=0.01, Is this correct?

Thanks
Mona


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

Re: [Freesurfer] high pass filter cutoff

[Nasiriavanaki, Zahra]

Hi Doug

Thanks so much for your reply. This is a question that a reviewer has pointed 
out. They were concerned that with the stimuli duration of 16 sec, maybe I am 
not using the correct hpf cutoff.
Could you please refer me a paper about this?

Thanks
Mona


> On Aug 7, 2020, at 10:15 AM, Douglas N. Greve  wrote:
> 
> There is not a hard and fast formula. With a block length of 16 sec, you 
> will have frequencies at 0.0625Hz and multiples thereof. The closer you 
> are to 0.625, the more signal you are going to lose. Also, if you don't 
> remove the whitening, then FSFAST will compute a highpass filter for 
> you. I think that .01Hz is probably fine, but you could bump it up to 
> .02Hz too
> 
> On 8/6/2020 6:11 PM, Nasiriavanaki, Zahra wrote:
>> Hi Freesurferers
>> 
>> Could you please let me know how I should calculate the high pass filter 
>> cutoff? I have seen a bunch of different formulas (i.e 1.5*the stimulation 
>> period)?
>> My task is a block-designed task, each stimuli takes 16 seconds and is 
>> followed by the next stimuli without an ITI. TR=2, number of conditions=8.
>> I have used a hpf=0.01, Is this correct?
>> 
>> Thanks
>> Mona
>> 
>> 
>> ___
>> 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


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

Re: [Freesurfer] high pass filter cutoff

[Nasiriavanaki, Zahra]

Could you please explain how you came up with “0.0625 Hz”?
You mentioned in your first email: “With a block length of 16 sec, you will 
have frequencies at 0.0625Hz and multiples thereof.”

Thanks
Mona

> On Aug 7, 2020, at 10:42 AM, Douglas N. Greve  wrote:
> 
> Sorry, I don't have a paper on it
> 
> On 8/7/2020 10:27 AM, Nasiriavanaki, Zahra wrote:
>> Hi Doug
>> 
>> Thanks so much for your reply. This is a question that a reviewer has 
>> pointed out. They were concerned that with the stimuli duration of 16 sec, 
>> maybe I am not using the correct hpf cutoff.
>> Could you please refer me a paper about this?
>> 
>> Thanks
>> Mona
>> 
>> 
>>> On Aug 7, 2020, at 10:15 AM, Douglas N. Greve  
>>> wrote:
>>> 
>>> There is not a hard and fast formula. With a block length of 16 sec, you
>>> will have frequencies at 0.0625Hz and multiples thereof. The closer you
>>> are to 0.625, the more signal you are going to lose. Also, if you don't
>>> remove the whitening, then FSFAST will compute a highpass filter for
>>> you. I think that .01Hz is probably fine, but you could bump it up to
>>> .02Hz too
>>> 
>>> On 8/6/2020 6:11 PM, Nasiriavanaki, Zahra wrote:
>>>> Hi Freesurferers
>>>> 
>>>> Could you please let me know how I should calculate the high pass filter 
>>>> cutoff? I have seen a bunch of different formulas (i.e 1.5*the stimulation 
>>>> period)?
>>>> My task is a block-designed task, each stimuli takes 16 seconds and is 
>>>> followed by the next stimuli without an ITI. TR=2, number of conditions=8.
>>>> I have used a hpf=0.01, Is this correct?
>>>> 
>>>> Thanks
>>>> Mona
>>>> 
>>>> 
>>>> ___
>>>> 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
>> 
>> ___
>> 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


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

[Freesurfer] POSTDOC and PhD POSITION- photoacoustic imaging , machine learning and OCT image analysis

[Nasiriavanaki, Zahra]

Hi all

Please see below for available postdoc and PhD positions at the Biomedical 
Engineering Department, University of Illinois at Chicago.

Best,
Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129


We have openings for two postdocs, one with expertise in the area of 
photoacoustic imaging instrumentation, and the other one in the area of machine 
learning and OCT image analysis. We also have one Ph.D. position available in 
the area of photoacoustic imaging. Please share this with your qualified 
colleagues/friends. See more details at: 
https://engineering.academickeys.com/seeker_job_display.php?dothis=display&job[IDX]=145660

[http://engineering.academickeys.com/seeker_job_attachments.php?dothis=display&job_file[IDX]=20637]
Two postdoctoral positions and a PhD position at the Biomedical Engineering 
Department , Biomedical Engineering Department , The University of Illinois at 
Chicago 
(UIC)
Two postdoctoral positions and one PhD position are available in OPIRA lab in 
the Biomedical Engineering Department, the University of Illinois at Chicago 
(UIC). 1. The first postdoctoral fellow will contribute to the design, 
development, and optimizati...
engineering.academickeys.com

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

[Freesurfer] mri_segstats quetsion

[Nasiriavanaki, Zahra]

Dear Freesurferers

Hi

I am trying to extract the BOLD signal values from a functional subcortical 
area. I did the below steps to make the functional thalamus ROI and then used 
the mri_segstats to extract the BOLD signal from it.
I would like to know 1-if my approach is correct? 2- should I use “lhthal3” as 
a mask? if so, what should I use as an input? 3-I see that the “mri_segstats” 
outputs one value for each voxel inside my ROI, is there a way to get one value 
across the whole ROI (lhthal3.nii.gz)?

fslmaths 'aseg.nii.gz' -thr 10 -uthr 10 'lhthal.nii.gz'
fslmaths 'lhthal.nii.gz' -mul 'sig.nii.gz' 'lhthal2.nii.gz'
fslmaths 'lhthal2.nii.gz' -bin 'lhthal3.nii.gz'

mri_segstats --seg aseg.nii.gz --i lhthal3.nii.gz  --sfavg this.txt

Thanks a lot
M0na

Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129

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

Re: [Freesurfer] mri_segstats quetsion

[Nasiriavanaki, Zahra]

Great. thanks Doug!

Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129

On Sep 4, 2020, at 1:07 PM, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:

I'm not entirely sure what those steps are trying to do. Extract out signal 
from voxels in thalamus that have a positive sig? You can do that with one call 
to mri_segstats. This page has an example:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview

On 9/4/2020 11:56 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurferers

Hi

I am trying to extract the BOLD signal values from a functional subcortical 
area. I did the below steps to make the functional thalamus ROI and then used 
the mri_segstats to extract the BOLD signal from it.
I would like to know 1-if my approach is correct? 2- should I use “lhthal3” as 
a mask? if so, what should I use as an input? 3-I see that the “mri_segstats” 
outputs one value for each voxel inside my ROI, is there a way to get one value 
across the whole ROI (lhthal3.nii.gz)?

fslmaths 'aseg.nii.gz' -thr 10 -uthr 10 'lhthal.nii.gz'
fslmaths 'lhthal.nii.gz' -mul 'sig.nii.gz' 'lhthal2.nii.gz'
fslmaths 'lhthal2.nii.gz' -bin 'lhthal3.nii.gz'

mri_segstats --seg aseg.nii.gz --i lhthal3.nii.gz  --sfavg this.txt

Thanks a lot
M0na

Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129




___
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] mri_volsynth question

[Nasiriavanaki, Zahra]

Hi

I am trying to make a subcortical 5 mm sphere ROI around a talairach 
coordinate. I am using the below command, but when I visualize it, it doesn’t 
look at the correct location. I see the same question in forum 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67295.html), I 
should probably use -pdf delta but I don’t know how to get the col, row and 
slice indices of the vertex where it should go.

mri_volsynth --template $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --c_ras -21.8 
-12.2 -10.3  --dim 5 5 5 5 —o new.mgh

I appreciate your help.

Thanks
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129

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

Re: [Freesurfer] mri_volsynth question

[Nasiriavanaki, Zahra]

Hi Doug

Thanks for your reply.
I did so, I'm getting the error below:

line 43:  8101 Segmentation fault  (core dumped) mri_volsynth --template 
$SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --c_ras -21.8 -12.2 -10.3 --pdf delta 
--delta-crsf 150 138 116 0 --dim 5 5 5 5 --o delta.mgh

I appreciate your help.

Thanks

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Wednesday, September 9, 2020 6:23 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_volsynth question

Load $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz into freeview and find the voxel 
where you want it to be centered. Then run
mri_volsynth as you have below but add --delta-crsf C R S 0
where C, R, S are the col, row, slice from the voxel you found in freeview

On 9/9/2020 5:39 PM, Nasiriavanaki, Zahra wrote:
Hi

I am trying to make a subcortical 5 mm sphere ROI around a talairach 
coordinate. I am using the below command, but when I visualize it, it doesn’t 
look at the correct location. I see the same question in forum 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67295.html), I 
should probably use -pdf delta but I don’t know how to get the col, row and 
slice indices of the vertex where it should go.

mri_volsynth --template $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --c_ras -21.8 
-12.2 -10.3  --dim 5 5 5 5 —o new.mgh

I appreciate your help.

Thanks
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129




___
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

Re: [Freesurfer] mri_volsynth question

[Nasiriavanaki, Zahra]

Sure, sorry for the inconvenience.
Here is the full output:

[bee:ROI_analysis] (nmr-stable6-env) ./make_flabels.sh
voliddelta.mgh
volfmt   (null)
Using 
/autofs/space/oprah_001/users/zn025/looming_3T/SUBJECTS_DIR/fsaverage/mri/brainmask.mgz
 as template
fwhm = 0, gstd  = 0
seed 1600286417
pdf   delta
SpikeTP -1
DoCurv 0
DoAbs  0
Diagnostic Level -1
INFO: reading template header
Synthesizing
delta set to 1 at 150 138 116 0
./make_flabels.sh: line 43: 20329 Segmentation fault  (core dumped) 
mri_volsynth --template $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --c_ras -21.8 
-12.2 -10.3 --pdf delta --delta-crsf 150 138 116 0 --dim 5 5 5 5 --o delta.mgh



Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129

On Sep 10, 2020, at 12:39 PM, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:

please send the full terminal output

On 9/10/2020 11:24 AM, Nasiriavanaki, Zahra wrote:
Hi Doug

Thanks for your reply.
I did so, I'm getting the error below:

line 43:  8101 Segmentation fault  (core dumped) mri_volsynth --template 
$SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --c_ras -21.8 -12.2 -10.3 --pdf delta 
--delta-crsf 150 138 116 0 --dim 5 5 5 5 --o delta.mgh

I appreciate your help.

Thanks
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, September 9, 2020 6:23 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_volsynth question

Load $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz into freeview and find the voxel 
where you want it to be centered. Then run
mri_volsynth as you have below but add --delta-crsf C R S 0
where C, R, S are the col, row, slice from the voxel you found in freeview

On 9/9/2020 5:39 PM, Nasiriavanaki, Zahra wrote:
Hi

I am trying to make a subcortical 5 mm sphere ROI around a talairach 
coordinate. I am using the below command, but when I visualize it, it doesn’t 
look at the correct location. I see the same question in forum 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67295.html), I 
should probably use -pdf delta but I don’t know how to get the col, row and 
slice indices of the vertex where it should go.

mri_volsynth --template $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --c_ras -21.8 
-12.2 -10.3  --dim 5 5 5 5 —o new.mgh

I appreciate your help.

Thanks
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129



___
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<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